diff --git a/QA.html b/QA.html
index 13d8b56..1032c8f 100644
--- a/QA.html
+++ b/QA.html
@@ -42,9 +42,14 @@
 <h2 id="are-you-keeping-the-uploaded-data">Are you keeping the uploaded data?<a class="anchor" aria-label="anchor" href="#are-you-keeping-the-uploaded-data"></a></h2>
 <p>No! All uploaded data is deleted when the session ends, so only stored for your analyses and the immediately deleted.</p>
 </div>
+<div class="section level2">
+<h2 id="how-do-i-merge-multiple-datasets">How do I merge multiple datasets?<a class="anchor" aria-label="anchor" href="#how-do-i-merge-multiple-datasets"></a></h2>
+<p>You can merge multiple sheets from ods or xls(x) files on import when a common key variable is present in selected sheets. Multiple file upload/merge is currently not supported.</p>
+</div>
 </div>
 
-  </main></div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
diff --git a/articles/freesearcheR.html b/articles/freesearcheR.html
index d2d2380..c53e94c 100644
--- a/articles/freesearcheR.html
+++ b/articles/freesearcheR.html
@@ -116,6 +116,46 @@ identically.</p>
 </h4>
 </div>
 </div>
+<div class="section level3">
+<h3 id="evaluate">Evaluate<a class="anchor" aria-label="anchor" href="#evaluate"></a>
+</h3>
+<div class="section level4">
+<h4 id="baseline">Baseline<a class="anchor" aria-label="anchor" href="#baseline"></a>
+</h4>
+</div>
+<div class="section level4">
+<h4 id="correlation-matrix">Correlation matrix<a class="anchor" aria-label="anchor" href="#correlation-matrix"></a>
+</h4>
+</div>
+</div>
+<div class="section level3">
+<h3 id="visualise">Visualise<a class="anchor" aria-label="anchor" href="#visualise"></a>
+</h3>
+<ul>
+<li>Would be nice to have a table of possible plots, their description
+and data options</li>
+</ul>
+</div>
+<div class="section level3">
+<h3 id="regression">Regression<a class="anchor" aria-label="anchor" href="#regression"></a>
+</h3>
+</div>
+<div class="section level3">
+<h3 id="download">Download<a class="anchor" aria-label="anchor" href="#download"></a>
+</h3>
+<div class="section level4">
+<h4 id="report">Report<a class="anchor" aria-label="anchor" href="#report"></a>
+</h4>
+</div>
+<div class="section level4">
+<h4 id="data">Data<a class="anchor" aria-label="anchor" href="#data"></a>
+</h4>
+</div>
+<div class="section level4">
+<h4 id="code">Code<a class="anchor" aria-label="anchor" href="#code"></a>
+</h4>
+</div>
+</div>
 </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside>
diff --git a/pkgdown.yml b/pkgdown.yml
index ad85724..bfd8465 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   freesearcheR: freesearcheR.html
-last_built: 2025-03-17T19:43Z
+last_built: 2025-03-17T20:30Z
 urls:
   reference: https://agdamsbo.github.io/freesearcheR/reference
   article: https://agdamsbo.github.io/freesearcheR/articles
diff --git a/reference/getfun.html b/reference/getfun.html
index 80d2e40..5e9e97e 100644
--- a/reference/getfun.html
+++ b/reference/getfun.html
@@ -133,7 +133,7 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span>         z$qr &lt;- NULL</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>     z</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;bytecode: 0x560e4a1f0950&gt;</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;bytecode: 0x5629d0813b78&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: namespace:stats&gt;</span>
 </code></pre></div>
     </div>
diff --git a/search.json b/search.json
index e7bed1d..206ea91 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
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Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. 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Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU Affero General Public License","title":"GNU Affero General Public License","text":"Version 3, 19 November 2007 Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU Affero General Public License","text":"GNU Affero General Public License free, copyleft license software kinds works, specifically designed ensure cooperation community case network server software. licenses software practical works designed take away freedom share change works. contrast, General Public Licenses intended guarantee freedom share change versions program–make sure remains free software users. speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. Developers use General Public Licenses protect rights two steps: (1) assert copyright software, (2) offer License gives legal permission copy, distribute /modify software. secondary benefit defending users’ freedom improvements made alternate versions program, receive widespread use, become available developers incorporate. Many developers free software heartened encouraged resulting cooperation. However, case software used network servers, result may fail come . GNU General Public License permits making modified version letting public access server without ever releasing source code public. 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Definitions.","title":"GNU Affero General Public License","text":"“License” refers version 3 GNU Affero General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. 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Program specifies certain numbered version GNU Affero General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU Affero General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU Affero General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty.","title":"GNU Affero General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_16-limitation-of-liability","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"16. Limitation of Liability.","title":"GNU Affero General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16.","title":"GNU Affero General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU Affero General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. software can interact users remotely computer network, also make sure provides way users get source. example, program web application, interface display “Source” link leads users archive code. many ways offer source, different solutions better different programs; see section 13 specific requirements. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU AGPL, see https://www.gnu.org/licenses/.","code":"<one line to give the program's name and a brief idea of what it does.>     Copyright (C) <year>  <name of author>      This program is free software: you can redistribute it and/or modify     it under the terms of the GNU Affero General Public License as     published by the Free Software Foundation, either version 3 of the     License, or (at your option) any later version.      This program is distributed in the hope that it will be useful,     but WITHOUT ANY WARRANTY; without even the implied warranty of     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the     GNU Affero General Public License for more details.      You should have received a copy of the GNU Affero General Public License     along with this program.  If not, see <https://www.gnu.org/licenses/>."},{"path":"https://agdamsbo.github.io/freesearcheR/QA.html","id":null,"dir":"","previous_headings":"","what":"Questions and answers","title":"Questions and answers","text":"complete instructions set available, collection questions answers project use app.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/QA.html","id":"are-you-keeping-the-uploaded-data","dir":"","previous_headings":"","what":"Are you keeping the uploaded data?","title":"Questions and answers","text":"! uploaded data deleted session ends, stored analyses immediately deleted.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/ROADMAP.html","id":null,"dir":"","previous_headings":"","what":"Project roadmap","title":"Project roadmap","text":"current state app considered experimental, lot things still changing. , however, usable state, basic functions available user. (actual list quite long growing) planned features improvements: Stratified analyses Additional study designs: Cross-sectional data analyses Longitudinal data analyses Survival analysis detailed variable browser Add histograms data distribution. 2025-01-16 Option edit labels. 2025-01-16 output controls Theming output tables Select analyses include report Export modified data. 2025-01-16 Include reproducible code steps (maybe , steps, final dataset can exported) Modify factor levels Factor level modifications possible converting factors numeric > cutting numeric desired fixed values. 2024-12-12 options date/datetime/time grouping/factoring. Included weekday month-options. 2024-12-12 Graphs plots Correlation matrix plot data exploration 2025-2-20 Grotta bars ordianl outcomes (sankey) 2025-3-17 Coefficient plotting regression analyses (forest plot) 2025-2-20","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/articles/freesearcheR.html","id":"getting-started-with-freesearcher","dir":"Articles","previous_headings":"","what":"Getting started with freesearcheR","title":"freesearcheR","text":"simple walk-trough basic instructions functions freesearcheR app.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/articles/freesearcheR.html","id":"launching","dir":"Articles","previous_headings":"Getting started with freesearcheR","what":"Launching","title":"freesearcheR","text":"easiest way get started launch hosted version app shinyapps.io (click link). Additionally option run app locally access data current working environment. , open R (RStudio similar), run following code install latest version freesearcheR launch app: small note, standalone Windows app version drawing board well, time frame available.","code":"require(\"pak\") pak::pak(\"agdamsbo/freesearcheR\") library(freesearcheR) freesearcheR::launch_freesearcheR()"},{"path":"https://agdamsbo.github.io/freesearcheR/articles/freesearcheR.html","id":"importing-data","dir":"Articles","previous_headings":"Getting started with freesearcheR","what":"Importing data","title":"freesearcheR","text":"app “Import”, three options available importing data: file upload, REDCap server export local sample data. choosing data source, can set threshold filter data completenes manually specify variables include analyses.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/articles/freesearcheR.html","id":"file-upload","dir":"Articles","previous_headings":"Getting started with freesearcheR > Importing data","what":"File upload","title":"freesearcheR","text":"Currently several data file formats supported easy import (csv, txt, xls(x), ods, rds, dta). importing workbooks (xls(x) ods), prompted specify sheet(s) import. choosing multiple sheets, automatically merged common variable(s), please make sure key variables correctly named identically.","code":""},{"path":[]},{"path":[]},{"path":"https://agdamsbo.github.io/freesearcheR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Andreas Gammelgaard Damsbo. Author, maintainer.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Damsbo (2025). freesearcheR: Browser Based Data Analysis. R package version 25.3.2, https://agdamsbo.github.io/freesearcheR/, https://github.com/agdamsbo/freesearcheR.","code":"@Manual{,   title = {freesearcheR: Browser Based Data Analysis},   author = {Andreas Gammelgaard Damsbo},   year = {2025},   note = {R package version 25.3.2, https://agdamsbo.github.io/freesearcheR/},   url = {https://github.com/agdamsbo/freesearcheR}, }"},{"path":"https://agdamsbo.github.io/freesearcheR/index.html","id":"freesearcher","dir":"","previous_headings":"","what":"Browser Based Data Analysis","title":"Browser Based Data Analysis","text":"package backbone freesearcheR, free open-source browser based data exploration analysis tool clinicians researchers publication ready output. package freesearcheR-tool part larger initiative democratize health data analysis remove barriers clinicians engage health research. freesearcheR-tool online accessible : link app freely hosted shinyapps.io. feedback welcome can shared GitHub issue. Initiatives funding continued development tool surrounding initiatives ongoing.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/index.html","id":"install-locally","dir":"","previous_headings":"","what":"Install locally","title":"Browser Based Data Analysis","text":"freesearcheR-tool can also launched locally. data.frame available global environment accessible interface.","code":"require(\"devtools\") devtools::install_github(\"agdamsbo/freesearcheR\") library(freesearcheR) # By loading mtcars to the environment, it will be available # in the interface like any other data.frame data(mtcars) shiny_freesearcheR()"},{"path":"https://agdamsbo.github.io/freesearcheR/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Browser Based Data Analysis","text":"Please note freesearcheR project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert class grid column to icon — add_class_icon","title":"Convert class grid column to icon — add_class_icon","text":"Convert class grid column icon","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert class grid column to icon — add_class_icon","text":"","code":"add_class_icon(grid, column = \"class\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert class grid column to icon — add_class_icon","text":"grid grid column column","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert class grid column to icon — add_class_icon","text":"datagrid","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert class grid column to icon — add_class_icon","text":"","code":"mtcars |>   overview_vars() |>   toastui::datagrid() |>   add_class_icon()      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(Q1, Q3); n (%)     mtcars |> baseline_table(fun.args = list(by = \"gear\"))     Characteristic       3 N = 151       4 N = 121       5 N = 51     mpg 15.5 (14.3, 18.7) 22.8 (21.0, 28.9) 19.7 (15.8, 26.0)cyl       4 1 (6.7%) 8 (67%) 2 (40%)    6 2 (13%) 4 (33%) 1 (20%)    8 12 (80%) 0 (0%) 2 (40%)disp 318 (276, 400) 131 (79, 160) 145 (120, 301)hp 180 (150, 215) 94 (66, 110) 175 (113, 264)drat 3.08 (3.00, 3.21) 3.92 (3.90, 4.10) 3.77 (3.62, 4.22)wt 3.73 (3.44, 4.07) 2.70 (2.07, 3.17) 2.77 (2.14, 3.17)qsec 17.42 (17.02, 18.00) 18.76 (18.41, 19.69) 15.50 (14.60, 16.70)vs 3 (20%) 10 (83%) 1 (20%)am 0 (0%) 8 (67%) 5 (100%)carb       1 3 (20%) 4 (33%) 0 (0%)    2 4 (27%) 4 (33%) 2 (40%)    3 3 (20%) 0 (0%) 0 (0%)    4 5 (33%) 4 (33%) 1 (20%)    6 0 (0%) 0 (0%) 1 (20%)    8 0 (0%) 0 (0%) 1 (20%)1 Median (Q1, Q3); n (%)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/clean_date.html","id":null,"dir":"Reference","previous_headings":"","what":"Attempts at applying uniform date 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string","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/clean_sep.html","id":null,"dir":"Reference","previous_headings":"","what":"gsub wrapper for piping with default values for separator substituting — clean_sep","title":"gsub wrapper for piping with default values for separator substituting — clean_sep","text":"gsub wrapper piping default values separator substituting","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/clean_sep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"gsub wrapper for piping with default values for separator substituting — clean_sep","text":"","code":"clean_sep(data, old.sep = \"[-.,/]\", new.sep = \"-\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/clean_sep.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"gsub wrapper for piping with default values for separator substituting — clean_sep","text":"data character vector 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Three different methods available: c(\"relative\",\"perceived\",\"perceived_2\") ... parameter overflow. Ignored.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/contrast_text.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Contrast Text Color — contrast_text","text":"character string contains best contrast text color.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/contrast_text.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Contrast Text Color — contrast_text","text":"function aids deciding font color print given background. function based example provided teppo: https://stackoverflow.com//66669838/21019325. different methods provided based methods outlined StackOverflow thread: https://stackoverflow.com/questions/596216/formula--determine-perceived-brightness--rgb-color","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/contrast_text.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Contrast Text Color 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overview datagrid — create_overview_datagrid","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/create_overview_datagrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a data overview datagrid — create_overview_datagrid","text":"datagrid","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/create_overview_datagrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a data overview datagrid — create_overview_datagrid","text":"","code":"mtcars |>   overview_vars() |>   create_overview_datagrid()      {\"x\":{\"nrow\":11,\"ncol\":7,\"data\":[[\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\"],[\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\"],[\"mpg\",\"cyl\",\"disp\",\"hp\",\"drat\",\"wt\",\"qsec\",\"vs\",\"am\",\"gear\",\"carb\"],[0,0,0,0,0,0,0,0,0,0,0],[1,1,1,1,1,1,1,1,1,1,1],[25,3,27,22,22,29,30,2,2,3,6],[[21,21,22.8,21.4,18.7,18.1,14.3,24.4,22.8,19.2,17.8,16.4,17.3,15.2,10.4,10.4,14.7,32.4,30.4,33.9,21.5,15.5,15.2,13.3,19.2,27.3,26,30.4,15.8,19.7,15,21.4],[6,6,4,6,8,6,8,4,4,6,6,8,8,8,8,8,8,4,4,4,4,8,8,8,8,4,4,4,8,6,8,4],[160,160,108,258,360,225,360,146.7,140.8,167.6,167.6,275.8,275.8,275.8,472,460,440,78.7,75.7,71.09999999999999,120.1,318,304,350,400,79,120.3,95.09999999999999,351,145,301,121],[110,110,93,110,175,105,245,62,95,123,123,180,180,180,205,215,230,66,52,65,97,150,150,245,175,66,91,113,264,175,335,109],[3.9,3.9,3.85,3.08,3.15,2.76,3.21,3.69,3.92,3.92,3.92,3.07,3.07,3.07,2.93,3,3.23,4.08,4.93,4.22,3.7,2.76,3.15,3.73,3.08,4.08,4.43,3.77,4.22,3.62,3.54,4.11],[2.62,2.875,2.32,3.215,3.44,3.46,3.57,3.19,3.15,3.44,3.44,4.07,3.73,3.78,5.25,5.424,5.345,2.2,1.615,1.835,2.465,3.52,3.435,3.84,3.845,1.935,2.14,1.513,3.17,2.77,3.57,2.78],[16.46,17.02,18.61,19.44,17.02,20.22,15.84,20,22.9,18.3,18.9,17.4,17.6,18,17.98,17.82,17.42,19.47,18.52,19.9,20.01,16.87,17.3,15.41,17.05,18.9,16.7,16.9,14.5,15.5,14.6,18.6],[0,0,1,1,0,1,0,1,1,1,1,0,0,0,0,0,0,1,1,1,1,0,0,0,0,1,0,1,0,0,0,1],[1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,1,1,1,1,1],[4,4,4,3,3,3,3,4,4,4,4,3,3,3,3,3,3,4,4,4,3,3,3,3,3,4,5,5,5,5,5,4],[4,4,1,1,2,1,4,2,2,4,4,3,3,3,4,4,4,1,2,1,1,2,2,4,2,1,2,2,4,6,8,2]]],\"colnames\":[\"class\",\"type\",\"name\",\"n_missing\",\"p_complete\",\"n_unique\",\"vals\"],\"options\":{\"columns\":[{\"header\":\" 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bslib::bs_theme()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/custom_theme.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom theme based on unity — custom_theme","text":"theme list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut-variable.html","id":null,"dir":"Reference","previous_headings":"","what":"Module to Convert Numeric to Factor — cut-variable","title":"Module to Convert Numeric to Factor — cut-variable","text":"module contain interface cut numeric several intervals.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut-variable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module to Convert Numeric to Factor — cut-variable","text":"","code":"cut_variable_ui(id)  cut_variable_server(id, data_r = reactive(NULL))  modal_cut_variable(   id,   title = i18n(\"Convert Numeric to Factor\"),   easyClose = TRUE,   size = \"l\",   footer = NULL )  winbox_cut_variable(   id,   title = i18n(\"Convert Numeric to Factor\"),   options = shinyWidgets::wbOptions(),   controls = shinyWidgets::wbControls() )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut-variable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module to Convert Numeric to Factor — cut-variable","text":"id Module ID. data_r shiny::reactive() function returning data.frame. title optional title dialog. easyClose TRUE, modal dialog can dismissed clicking outside dialog box, pressing Escape key. FALSE (default), modal dialog dismissed ways; instead must dismissed clicking modalButton(), call removeModal() server. size One \"s\" small, \"m\" (default) medium, \"l\" large, \"xl\" extra large. Note \"xl\" works Bootstrap 4 (opt-Bootstrap 4+, pass bslib::bs_theme() theme argument page container like fluidPage()). footer UI footer. Use NULL footer. options List options, see wbOptions(). controls List controls, see wbControls().","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut-variable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module to Convert Numeric to Factor — cut-variable","text":"shiny::reactive() function returning data.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut.html","id":null,"dir":"Reference","previous_headings":"","what":"Extended cutting function — cut.hms","title":"Extended cutting function — cut.hms","text":"Extended cutting function","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extended cutting function — cut.hms","text":"","code":"# S3 method for class 'hms' cut(x, breaks, ...)  # S3 method for class 'POSIXt' cut(   x,   breaks,   right = FALSE,   include.lowest = TRUE,   start.on.monday = TRUE,   ... )  # S3 method for class 'POSIXct' cut(   x,   breaks,   right = FALSE,   include.lowest = TRUE,   start.on.monday = TRUE,   ... )  # S3 method for class 'Date' cut(x, breaks, start.on.monday = TRUE, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extended cutting function — cut.hms","text":"x object inheriting class \"POSIXct\" ... passed ","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extended cutting function — cut.hms","text":"factor","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extended cutting function — cut.hms","text":"","code":"readr::parse_time(c(\"01:00:20\", \"03:00:20\", \"01:20:20\", \"08:20:20\", \"21:20:20\", \"03:02:20\")) |> cut(2) #> [1] 01:00:20 01:00:20 01:00:20 03:01:20 <NA>     03:01:20 #> attr(,\"brks\") #> 01:00:20 #> 03:01:20 #> 21:20:20 #> Levels: 01:00:20 03:01:20 readr::parse_time(c(\"01:00:20\", \"03:00:20\", \"01:20:20\", \"08:20:20\", \"21:20:20\", \"03:02:20\")) |> cut(\"min\") #> [1] 01:00:00 03:00:00 01:20:00 08:20:00 21:20:00 03:02:00 #> attr(,\"brks\") #> 01:00:00 #> 01:20:00 #> 03:00:00 #> 03:02:00 #> 08:20:00 #> 21:20:00 #> 21:20:20 #> Levels: 01:00:00 01:20:00 03:00:00 03:02:00 08:20:00 21:20:00 readr::parse_time(c(\"01:00:20\", \"03:00:20\", \"01:20:20\", \"08:20:20\", \"21:20:20\", \"03:02:20\")) |> cut(breaks = \"hour\") #> [1] 01:00:00 03:00:00 01:00:00 08:00:00 21:00:00 03:00:00 #> attr(,\"brks\") #> 01:00:00 #> 03:00:00 #> 08:00:00 #> 21:00:00 #> 21:20:20 #> Levels: 01:00:00 03:00:00 08:00:00 21:00:00 readr::parse_time(c(\"01:00:20\", \"03:00:20\", \"01:20:20\", \"08:20:20\", \"21:20:20\", \"03:02:20\")) |> cut(breaks = hms::as_hms(c(\"01:00:00\", \"03:01:20\", \"9:20:20\"))) #> [1] 01:00:00 01:00:00 01:00:00 03:01:20 <NA>     03:01:20 #> attr(,\"brks\") #> 01:00:00 #> 03:01:20 #> 09:20:20 #> Levels: 01:00:00 03:01:20 d_t <- readr::parse_time(c(\"01:00:20\", \"03:00:20\", \"01:20:20\", \"03:02:20\", NA)) f <- d_t |> cut(2) readr::parse_time(c(\"01:00:20\", \"03:00:20\", \"01:20:20\", \"03:02:20\", NA)) |> cut(breaks = lubridate::as_datetime(c(hms::as_hms(levels(f)), hms::as_hms(max(d_t, na.rm = TRUE) + 1))), right = FALSE) #> Warning: tz(): Don't know how to compute timezone for object of class hms/difftime; returning \"UTC\". #> [1] 01:00:20 02:10:20 01:00:20 02:10:20 <NA>     #> attr(,\"brks\") #> 01:00:20 #> 02:10:20 #> 03:02:21 #> Levels: 01:00:20 02:10:20 readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(2) #> [1] 1992-02-01 01:00:20 1992-02-01 01:00:20 1992-02-01 01:00:20 #> [4] 1992-02-01 01:00:20 1999-02-01 21:20:20 1992-02-01 01:00:20 #> Levels: 1992-02-01 01:00:20 1999-02-01 21:20:20 readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(breaks=\"weekday\") #> Error in cut.POSIXt(readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\",     \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\",     \"1992-12-01 03:02:20\")), breaks = \"weekday\"): invalid specification of 'breaks' readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(breaks=\"month_only\") #> Error in cut.POSIXt(readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\",     \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\",     \"1992-12-01 03:02:20\")), breaks = \"month_only\"): invalid specification of 'breaks' as.Date(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(2) #> [1] 1992-02-01 1992-02-01 1992-02-01 1992-02-01 1999-02-01 1992-02-01 #> Levels: 1992-02-01 1999-02-01 as.Date(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(breaks=\"weekday\") #> Error in cut.Date(as.Date(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\",     \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\",     \"1992-12-01 03:02:20\")), breaks = \"weekday\"): invalid specification of 'breaks'"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":null,"dir":"Reference","previous_headings":"","what":"Data correlations evaluation module — data-correlations","title":"Data correlations evaluation module — data-correlations","text":"Data correlations evaluation module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data correlations evaluation module — data-correlations","text":"","code":"data_correlations_ui(id, ...)  data_correlations_server(id, data, include.class = NULL, cutoff = 0.7, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data correlations evaluation module — data-correlations","text":"id Module id. (Use 'ns(\"id\")') ... arguments passed toastui::datagrid data data color.main main color color.sec secondary color","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data correlations evaluation module — data-correlations","text":"Shiny ui module shiny server module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-import.html","id":null,"dir":"Reference","previous_headings":"","what":"Test app for the data-import module — data_import_demo_app","title":"Test app for the data-import module — data_import_demo_app","text":"Test app data-import module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-import.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test app for the data-import module — data_import_demo_app","text":"","code":"data_import_demo_app()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-import.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test app for the data-import module — data_import_demo_app","text":"","code":"if (FALSE) { # \\dontrun{ data_import_demo_app() } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Data correlations evaluation module — data-plots","title":"Data correlations evaluation module — data-plots","text":"Data correlations evaluation module Wrapper create plot based provided type Nice horizontal stacked bars (Grotta bars) Plot nice ridge plot Readying data sankey plot Beautiful sankey plot option split tertiary group Beautiful violin plot Beatiful violin plot","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data correlations evaluation module — data-plots","text":"","code":"data_visuals_ui(id, tab_title = \"Plots\", ...)  data_visuals_server(id, data, ...)  create_plot(data, type, x, y, z = NULL, ...)  plot_hbars(data, x, y, z = NULL)  plot_ridge(data, x, y, z = NULL, ...)  sankey_ready(data, x, y, numbers = \"count\", ...)  plot_sankey(data, x, y, z = NULL, color.group = \"x\", colors = NULL)  plot_scatter(data, x, y, z = NULL)  plot_violin(data, x, y, z = NULL)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data correlations evaluation module — data-plots","text":"id Module id. (Use 'ns(\"id\")') ... ignored now data data.frame type plot type (derived possible_plots() matches custom function) x primary variable y secondary variable z tertiary variable","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data correlations evaluation module — data-plots","text":"Shiny ui module shiny server module ggplot2 object ggplot2 object ggplot2 object data.frame ggplot2 object ggplot2 object ggplot2 object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data correlations evaluation module — data-plots","text":"","code":"create_plot(mtcars, \"plot_violin\", \"mpg\", \"cyl\") #> Error in if (!z %in% names(data)) {    z <- NULL}: argument is of length zero mtcars |> plot_hbars(x = \"carb\", y = \"cyl\") #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale.  mtcars |> plot_hbars(x = \"carb\", y = NULL) #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale.  mtcars |>   default_parsing() |>   plot_ridge(x = \"mpg\", y = \"cyl\") #> Picking joint bandwidth of 1.38  mtcars |> plot_ridge(x = \"mpg\", y = \"cyl\", z = \"gear\") #> Picking joint bandwidth of 1.52 #> Warning: The following aesthetics were dropped during statistical transformation: y and #> fill. #> ℹ This can happen when ggplot fails to infer the correct grouping structure in #>   the data. #> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical #>   variable into a factor? #> Error in ggridges::geom_density_ridges(): Problem while setting up geom. #> ℹ Error occurred in the 1st layer. #> Caused by error in `compute_geom_1()`: #> ! `geom_density_ridges()` requires the following missing aesthetics: y. ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = sample(c(letters[1:4], NA), 100, TRUE, prob = c(rep(.23, 4), .08))) ds |> sankey_ready(\"first\", \"last\") #> # A tibble: 19 × 7 #>    first last      n gx.sum gy.sum lx          ly          #>    <fct> <fct> <int>  <int>  <int> <fct>       <fct>       #>  1 c     c         5     28     15 \"c\\n(n=28)\" \"c\\n(n=15)\" #>  2 c     a         7     28     32 \"c\\n(n=28)\" \"a\\n(n=32)\" #>  3 c     b         6     28     26 \"c\\n(n=28)\" \"b\\n(n=26)\" #>  4 c     d         6     28     17 \"c\\n(n=28)\" \"d\\n(n=17)\" #>  5 c     NA        4     28     10 \"c\\n(n=28)\"  NA         #>  6 a     c         6     24     15 \"a\\n(n=24)\" \"c\\n(n=15)\" #>  7 a     a         9     24     32 \"a\\n(n=24)\" \"a\\n(n=32)\" #>  8 a     b         6     24     26 \"a\\n(n=24)\" \"b\\n(n=26)\" #>  9 a     d         1     24     17 \"a\\n(n=24)\" \"d\\n(n=17)\" #> 10 a     NA        2     24     10 \"a\\n(n=24)\"  NA         #> 11 b     c         4     20     15 \"b\\n(n=20)\" \"c\\n(n=15)\" #> 12 b     a         8     20     32 \"b\\n(n=20)\" \"a\\n(n=32)\" #> 13 b     b         5     20     26 \"b\\n(n=20)\" \"b\\n(n=26)\" #> 14 b     d         2     20     17 \"b\\n(n=20)\" \"d\\n(n=17)\" #> 15 b     NA        1     20     10 \"b\\n(n=20)\"  NA         #> 16 d     a         8     28     32 \"d\\n(n=28)\" \"a\\n(n=32)\" #> 17 d     b         9     28     26 \"d\\n(n=28)\" \"b\\n(n=26)\" #> 18 d     d         8     28     17 \"d\\n(n=28)\" \"d\\n(n=17)\" #> 19 d     NA        3     28     10 \"d\\n(n=28)\"  NA         ds |> sankey_ready(\"first\", \"last\", numbers = \"percentage\") #> # A tibble: 19 × 7 #>    first last      n gx.sum gy.sum lx         ly         #>    <fct> <fct> <int>  <int>  <int> <fct>      <fct>      #>  1 c     c         5     28     15 \"c\\n(28%)\" \"c\\n(15%)\" #>  2 c     a         7     28     32 \"c\\n(28%)\" \"a\\n(32%)\" #>  3 c     b         6     28     26 \"c\\n(28%)\" \"b\\n(26%)\" #>  4 c     d         6     28     17 \"c\\n(28%)\" \"d\\n(17%)\" #>  5 c     NA        4     28     10 \"c\\n(28%)\"  NA        #>  6 a     c         6     24     15 \"a\\n(24%)\" \"c\\n(15%)\" #>  7 a     a         9     24     32 \"a\\n(24%)\" \"a\\n(32%)\" #>  8 a     b         6     24     26 \"a\\n(24%)\" \"b\\n(26%)\" #>  9 a     d         1     24     17 \"a\\n(24%)\" \"d\\n(17%)\" #> 10 a     NA        2     24     10 \"a\\n(24%)\"  NA        #> 11 b     c         4     20     15 \"b\\n(20%)\" \"c\\n(15%)\" #> 12 b     a         8     20     32 \"b\\n(20%)\" \"a\\n(32%)\" #> 13 b     b         5     20     26 \"b\\n(20%)\" \"b\\n(26%)\" #> 14 b     d         2     20     17 \"b\\n(20%)\" \"d\\n(17%)\" #> 15 b     NA        1     20     10 \"b\\n(20%)\"  NA        #> 16 d     a         8     28     32 \"d\\n(28%)\" \"a\\n(32%)\" #> 17 d     b         9     28     26 \"d\\n(28%)\" \"b\\n(26%)\" #> 18 d     d         8     28     17 \"d\\n(28%)\" \"d\\n(17%)\" #> 19 d     NA        3     28     10 \"d\\n(28%)\"  NA        data.frame(   g = sample(LETTERS[1:2], 100, TRUE),   first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)),   last = sample(c(TRUE, FALSE, FALSE), 100, TRUE) ) |>   sankey_ready(\"first\", \"last\") #> # A tibble: 8 × 7 #>   first last      n gx.sum gy.sum lx          ly              #>   <fct> <fct> <int>  <int>  <int> <fct>       <fct>           #> 1 a     FALSE    21     29     61 \"a\\n(n=29)\" \"FALSE\\n(n=61)\" #> 2 a     TRUE      8     29     39 \"a\\n(n=29)\" \"TRUE\\n(n=39)\"  #> 3 d     FALSE    12     22     61 \"d\\n(n=22)\" \"FALSE\\n(n=61)\" #> 4 d     TRUE     10     22     39 \"d\\n(n=22)\" \"TRUE\\n(n=39)\"  #> 5 b     FALSE    13     26     61 \"b\\n(n=26)\" \"FALSE\\n(n=61)\" #> 6 b     TRUE     13     26     39 \"b\\n(n=26)\" \"TRUE\\n(n=39)\"  #> 7 c     FALSE    15     23     61 \"c\\n(n=23)\" \"FALSE\\n(n=61)\" #> 8 c     TRUE      8     23     39 \"c\\n(n=23)\" \"TRUE\\n(n=39)\"  ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE))) ds |> plot_sankey(\"first\", \"last\") #> Loading required package: ggplot2  ds |> plot_sankey(\"first\", \"last\", color.group = \"y\")  ds |> plot_sankey(\"first\", \"last\", z = \"g\", color.group = \"y\")  mtcars |> plot_scatter(x = \"mpg\", y = \"wt\")  mtcars |> plot_violin(x = \"mpg\", y = \"cyl\", z = \"gear\") #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 1: `cyl = 4`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 1: `cyl = 4`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 2: `cyl = 6`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 2: `cyl = 6`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: Groups with fewer than two datapoints have been dropped. #> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes. #> Warning: Groups with fewer than two datapoints have been dropped. #> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes. #> Warning: Groups with fewer than two datapoints have been dropped. #> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes. #> Warning: Groups with fewer than two datapoints have been dropped. #> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes. #> Warning: Removed 2 rows containing non-finite outside the scale range #> (`stat_ydensity()`). #> Warning: Groups with fewer than two datapoints have been dropped. #> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes. #> Warning: Removed 1 row containing missing values or values outside the scale range #> (`geom_point()`). #> Warning: Removed 4 rows containing non-finite outside the scale range #> (`stat_ydensity()`). #> Warning: Removed 1 row containing missing values or values outside the scale range #> (`geom_point()`). #> Warning: Removed 1 row containing non-finite outside the scale range #> (`stat_ydensity()`). #> Warning: Removed 1 row containing missing values or values outside the scale range #> (`geom_point()`)."},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Data summary module — data-summary","title":"Data summary module — data-summary","text":"Data summary module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data summary module — data-summary","text":"","code":"data_summary_ui(id)  data_summary_server(id, data, color.main, color.sec, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data summary module — data-summary","text":"id Module id. (Use 'ns(\"id\")') data data color.main main color color.sec secondary color ... arguments passed toastui::datagrid","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data summary module — data-summary","text":"Shiny ui module shiny server module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_format_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Defaults qmd formats — default_format_arguments","title":"Defaults qmd formats — default_format_arguments","text":"Defaults qmd formats","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_format_arguments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Defaults qmd formats — default_format_arguments","text":"","code":"default_format_arguments()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_format_arguments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Defaults qmd formats — default_format_arguments","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":null,"dir":"Reference","previous_headings":"","what":"Default data parsing — default_parsing","title":"Default data parsing — default_parsing","text":"Default data parsing","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Default data parsing — default_parsing","text":"","code":"default_parsing(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Default data parsing — default_parsing","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Default data parsing — default_parsing","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Default data parsing — default_parsing","text":"","code":"mtcars |> str() #> 'data.frame':\t32 obs. of  11 variables: #>  $ mpg : num  21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : num  6 6 4 6 8 6 8 4 4 6 ... #>  $ disp: num  160 160 108 258 360 ... #>  $ hp  : num  110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num  3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num  2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num  16.5 17 18.6 19.4 17 ... #>  $ vs  : num  0 0 1 1 0 1 0 1 1 1 ... #>  $ am  : num  1 1 1 0 0 0 0 0 0 0 ... #>  $ gear: num  4 4 4 3 3 3 3 4 4 4 ... #>  $ carb: num  4 4 1 1 2 1 4 2 2 4 ... mtcars |>   default_parsing() |>   str() #> tibble [32 × 11] (S3: tbl_df/tbl/data.frame) #>  $ mpg : num [1:32] 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : Factor w/ 3 levels \"4\",\"6\",\"8\": 2 2 1 2 3 2 3 1 1 2 ... #>  $ disp: num [1:32] 160 160 108 258 360 ... #>  $ hp  : num [1:32] 110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num [1:32] 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num [1:32] 2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num [1:32] 16.5 17 18.6 19.4 17 ... #>  $ vs  : Factor w/ 2 levels \"0\",\"1\": 1 1 2 2 1 2 1 2 2 2 ... #>  $ am  : Factor w/ 2 levels \"0\",\"1\": 2 2 2 1 1 1 1 1 1 1 ... #>  $ gear: Factor w/ 3 levels \"3\",\"4\",\"5\": 2 2 2 1 1 1 1 2 2 2 ... #>  $ carb: Factor w/ 6 levels \"1\",\"2\",\"3\",\"4\",..: 4 4 1 1 2 1 4 2 2 4 ..."},{"path":"https://agdamsbo.github.io/freesearcheR/reference/drop_empty_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Drop empty events from REDCap export — drop_empty_event","title":"Drop empty events from REDCap export — drop_empty_event","text":"Drop empty events REDCap export","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/drop_empty_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Drop empty events from REDCap export — drop_empty_event","text":"","code":"drop_empty_event(data, event = \"redcap_event_name\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/drop_empty_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Drop empty events from REDCap export — drop_empty_event","text":"data data event \"redcap_event_name\", \"redcap_repeat_instrument\" \"redcap_repeat_instance\"","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/drop_empty_event.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Drop empty events from REDCap export — drop_empty_event","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":null,"dir":"Reference","previous_headings":"","what":"Factorize variables in data.frame — factorize","title":"Factorize variables in data.frame — factorize","text":"Factorize variables data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Factorize variables in data.frame — factorize","text":"","code":"factorize(data, vars)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Factorize variables in data.frame — factorize","text":"data data.frame vars variables force factorize","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Factorize variables in data.frame — factorize","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":null,"dir":"Reference","previous_headings":"","what":"Title — file_export","title":"Title — file_export","text":"Title","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title — file_export","text":"","code":"file_export(data, output.format = c(\"df\", \"teal\", \"list\"), filename, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title — file_export","text":"data data output.format output filename filename ... passed ","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title — file_export","text":"data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":null,"dir":"Reference","previous_headings":"","what":"Merges list of named arguments for qmd header generation — format_writer","title":"Merges list of named arguments for qmd header generation — format_writer","text":"Merges list named arguments qmd header generation","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Merges list of named arguments for qmd header generation — format_writer","text":"","code":"format_writer(data, name)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Merges list of named arguments for qmd header generation — format_writer","text":"data vector name name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Merges list of named arguments for qmd header generation — format_writer","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the function options based on the selected function description — get_fun_options","title":"Get the function options based on the selected function description — get_fun_options","text":"Get function options based selected function description","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the function options based on the selected function description — get_fun_options","text":"","code":"get_fun_options(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the function options based on the selected function description — get_fun_options","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the function options based on the selected function description — get_fun_options","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the function options based on the selected function description — get_fun_options","text":"","code":"mtcars |>   default_parsing() |>   dplyr::pull(mpg) |>   possible_functions(design = \"cross-sectional\") |>   (\\(.x){     .x[[1]]   })() |>   get_fun_options() #> $lm #> $lm$descr #> [1] \"Linear regression model\" #>  #> $lm$design #> [1] \"cross-sectional\" #>  #> $lm$out.type #> [1] \"continuous\" #>  #> $lm$fun #> [1] \"stats::lm\" #>  #> $lm$args.list #> NULL #>  #> $lm$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $lm$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $lm$table.args.list #> $lm$table.args.list$exponentiate #> [1] FALSE #>  #>  #>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Print label, and if missing print variable name — get_label","title":"Print label, and if missing print variable name — get_label","text":"Print label, missing print variable name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print label, and if missing print variable name — get_label","text":"","code":"get_label(data, var = NULL)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print label, and if missing print variable name — get_label","text":"data vector data frame var variable name. Optional.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print label, and if missing print variable name — get_label","text":"character string","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Print label, and if missing print variable name — get_label","text":"","code":"mtcars |> get_label(var = \"mpg\") #> [1] \"mpg\" mtcars |> get_label() #> [1] \"mtcars\" mtcars$mpg |> get_label() #> [1] \"mtcars$mpg\" gtsummary::trial |> get_label(var = \"trt\") #> [1] \"Chemotherapy Treatment\" 1:10 |> get_label() #> [1] \"1:10\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the function options based on the selected function description — get_plot_options","title":"Get the function options based on the selected function description — get_plot_options","text":"Get function options based selected function description","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the function options based on the selected function description — get_plot_options","text":"","code":"get_plot_options(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the function options based on the selected function description — get_plot_options","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the function options based on the selected function description — get_plot_options","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the function options based on the selected function description — get_plot_options","text":"","code":"ls <- mtcars |>   default_parsing() |>   dplyr::pull(mpg) |>   possible_plots() |>   (\\(.x){     .x[[1]]   })() |>   get_plot_options()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"function follows idea comment: https://stackoverflow.com/questions/38983179/-call--function--r-without-loading--package","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"","code":"getfun(x)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"x function function name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"function character vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"","code":"getfun(\"stats::lm\") #> function (formula, data, subset, weights, na.action, method = \"qr\",  #>     model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, offset, ...)  #> { #>     ret.x <- x #>     ret.y <- y #>     cl <- match.call() #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (method == \"model.frame\")  #>         return(mf) #>     else if (method != \"qr\")  #>         warning(gettextf(\"method = '%s' is not supported. Using 'qr'\",  #>             method), domain = NA) #>     mt <- attr(mf, \"terms\") #>     y <- model.response(mf, \"numeric\") #>     w <- as.vector(model.weights(mf)) #>     if (!is.null(w) && !is.numeric(w))  #>         stop(\"'weights' must be a numeric vector\") #>     offset <- model.offset(mf) #>     mlm <- is.matrix(y) #>     ny <- if (mlm)  #>         nrow(y) #>     else length(y) #>     if (!is.null(offset)) { #>         if (!mlm)  #>             offset <- as.vector(offset) #>         if (NROW(offset) != ny)  #>             stop(gettextf(\"number of offsets is %d, should equal %d (number of observations)\",  #>                 NROW(offset), ny), domain = NA) #>     } #>     if (is.empty.model(mt)) { #>         x <- NULL #>         z <- list(coefficients = if (mlm) matrix(NA_real_, 0,  #>             ncol(y)) else numeric(), residuals = y, fitted.values = 0 *  #>             y, weights = w, rank = 0L, df.residual = if (!is.null(w)) sum(w !=  #>             0) else ny) #>         if (!is.null(offset)) { #>             z$fitted.values <- offset #>             z$residuals <- y - offset #>         } #>     } #>     else { #>         x <- model.matrix(mt, mf, contrasts) #>         z <- if (is.null(w))  #>             lm.fit(x, y, offset = offset, singular.ok = singular.ok,  #>                 ...) #>         else lm.wfit(x, y, w, offset = offset, singular.ok = singular.ok,  #>             ...) #>     } #>     class(z) <- c(if (mlm) \"mlm\", \"lm\") #>     z$na.action <- attr(mf, \"na.action\") #>     z$offset <- offset #>     z$contrasts <- attr(x, \"contrasts\") #>     z$xlevels <- .getXlevels(mt, mf) #>     z$call <- cl #>     z$terms <- mt #>     if (model)  #>         z$model <- mf #>     if (ret.x)  #>         z$x <- x #>     if (ret.y)  #>         z$y <- y #>     if (!qr)  #>         z$qr <- NULL #>     z #> } #> <bytecode: 0x560e4a1f0950> #> <environment: namespace:stats>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_export.html","id":null,"dir":"Reference","previous_headings":"","what":"GGplot default theme for plotting export objects — gg_theme_export","title":"GGplot default theme for plotting export objects — gg_theme_export","text":"GGplot default theme plotting export objects","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_export.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GGplot default theme for plotting export objects — gg_theme_export","text":"","code":"gg_theme_export()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_export.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GGplot default theme for plotting export objects — gg_theme_export","text":"data ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_export.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"GGplot default theme for plotting export objects — gg_theme_export","text":"ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_shiny.html","id":null,"dir":"Reference","previous_headings":"","what":"GGplot default theme for plotting in Shiny — gg_theme_shiny","title":"GGplot default theme for plotting in Shiny — gg_theme_shiny","text":"GGplot default theme plotting Shiny","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_shiny.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GGplot default theme for plotting in Shiny — gg_theme_shiny","text":"","code":"gg_theme_shiny()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_shiny.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GGplot default theme for plotting in Shiny — gg_theme_shiny","text":"data ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_shiny.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"GGplot default theme for plotting in Shiny — gg_theme_shiny","text":"ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/ggeulerr.html","id":null,"dir":"Reference","previous_headings":"","what":"Area proportional venn diagrams — ggeulerr","title":"Area proportional venn diagrams — ggeulerr","text":"slightly modified https://gist.github.com/danlooo/d23d8bcf8856c7dd8e86266097404ded functions uses eulerr::euler plot area proportional venn diagramms plots using ggplot2","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/ggeulerr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Area proportional venn diagrams — ggeulerr","text":"","code":"ggeulerr(combinations, show_quantities = TRUE, show_labels = TRUE, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/ggeulerr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Area proportional venn diagrams — ggeulerr","text":"combinations set relationships named numeric vector, matrix, data.frame(See eulerr::euler) show_quantities whether show number intersecting elements show_labels whether show set names ... arguments passed eulerr::euler","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/grepl_fix.html","id":null,"dir":"Reference","previous_headings":"","what":"Matches pattern to vector based on match type — grepl_fix","title":"Matches pattern to vector based on match type — grepl_fix","text":"Matches pattern vector based match type","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/grepl_fix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Matches pattern to vector based on match type — grepl_fix","text":"","code":"grepl_fix(data, pattern, type = c(\"prefix\", \"infix\", \"suffix\"))"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/grepl_fix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Matches pattern to vector based on match type — grepl_fix","text":"data vector pattern pattern(s) match. Character vector length 1 . type type match. can one \"prefix\",\"infix\" \"suffix\".","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/grepl_fix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Matches pattern to vector based on match type — grepl_fix","text":"logical vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/grepl_fix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Matches pattern to vector based on match type — grepl_fix","text":"","code":"c(\"id\", \"age\", \"weight_0\", \"weight_1\") |> grepl_fix(pattern = c(\"_0\", \"_1\"), type = \"suffix\") #> [1] FALSE FALSE  TRUE  TRUE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file-type.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to ease data file import — import-file-type","title":"Wrapper to ease data file import — import-file-type","text":"Wrapper ease data file import","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file-type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to ease data file import — import-file-type","text":"","code":"import_delim(file, skip, encoding, na.strings)  import_xls(file, sheet, skip, na.strings)  import_ods(file, sheet, skip, na.strings)  import_dta(file)  import_rds(file)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file-type.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to ease data file import — import-file-type","text":"file path file skip number row skip encoding file encoding na.strings character(s) interpret missing values. sheet Excel files, sheet read","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file-type.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper to ease data file import — import-file-type","text":"data.frame data.frame data.frame data.frame data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file.html","id":null,"dir":"Reference","previous_headings":"","what":"Import data from a file — import-file","title":"Import data from a file — import-file","text":"Let user upload file import data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Import data from a file — import-file","text":"","code":"import_file_ui(   id,   title = \"\",   preview_data = TRUE,   file_extensions = c(\".csv\", \".txt\", \".xls\", \".xlsx\", \".rds\", \".fst\", \".sas7bdat\",     \".sav\"),   layout_params = c(\"dropdown\", \"inline\") )  import_file_server(   id,   btn_show_data = TRUE,   show_data_in = c(\"popup\", \"modal\"),   trigger_return = c(\"button\", \"change\"),   return_class = c(\"data.frame\", \"data.table\", \"tbl_df\", \"raw\"),   reset = reactive(NULL) )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Import data from a file — import-file","text":"preview_data Show preview data file input. file_extensions File extensions accepted shiny::fileInput(), can also MIME type. layout_params display import parameters : dropdown button inline file input.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file_module.html","id":null,"dir":"Reference","previous_headings":"","what":"Test app for the import_file module — import_file_demo_app","title":"Test app for the import_file module — import_file_demo_app","text":"Test app import_file module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file_module.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test app for the import_file module — import_file_demo_app","text":"","code":"import_file_demo_app()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file_module.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test app for the import_file module — import_file_demo_app","text":"","code":"if (FALSE) { # \\dontrun{ import_file_demo_app() } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/index_embed.html","id":null,"dir":"Reference","previous_headings":"","what":"Split vector by an index and embed addition — index_embed","title":"Split vector by an index and embed addition — index_embed","text":"Split vector index embed addition","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/index_embed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split vector by an index and embed addition — index_embed","text":"","code":"index_embed(data, index, add = NULL)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/index_embed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split vector by an index and embed addition — index_embed","text":"data vector index split index add addition","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/index_embed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split vector by an index and embed addition — index_embed","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":null,"dir":"Reference","previous_headings":"","what":"Test class — is_any_class","title":"Test class — is_any_class","text":"Test class","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test class — is_any_class","text":"","code":"is_any_class(data, class.vec)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test class — is_any_class","text":"data data class.vec vector class names test","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test class — is_any_class","text":"factor","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test class — is_any_class","text":"","code":"if (FALSE) { # \\dontrun{ vapply(REDCapCAST::redcapcast_data, \\(.x){   is_any_class(.x, c(\"hms\", \"Date\", \"POSIXct\", \"POSIXt\")) }, logical(1)) } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"Checks elements vector equally spaced indication ID","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"","code":"is_consecutive(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"logical","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"","code":"1:10 |> is_consecutive() #> [1] TRUE sample(1:100,40) |> is_consecutive() #> [1] FALSE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":null,"dir":"Reference","previous_headings":"","what":"Test is date/datetime/time — is_datetime","title":"Test is date/datetime/time — is_datetime","text":"Test date/datetime/time","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test is date/datetime/time — is_datetime","text":"","code":"is_datetime(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test is date/datetime/time — is_datetime","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test is date/datetime/time — is_datetime","text":"factor","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test is date/datetime/time — is_datetime","text":"","code":"vapply(REDCapCAST::redcapcast_data, is_datetime, logical(1)) #>                    record_id            redcap_event_name  #>                        FALSE                        FALSE  #>     redcap_repeat_instrument       redcap_repeat_instance  #>                        FALSE                        FALSE  #>                          cpr                    inclusion  #>                        FALSE                         TRUE  #>               inclusion_time                          dob  #>                         TRUE                         TRUE  #>                          age                  age_integer  #>                        FALSE                        FALSE  #>                          sex                 cohabitation  #>                        FALSE                        FALSE  #>                 hypertension                     diabetes  #>                        FALSE                        FALSE  #>                       region baseline_data_start_complete  #>                        FALSE                        FALSE  #>                 mrs_assessed                     mrs_date  #>                        FALSE                         TRUE  #>                    mrs_score                 mrs_complete  #>                        FALSE                        FALSE  #>                      con_mrs                     con_calc  #>                        FALSE                        FALSE  #>           consensus_complete               event_datetime  #>                        FALSE                         TRUE  #>                    event_age                   event_type  #>                        FALSE                        FALSE  #>           new_event_complete  #>                        FALSE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if url is valid format for REDCap API — is_valid_redcap_url","title":"Test if url is valid format for REDCap API — is_valid_redcap_url","text":"Test url valid format REDCap API","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if url is valid format for REDCap API — is_valid_redcap_url","text":"","code":"is_valid_redcap_url(url)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if url is valid format for REDCap API — is_valid_redcap_url","text":"url url","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test if url is valid format for REDCap API — is_valid_redcap_url","text":"logical","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test if url is valid format for REDCap API — is_valid_redcap_url","text":"","code":"url <- c(   \"www.example.com\",   \"redcap.your.inst/api/\",   \"https://redcap.your.inst/api/\",   \"https://your.inst/redcap/api/\",   \"https://www.your.inst/redcap/api/\" ) is_valid_redcap_url(url) #> [1] FALSE FALSE  TRUE  TRUE  TRUE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate REDCap token — is_valid_token","title":"Validate REDCap token — is_valid_token","text":"Validate REDCap token","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate REDCap token — is_valid_token","text":"","code":"is_valid_token(token, pattern_env = NULL, nchar = 32)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate REDCap token — is_valid_token","text":"token token pattern_env pattern","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate REDCap token — is_valid_token","text":"logical","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate REDCap token — is_valid_token","text":"","code":"token <- paste(sample(c(1:9, LETTERS[1:6]), 32, TRUE), collapse = \"\") is_valid_token(token) #> [1] TRUE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":null,"dir":"Reference","previous_headings":"","what":"Easily launch the freesearcheR app — launch_freesearcheR","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"Easily launch freesearcheR app","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"","code":"launch_freesearcheR(...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"... passed shiny::runApp()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"shiny app","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":null,"dir":"Reference","previous_headings":"","what":"Line breaking at given number of characters for nicely plotting labels — line_break","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"Line breaking given number characters nicely plotting labels","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"","code":"line_break(data, lineLength = 20, fixed = FALSE)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"data string lineLength maximum line length fixed flag force split exactly value given lineLength. Default FALSE, splitting spaces.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"character string","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"","code":"\"Lorem ipsum... you know the routine\" |> line_break() #> [1] \"Lorem ipsum... you\\nknow the routine\" paste(sample(letters[1:10], 100, TRUE), collapse = \"\") |> line_break(fixed = TRUE) #> [1] \"jdhegaaegchcffhcedhcgghhdifbfjheabacfibfhecjigehjdgdjfaffbfhfcghgefddidiihdhbgedgdgaahcjicggefhgfjhb\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":null,"dir":"Reference","previous_headings":"","what":"Shiny UI module to load a data file — m_datafileUI","title":"Shiny UI module to load a data file — m_datafileUI","text":"Shiny UI module load data file","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shiny UI module to load a data file — m_datafileUI","text":"","code":"m_datafileUI(id)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shiny UI module to load a data file — m_datafileUI","text":"id id","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shiny UI module to load a data file — m_datafileUI","text":"shiny UI","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"Wrapper pivot gtsummary table data long plotting","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"","code":"merge_long(list, model.names)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"list custom regression models list model.names names models include","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/missing_fraction.html","id":null,"dir":"Reference","previous_headings":"","what":"Get missingsness fraction — missing_fraction","title":"Get missingsness fraction — missing_fraction","text":"Get missingsness fraction","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/missing_fraction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get missingsness fraction — missing_fraction","text":"","code":"missing_fraction(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/missing_fraction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get missingsness fraction — missing_fraction","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/missing_fraction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get missingsness fraction — missing_fraction","text":"numeric vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/missing_fraction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get missingsness fraction — missing_fraction","text":"","code":"c(NA,1:10,rep(NA,3)) |> missing_fraction() #> [1] 0.2857143"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to modify quarto file to render specific formats — modify_qmd","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"Wrapper modify quarto file render specific formats","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"","code":"modify_qmd(file, format)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"file filename format desired output","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"none","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":null,"dir":"Reference","previous_headings":"","what":"Outcome data type assessment — outcome_type","title":"Outcome data type assessment — outcome_type","text":"Outcome data type assessment","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Outcome data type assessment — outcome_type","text":"","code":"outcome_type(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Outcome data type assessment — outcome_type","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Outcome data type assessment — outcome_type","text":"outcome type","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Outcome data type assessment — outcome_type","text":"","code":"mtcars |>   default_parsing() |>   lapply(outcome_type) #> $mpg #> [1] \"continuous\" #>  #> $cyl #> [1] \"ordinal\" #>  #> $disp #> [1] \"continuous\" #>  #> $hp #> [1] \"continuous\" #>  #> $drat #> [1] \"continuous\" #>  #> $wt #> [1] \"continuous\" #>  #> $qsec #> [1] \"continuous\" #>  #> $vs #> [1] \"dichotomous\" #>  #> $am #> [1] \"dichotomous\" #>  #> $gear #> [1] \"ordinal\" #>  #> $carb #> [1] \"ordinal\" #>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a data overview data.frame ready for sparklines — overview_vars","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"Create data overview data.frame ready sparklines","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"","code":"overview_vars(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"","code":"mtcars |> overview_vars() #> # A tibble: 11 × 7 #>    class   type    name  n_missing p_complete n_unique vals         #>    <chr>   <chr>   <chr>     <dbl>      <dbl>    <int> <named list> #>  1 numeric numeric mpg           0          1       25 <dbl [32]>   #>  2 numeric numeric cyl           0          1        3 <dbl [32]>   #>  3 numeric numeric disp          0          1       27 <dbl [32]>   #>  4 numeric numeric hp            0          1       22 <dbl [32]>   #>  5 numeric numeric drat          0          1       22 <dbl [32]>   #>  6 numeric numeric wt            0          1       29 <dbl [32]>   #>  7 numeric numeric qsec          0          1       30 <dbl [32]>   #>  8 numeric numeric vs            0          1        2 <dbl [32]>   #>  9 numeric numeric am            0          1        2 <dbl [32]>   #> 10 numeric numeric gear          0          1        3 <dbl [32]>   #> 11 numeric numeric carb          0          1        6 <dbl [32]>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"Regression coef plot gtsummary. Slightly modified pass arguments","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"","code":"# S3 method for class 'tbl_regression' plot(x, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"x (tbl_regression, tbl_uvregression) 'tbl_regression' 'tbl_uvregression' object ... arguments passed ggstats::ggcoef_plot(...)","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"","code":"if (FALSE) { # \\dontrun{ mod <- lm(mpg ~ ., mtcars) p <- mod |>   gtsummary::tbl_regression() |>   plot(colour = \"variable\") } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler.html","id":null,"dir":"Reference","previous_headings":"","what":"Easily plot euler diagrams — plot_euler","title":"Easily plot euler diagrams — plot_euler","text":"Easily plot euler diagrams","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Easily plot euler diagrams — plot_euler","text":"","code":"plot_euler(data, x, y, z = NULL, seed = 2103)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Easily plot euler diagrams — plot_euler","text":"data data x name main variable y name secondary variables z grouping variable seed seed","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Easily plot euler diagrams — plot_euler","text":"patchwork object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Easily plot euler diagrams — plot_euler","text":"","code":"data.frame(   A = sample(c(TRUE, TRUE, FALSE), 50, TRUE),   B = sample(c(\"A\", \"C\"), 50, TRUE),   C = sample(c(TRUE, FALSE, FALSE, FALSE), 50, TRUE),   D = sample(c(TRUE, FALSE, FALSE, FALSE), 50, TRUE) ) |> plot_euler(\"A\", c(\"B\", \"C\"), \"D\", seed = 4)  mtcars |> plot_euler(\"vs\", \"am\", seed = 1) #> [[1]]  #>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler_single.html","id":null,"dir":"Reference","previous_headings":"","what":"Easily plot single euler diagrams — plot_euler_single","title":"Easily plot single euler diagrams — plot_euler_single","text":"Easily plot single euler diagrams","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler_single.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Easily plot single euler diagrams — plot_euler_single","text":"","code":"plot_euler_single(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler_single.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Easily plot single euler diagrams — plot_euler_single","text":"ggplot2 object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler_single.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Easily plot single euler diagrams — plot_euler_single","text":"","code":"data.frame(   A = sample(c(TRUE, TRUE, FALSE), 50, TRUE),   B = sample(c(\"A\", \"C\"), 50, TRUE),   C = sample(c(TRUE, FALSE, FALSE, FALSE), 50, TRUE),   D = sample(c(TRUE, FALSE, FALSE, FALSE), 50, TRUE) ) |> plot_euler_single()  mtcars[c(\"vs\", \"am\")] |> plot_euler_single()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":null,"dir":"Reference","previous_headings":"","what":"Beautiful sankey plot — plot_sankey_single","title":"Beautiful sankey plot — plot_sankey_single","text":"Beautiful sankey plot","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Beautiful sankey plot — plot_sankey_single","text":"","code":"plot_sankey_single(data, x, y, color.group = c(\"x\", \"y\"), colors = NULL, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Beautiful sankey plot — plot_sankey_single","text":"color.group set group colour . \"x\" \"y\". colors optinally specify colors. Give NA color, color level primary group color level secondary group. ... passed sankey_ready()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Beautiful sankey plot — plot_sankey_single","text":"ggplot2 object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Beautiful sankey plot — plot_sankey_single","text":"","code":"ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE))) ds |> plot_sankey_single(\"first\", \"last\") #> Warning: Some strata appear at multiple axes. #> Warning: Some strata appear at multiple axes. #> Warning: Some strata appear at multiple axes.  ds |> plot_sankey_single(\"first\", \"last\", color.group = \"y\") #> Warning: Some strata appear at multiple axes. #> Warning: Some strata appear at multiple axes. #> Warning: Some strata appear at multiple axes.  data.frame(   g = sample(LETTERS[1:2], 100, TRUE),   first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)),   last = sample(c(TRUE, FALSE, FALSE), 100, TRUE) ) |>   plot_sankey_single(\"first\", \"last\", color.group = \"x\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Get possible regression models — possible_functions","title":"Get possible regression models — possible_functions","text":"Get possible regression models","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get possible regression models — possible_functions","text":"","code":"possible_functions(data, design = c(\"cross-sectional\"))"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get possible regression models — possible_functions","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get possible regression models — possible_functions","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get possible regression models — possible_functions","text":"","code":"mtcars |>   default_parsing() |>   dplyr::pull(\"cyl\") |>   possible_functions(design = \"cross-sectional\") #> [1] \"Ordinal logistic regression model\"  mtcars |>   default_parsing() |>   dplyr::select(\"cyl\") |>   possible_functions(design = \"cross-sectional\") #> [1] \"Ordinal logistic regression model\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Get possible regression models — possible_plots","title":"Get possible regression models — possible_plots","text":"Get possible regression models","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get possible regression models — possible_plots","text":"","code":"possible_plots(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get possible regression models — possible_plots","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get possible regression models — possible_plots","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get possible regression models — possible_plots","text":"","code":"mtcars |>   default_parsing() |>   dplyr::pull(\"cyl\") |>   possible_plots() #> [1] \"Stacked horizontal bars\" \"Violin plot\"             #> [3] \"Sankey plot\"              mtcars |>   default_parsing() |>   dplyr::select(\"mpg\") |>   possible_plots() #> [1] \"Violin plot\"  \"Scatter plot\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Flexible file import based on extension — read_input","title":"Flexible file import based on extension — read_input","text":"Flexible file import based extension","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Flexible file import based on extension — read_input","text":"","code":"read_input(file, consider.na = c(\"NA\", \"\\\"\\\"\", \"\"))"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Flexible file import based on extension — read_input","text":"file file name consider.na character vector strings consider NAs","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Flexible file import based on extension — read_input","text":"tibble","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Flexible file import based on extension — read_input","text":"","code":"read_input(\"https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv\") #> Rows: 28 Columns: 8 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> dbl (8): id, ab, age, imm, vis, ver, att, del #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> # A tibble: 28 × 8 #>       id    ab   age   imm   vis   ver   att   del #>    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1     1     1    74    38    35    30    29    35 #>  2     1     2    69    36    36    21    27    37 #>  3     2     1    63    32    31    26    34    38 #>  4     2     2    64    37    34    26    36    46 #>  5     3     1    69    39    33    31    47    29 #>  6     3     2    70    40    36    31    46    25 #>  7     4     1    79    44    37    20    37    36 #>  8     4     2    81    35    36    31    37    40 #>  9     5     1    77    35    26    17    20    36 #> 10     5     2    80    29    34    18    23    36 #> # ℹ 18 more rows"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":null,"dir":"Reference","previous_headings":"","what":"Shiny module to browser and export REDCap data — m_redcap_readUI","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"Shiny module browser export REDCap data Test app redcap_read_shiny_module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"","code":"m_redcap_readUI(id, title = TRUE)  m_redcap_readServer(id)  redcap_demo_app()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"id Namespace id include_title logical include title","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"shiny ui element shiny server module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"","code":"if (FALSE) { # \\dontrun{ redcap_demo_app() } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a regression model programatically — regression_model","title":"Create a regression model programatically — regression_model","text":"Output concatenated list model information model","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a regression model programatically — regression_model","text":"","code":"regression_model(   data,   outcome.str,   auto.mode = FALSE,   formula.str = NULL,   args.list = NULL,   fun = NULL,   vars = NULL,   ... )  regression_model_uv(   data,   outcome.str,   args.list = NULL,   fun = NULL,   vars = NULL,   ... )  regression_model_list(   data,   outcome.str,   fun.descr,   fun = NULL,   formula.str = NULL,   args.list = NULL,   vars = NULL,   ... )  regression_model_uv_list(   data,   outcome.str,   fun.descr,   fun = NULL,   formula.str = NULL,   args.list = NULL,   vars = NULL,   ... )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a regression model programatically — regression_model","text":"data data outcome.str name outcome variable auto.mode Make assumptions function dependent outcome data format. Overwrites arguments. formula.str custom formula glue string. Default NULL. args.list custom character string converted using argsstring2list() list arguments. Default NULL. fun name custom function. Default NULL. vars character vector variables include ... ignored fun.descr Description chosen function matching description \"supported_functions()\"","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a regression model programatically — regression_model","text":"object standard class fun object standard class fun list list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a regression model programatically — regression_model","text":"","code":"gtsummary::trial |>   regression_model(outcome.str = \"age\") #>  #> Call: #> (function (formula, data, subset, weights, na.action, method = \"qr\",  #>     model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, offset, ...)  #> { #>     ret.x <- x #>     ret.y <- y #>     cl <- match.call() #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (method == \"model.frame\")  #>         return(mf) #>     else if (method != \"qr\")  #>         warning(gettextf(\"method = '%s' is not supported. Using 'qr'\",  #>             method), domain = NA) #>     mt <- attr(mf, \"terms\") #>     y <- model.response(mf, \"numeric\") #>     w <- as.vector(model.weights(mf)) #>     if (!is.null(w) && !is.numeric(w))  #>         stop(\"'weights' must be a numeric vector\") #>     offset <- model.offset(mf) #>     mlm <- is.matrix(y) #>     ny <- if (mlm)  #>         nrow(y) #>     else length(y) #>     if (!is.null(offset)) { #>         if (!mlm)  #>             offset <- as.vector(offset) #>         if (NROW(offset) != ny)  #>             stop(gettextf(\"number of offsets is %d, should equal %d (number of observations)\",  #>                 NROW(offset), ny), domain = NA) #>     } #>     if (is.empty.model(mt)) { #>         x <- NULL #>         z <- list(coefficients = if (mlm) matrix(NA_real_, 0,  #>             ncol(y)) else numeric(), residuals = y, fitted.values = 0 *  #>             y, weights = w, rank = 0L, df.residual = if (!is.null(w)) sum(w !=  #>             0) else ny) #>         if (!is.null(offset)) { #>             z$fitted.values <- offset #>             z$residuals <- y - offset #>         } #>     } #>     else { #>         x <- model.matrix(mt, mf, contrasts) #>         z <- if (is.null(w))  #>             lm.fit(x, y, offset = offset, singular.ok = singular.ok,  #>                 ...) #>         else lm.wfit(x, y, w, offset = offset, singular.ok = singular.ok,  #>             ...) #>     } #>     class(z) <- c(if (mlm) \"mlm\", \"lm\") #>     z$na.action <- attr(mf, \"na.action\") #>     z$offset <- offset #>     z$contrasts <- attr(x, \"contrasts\") #>     z$xlevels <- .getXlevels(mt, mf) #>     z$call <- cl #>     z$terms <- mt #>     if (model)  #>         z$model <- mf #>     if (ret.x)  #>         z$x <- x #>     if (ret.y)  #>         z$y <- y #>     if (!qr)  #>         z$qr <- NULL #>     z #> })(formula = age ~ trt + marker + stage + grade + response +  #>     death + ttdeath, data = structure(list(trt = structure(c(1L,  #> 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L,  #> 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L,  #> 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L,  #> 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L,  #> 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L,  #> 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L,  #> 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L,  #> 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L,  #> 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,  #> 2L, 1L, 2L, 1L, 1L, 1L, 1L), levels = c(\"Drug A\", \"Drug B\"), class = \"factor\", label = \"Chemotherapy Treatment\"),  #>     age = structure(c(23, 9, 31, NA, 51, 39, 37, 32, 31, 34,  #>     42, 63, 54, 21, 48, 71, 38, 49, 57, 46, 47, 52, 61, 38, 34,  #>     49, 63, 67, 68, 78, 36, 37, 53, 36, 51, 48, 57, 31, 37, 28,  #>     40, 49, 61, 56, 54, 71, 38, 31, 48, NA, 83, 52, 32, 53, 69,  #>     60, 45, 39, NA, 38, 36, 71, 31, 43, 57, 53, 25, 44, 25, 30,  #>     51, 40, NA, 43, 21, 54, 67, 43, 54, 41, 34, 34, 6, 39, 36,  #>     58, 27, 47, NA, 50, 61, 47, 52, 51, 68, 33, 65, 34, 38, 60,  #>     10, 49, 56, 50, 60, 49, 54, 39, 48, 65, 47, 61, 34, NA, NA,  #>     58, 26, 44, 17, 68, 57, 66, 44, NA, 67, 48, 62, 35, 53, 53,  #>     66, 55, 57, 47, 58, 43, 45, 44, 63, 59, 44, 53, 51, 28, 65,  #>     63, 76, 61, 33, 48, 42, 36, 55, 20, 26, 50, 47, 74, 50, 31,  #>     45, 51, 66, 76, 47, 48, 56, 70, 46, 43, 41, 41, 19, 49, 43,  #>     43, 75, 52, 42, 37, 45, 35, 67, 38, 44, 45, 39, 46, NA, 42,  #>     60, 31, 45, 38, NA, 19, 69, 66, NA, 64), label = \"Age\"),  #>     marker = structure(c(0.16, 1.107, 0.277, 2.067, 2.767, 0.613,  #>     0.354, 1.739, 0.144, 0.205, 0.513, 0.06, 0.831, 0.258, 0.128,  #>     0.445, 2.083, 0.157, 0.066, 0.325, 0.266, 0.719, 1.713, 0.096,  #>     0.105, 0.043, 0.981, 1.156, 0.105, 0.175, 0.309, 1.869, 2.008,  #>     1.894, 0.16, 1.209, 0.108, 0.611, 0.222, 0.803, 0.37, NA,  #>     0.177, 1.479, 0.161, 0.737, 0.124, 0.092, 0.385, 0.21, 0.475,  #>     1.628, 0.583, NA, 0.702, 1.206, 2.213, 1.406, 0.101, 0.013,  #>     2.032, 1.046, 0.408, 2.636, 1.263, NA, 2.447, 1.041, 0.531,  #>     0.924, 1.087, 0.733, 2.157, 0.333, 1.527, 2.238, 0.153, 0.305,  #>     0.131, 0.386, 1.645, 1.321, 0.229, 0.615, 1.976, 1.941, 0.22,  #>     3.874, 0.982, 1.68, 1.091, 0.169, 0.511, 2.141, 0.599, NA,  #>     0.389, 0.005, 0.075, 1.491, 0.358, 1.709, 0.056, 1.354, 2.522,  #>     0.387, 0.592, 0.243, 0.215, 1.207, 0.29, 0.718, 0.589, 0.003,  #>     1.328, 0.308, 0.691, 3.249, 0.039, 1.804, 0.238, 2.702, 1.441,  #>     0.27, NA, NA, 0.062, 2.19, 0.976, 3.062, 0.124, 0.045, 1.892,  #>     0.711, 1.079, 1.061, 0.239, 0.361, 0.033, 1.133, 1.225, 1.418,  #>     3.751, 3.02, 0.086, 0.772, 1.882, 2.725, 2.41, 0.352, 0.895,  #>     0.215, 0.141, 2.288, 1.658, 1.255, 1.306, 0.081, 0.667, 0.046,  #>     0.662, 1.985, 1.063, 1.55, 0.015, 0.056, NA, 0.51, 0.929,  #>     2.345, 0.25, 0.816, 0.022, 0.16, 0.547, 3.642, 0.092, 1.2,  #>     1.512, 2.124, NA, 0.862, 0.182, 1.075, 0.021, 0.402, 0.063,  #>     1.129, 0.61, NA, 0.717, 0.205, 0.946, 0.386, 0.37, 1.148,  #>     NA, 0.136, 0.439, 1.148), label = \"Marker Level (ng/mL)\"),  #>     stage = structure(c(1L, 2L, 1L, 3L, 4L, 4L, 1L, 1L, 1L, 3L,  #>     1L, 3L, 4L, 4L, 1L, 4L, 4L, 2L, 1L, 1L, 2L, 2L, 4L, 4L, 4L,  #>     2L, 4L, 1L, 4L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 4L, 4L,  #>     3L, 1L, 4L, 3L, 4L, 1L, 1L, 2L, 1L, 4L, 1L, 2L, 2L, 3L, 3L,  #>     2L, 4L, 1L, 4L, 2L, 4L, 1L, 4L, 1L, 4L, 1L, 1L, 1L, 4L, 1L,  #>     2L, 2L, 2L, 1L, 4L, 4L, 2L, 2L, 4L, 4L, 3L, 2L, 4L, 3L, 2L,  #>     4L, 1L, 2L, 1L, 4L, 3L, 3L, 1L, 3L, 2L, 3L, 2L, 2L, 3L, 4L,  #>     4L, 3L, 3L, 2L, 3L, 2L, 2L, 3L, 2L, 1L, 1L, 3L, 4L, 1L, 4L,  #>     3L, 3L, 2L, 4L, 2L, 1L, 2L, 1L, 4L, 3L, 3L, 3L, 2L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 3L, 4L, 1L, 2L, 2L,  #>     1L, 3L, 4L, 2L, 4L, 2L, 1L, 2L, 3L, 1L, 3L, 4L, 2L, 2L, 1L,  #>     2L, 2L, 3L, 1L, 2L, 2L, 1L, 1L, 3L, 2L, 3L, 1L, 1L, 2L, 4L,  #>     2L, 4L, 4L, 2L, 3L, 4L, 3L, 4L, 4L, 1L, 1L, 4L, 4L, 4L, 1L,  #>     2L, 2L, 2L, 4L, 3L, 3L, 2L, 2L, 4L, 3L), levels = c(\"T1\",  #>     \"T2\", \"T3\", \"T4\"), class = \"factor\", label = \"T Stage\"),  #>     grade = structure(c(2L, 1L, 2L, 3L, 3L, 1L, 2L, 1L, 2L, 1L,  #>     3L, 1L, 3L, 1L, 1L, 3L, 3L, 2L, 3L, 2L, 1L, 2L, 1L, 1L, 2L,  #>     3L, 2L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 2L, 2L, 3L, 2L,  #>     2L, 3L, 3L, 1L, 3L, 1L, 3L, 2L, 2L, 2L, 3L, 3L, 3L, 2L, 3L,  #>     1L, 3L, 1L, 2L, 2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 3L, 2L,  #>     1L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L,  #>     3L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 1L,  #>     3L, 1L, 2L, 2L, 1L, 2L, 2L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 2L,  #>     3L, 3L, 2L, 1L, 3L, 2L, 1L, 2L, 2L, 2L, 1L, 3L, 3L, 2L, 3L,  #>     1L, 1L, 1L, 2L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L,  #>     2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, 2L, 1L, 2L, 1L, 2L, 3L, 2L,  #>     1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 2L, 1L,  #>     3L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L,  #>     3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 3L, 1L), levels = c(\"I\",  #>     \"II\", \"III\"), class = \"factor\", label = \"Grade\"), response = structure(c(0L,  #>     1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L,  #>     0L, 0L, 1L, 0L, NA, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     0L, 0L, 0L, NA, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     1L, 1L, NA, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, NA, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 0L, 0L,  #>     0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, NA, 0L, 1L,  #>     0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L,  #>     1L, 1L, 0L, 0L), label = \"Tumor Response\"), death = structure(c(0L,  #>     0L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L,  #>     0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 1L,  #>     1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L,  #>     1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L,  #>     1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L,  #>     0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     0L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 1L, 0L), label = \"Patient Died\"), ttdeath = structure(c(24,  #>     24, 24, 17.64, 16.43, 15.64, 24, 18.43, 24, 10.53, 24, 24,  #>     14.34, 12.89, 22.68, 8.71, 24, 15.21, 24, 24, 24, 24, 16.92,  #>     23.89, 6.32, 15.77, 24, 24, 15.45, 17.43, 24, 20.9, 24, 24,  #>     24, 21.19, 12.52, 24, 15.59, 18, 18.02, 12.43, 12.1, 24,  #>     17.42, 24, 24, 24, 12.19, 10.02, 18.23, 10.42, 24, 24, 19.34,  #>     12.21, 14.46, 19.34, 10.16, 13.15, 10.12, 24, 22.77, 24,  #>     24, 22.13, 24, 20.62, 23.23, 7.38, 24, 24, 24, 24, 24, 19.22,  #>     7.27, 23.88, 16.23, 24, 14.06, 24, 24, 24, 16.44, 23.81,  #>     24, 18.37, 11.44, 20.94, 5.33, 22.92, 10.33, 24, 24, 14.54,  #>     19.14, 24, 21.19, 16.07, 9.97, 24, 24, 24, 19.75, 16.67,  #>     11.18, 18.29, 24, 17.56, 17.45, 24, 22.86, 13.68, 24, 24,  #>     17.46, 24, 24, 24, 24, 24, 13, 9.73, 15.65, 24, 3.53, 20.35,  #>     23.41, 16.47, 24, 24, 14.65, 17.81, 24, 21.83, 24, 24, 21.49,  #>     12.68, 24, 24, 24, 24, 10.07, 24, 24, 24, 8.37, 20.33, 24,  #>     24, 21.33, 12.63, 13.08, 24, 15.1, 20.14, 10.55, 24, 24,  #>     24, 24, 23.6, 24, 19.98, 15.55, 23.72, 22.41, 19.54, 16.57,  #>     24, 24, 24, 21.91, 24, 12.53, 24, 18.63, 14.82, 16.46, 24,  #>     9.24, 17.77, 24, 24, 9.92, 16.16, 10.51, 20.81, 24, 16.44,  #>     24, 22.4, 11.76, 24, 21.6, 24, 19.81, 24), label = \"Months to Death/Censor\")), class = c(\"tbl_df\",  #> \"tbl\", \"data.frame\"), row.names = c(NA, -200L))) #>  #> Coefficients: #> (Intercept)    trtDrug B       marker      stageT2      stageT3      stageT4   #>     45.9247      -0.4052      -0.1435       2.0519       2.4437      -3.1573   #>     gradeII     gradeIII     response        death      ttdeath   #>      0.1750       1.6855       4.9885       3.0775      -0.1394   #>  gtsummary::trial |>   regression_model(     outcome.str = \"age\",     auto.mode = FALSE,     fun = \"stats::lm\",     formula.str = \"{outcome.str}~.\",     args.list = NULL   ) #>  #> Call: #> (function (formula, data, subset, weights, na.action, method = \"qr\",  #>     model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, offset, ...)  #> { #>     ret.x <- x #>     ret.y <- y #>     cl <- match.call() #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (method == \"model.frame\")  #>         return(mf) #>     else if (method != \"qr\")  #>         warning(gettextf(\"method = '%s' is not supported. Using 'qr'\",  #>             method), domain = NA) #>     mt <- attr(mf, \"terms\") #>     y <- model.response(mf, \"numeric\") #>     w <- as.vector(model.weights(mf)) #>     if (!is.null(w) && !is.numeric(w))  #>         stop(\"'weights' must be a numeric vector\") #>     offset <- model.offset(mf) #>     mlm <- is.matrix(y) #>     ny <- if (mlm)  #>         nrow(y) #>     else length(y) #>     if (!is.null(offset)) { #>         if (!mlm)  #>             offset <- as.vector(offset) #>         if (NROW(offset) != ny)  #>             stop(gettextf(\"number of offsets is %d, should equal %d (number of observations)\",  #>                 NROW(offset), ny), domain = NA) #>     } #>     if (is.empty.model(mt)) { #>         x <- NULL #>         z <- list(coefficients = if (mlm) matrix(NA_real_, 0,  #>             ncol(y)) else numeric(), residuals = y, fitted.values = 0 *  #>             y, weights = w, rank = 0L, df.residual = if (!is.null(w)) sum(w !=  #>             0) else ny) #>         if (!is.null(offset)) { #>             z$fitted.values <- offset #>             z$residuals <- y - offset #>         } #>     } #>     else { #>         x <- model.matrix(mt, mf, contrasts) #>         z <- if (is.null(w))  #>             lm.fit(x, y, offset = offset, singular.ok = singular.ok,  #>                 ...) #>         else lm.wfit(x, y, w, offset = offset, singular.ok = singular.ok,  #>             ...) #>     } #>     class(z) <- c(if (mlm) \"mlm\", \"lm\") #>     z$na.action <- attr(mf, \"na.action\") #>     z$offset <- offset #>     z$contrasts <- attr(x, \"contrasts\") #>     z$xlevels <- .getXlevels(mt, mf) #>     z$call <- cl #>     z$terms <- mt #>     if (model)  #>         z$model <- mf #>     if (ret.x)  #>         z$x <- x #>     if (ret.y)  #>         z$y <- y #>     if (!qr)  #>         z$qr <- NULL #>     z #> })(formula = age ~ ., data = structure(list(trt = structure(c(1L,  #> 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L,  #> 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L,  #> 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L,  #> 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L,  #> 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L,  #> 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L,  #> 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L,  #> 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L,  #> 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,  #> 2L, 1L, 2L, 1L, 1L, 1L, 1L), levels = c(\"Drug A\", \"Drug B\"), class = \"factor\", label = \"Chemotherapy Treatment\"),  #>     age = structure(c(23, 9, 31, NA, 51, 39, 37, 32, 31, 34,  #>     42, 63, 54, 21, 48, 71, 38, 49, 57, 46, 47, 52, 61, 38, 34,  #>     49, 63, 67, 68, 78, 36, 37, 53, 36, 51, 48, 57, 31, 37, 28,  #>     40, 49, 61, 56, 54, 71, 38, 31, 48, NA, 83, 52, 32, 53, 69,  #>     60, 45, 39, NA, 38, 36, 71, 31, 43, 57, 53, 25, 44, 25, 30,  #>     51, 40, NA, 43, 21, 54, 67, 43, 54, 41, 34, 34, 6, 39, 36,  #>     58, 27, 47, NA, 50, 61, 47, 52, 51, 68, 33, 65, 34, 38, 60,  #>     10, 49, 56, 50, 60, 49, 54, 39, 48, 65, 47, 61, 34, NA, NA,  #>     58, 26, 44, 17, 68, 57, 66, 44, NA, 67, 48, 62, 35, 53, 53,  #>     66, 55, 57, 47, 58, 43, 45, 44, 63, 59, 44, 53, 51, 28, 65,  #>     63, 76, 61, 33, 48, 42, 36, 55, 20, 26, 50, 47, 74, 50, 31,  #>     45, 51, 66, 76, 47, 48, 56, 70, 46, 43, 41, 41, 19, 49, 43,  #>     43, 75, 52, 42, 37, 45, 35, 67, 38, 44, 45, 39, 46, NA, 42,  #>     60, 31, 45, 38, NA, 19, 69, 66, NA, 64), label = \"Age\"),  #>     marker = structure(c(0.16, 1.107, 0.277, 2.067, 2.767, 0.613,  #>     0.354, 1.739, 0.144, 0.205, 0.513, 0.06, 0.831, 0.258, 0.128,  #>     0.445, 2.083, 0.157, 0.066, 0.325, 0.266, 0.719, 1.713, 0.096,  #>     0.105, 0.043, 0.981, 1.156, 0.105, 0.175, 0.309, 1.869, 2.008,  #>     1.894, 0.16, 1.209, 0.108, 0.611, 0.222, 0.803, 0.37, NA,  #>     0.177, 1.479, 0.161, 0.737, 0.124, 0.092, 0.385, 0.21, 0.475,  #>     1.628, 0.583, NA, 0.702, 1.206, 2.213, 1.406, 0.101, 0.013,  #>     2.032, 1.046, 0.408, 2.636, 1.263, NA, 2.447, 1.041, 0.531,  #>     0.924, 1.087, 0.733, 2.157, 0.333, 1.527, 2.238, 0.153, 0.305,  #>     0.131, 0.386, 1.645, 1.321, 0.229, 0.615, 1.976, 1.941, 0.22,  #>     3.874, 0.982, 1.68, 1.091, 0.169, 0.511, 2.141, 0.599, NA,  #>     0.389, 0.005, 0.075, 1.491, 0.358, 1.709, 0.056, 1.354, 2.522,  #>     0.387, 0.592, 0.243, 0.215, 1.207, 0.29, 0.718, 0.589, 0.003,  #>     1.328, 0.308, 0.691, 3.249, 0.039, 1.804, 0.238, 2.702, 1.441,  #>     0.27, NA, NA, 0.062, 2.19, 0.976, 3.062, 0.124, 0.045, 1.892,  #>     0.711, 1.079, 1.061, 0.239, 0.361, 0.033, 1.133, 1.225, 1.418,  #>     3.751, 3.02, 0.086, 0.772, 1.882, 2.725, 2.41, 0.352, 0.895,  #>     0.215, 0.141, 2.288, 1.658, 1.255, 1.306, 0.081, 0.667, 0.046,  #>     0.662, 1.985, 1.063, 1.55, 0.015, 0.056, NA, 0.51, 0.929,  #>     2.345, 0.25, 0.816, 0.022, 0.16, 0.547, 3.642, 0.092, 1.2,  #>     1.512, 2.124, NA, 0.862, 0.182, 1.075, 0.021, 0.402, 0.063,  #>     1.129, 0.61, NA, 0.717, 0.205, 0.946, 0.386, 0.37, 1.148,  #>     NA, 0.136, 0.439, 1.148), label = \"Marker Level (ng/mL)\"),  #>     stage = structure(c(1L, 2L, 1L, 3L, 4L, 4L, 1L, 1L, 1L, 3L,  #>     1L, 3L, 4L, 4L, 1L, 4L, 4L, 2L, 1L, 1L, 2L, 2L, 4L, 4L, 4L,  #>     2L, 4L, 1L, 4L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 4L, 4L,  #>     3L, 1L, 4L, 3L, 4L, 1L, 1L, 2L, 1L, 4L, 1L, 2L, 2L, 3L, 3L,  #>     2L, 4L, 1L, 4L, 2L, 4L, 1L, 4L, 1L, 4L, 1L, 1L, 1L, 4L, 1L,  #>     2L, 2L, 2L, 1L, 4L, 4L, 2L, 2L, 4L, 4L, 3L, 2L, 4L, 3L, 2L,  #>     4L, 1L, 2L, 1L, 4L, 3L, 3L, 1L, 3L, 2L, 3L, 2L, 2L, 3L, 4L,  #>     4L, 3L, 3L, 2L, 3L, 2L, 2L, 3L, 2L, 1L, 1L, 3L, 4L, 1L, 4L,  #>     3L, 3L, 2L, 4L, 2L, 1L, 2L, 1L, 4L, 3L, 3L, 3L, 2L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 3L, 4L, 1L, 2L, 2L,  #>     1L, 3L, 4L, 2L, 4L, 2L, 1L, 2L, 3L, 1L, 3L, 4L, 2L, 2L, 1L,  #>     2L, 2L, 3L, 1L, 2L, 2L, 1L, 1L, 3L, 2L, 3L, 1L, 1L, 2L, 4L,  #>     2L, 4L, 4L, 2L, 3L, 4L, 3L, 4L, 4L, 1L, 1L, 4L, 4L, 4L, 1L,  #>     2L, 2L, 2L, 4L, 3L, 3L, 2L, 2L, 4L, 3L), levels = c(\"T1\",  #>     \"T2\", \"T3\", \"T4\"), class = \"factor\", label = \"T Stage\"),  #>     grade = structure(c(2L, 1L, 2L, 3L, 3L, 1L, 2L, 1L, 2L, 1L,  #>     3L, 1L, 3L, 1L, 1L, 3L, 3L, 2L, 3L, 2L, 1L, 2L, 1L, 1L, 2L,  #>     3L, 2L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 2L, 2L, 3L, 2L,  #>     2L, 3L, 3L, 1L, 3L, 1L, 3L, 2L, 2L, 2L, 3L, 3L, 3L, 2L, 3L,  #>     1L, 3L, 1L, 2L, 2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 3L, 2L,  #>     1L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L,  #>     3L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 1L,  #>     3L, 1L, 2L, 2L, 1L, 2L, 2L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 2L,  #>     3L, 3L, 2L, 1L, 3L, 2L, 1L, 2L, 2L, 2L, 1L, 3L, 3L, 2L, 3L,  #>     1L, 1L, 1L, 2L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L,  #>     2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, 2L, 1L, 2L, 1L, 2L, 3L, 2L,  #>     1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 2L, 1L,  #>     3L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L,  #>     3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 3L, 1L), levels = c(\"I\",  #>     \"II\", \"III\"), class = \"factor\", label = \"Grade\"), response = structure(c(0L,  #>     1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L,  #>     0L, 0L, 1L, 0L, NA, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     0L, 0L, 0L, NA, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     1L, 1L, NA, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, NA, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 0L, 0L,  #>     0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, NA, 0L, 1L,  #>     0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L,  #>     1L, 1L, 0L, 0L), label = \"Tumor Response\"), death = structure(c(0L,  #>     0L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L,  #>     0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 1L,  #>     1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L,  #>     1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L,  #>     1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L,  #>     0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     0L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 1L, 0L), label = \"Patient Died\"), ttdeath = structure(c(24,  #>     24, 24, 17.64, 16.43, 15.64, 24, 18.43, 24, 10.53, 24, 24,  #>     14.34, 12.89, 22.68, 8.71, 24, 15.21, 24, 24, 24, 24, 16.92,  #>     23.89, 6.32, 15.77, 24, 24, 15.45, 17.43, 24, 20.9, 24, 24,  #>     24, 21.19, 12.52, 24, 15.59, 18, 18.02, 12.43, 12.1, 24,  #>     17.42, 24, 24, 24, 12.19, 10.02, 18.23, 10.42, 24, 24, 19.34,  #>     12.21, 14.46, 19.34, 10.16, 13.15, 10.12, 24, 22.77, 24,  #>     24, 22.13, 24, 20.62, 23.23, 7.38, 24, 24, 24, 24, 24, 19.22,  #>     7.27, 23.88, 16.23, 24, 14.06, 24, 24, 24, 16.44, 23.81,  #>     24, 18.37, 11.44, 20.94, 5.33, 22.92, 10.33, 24, 24, 14.54,  #>     19.14, 24, 21.19, 16.07, 9.97, 24, 24, 24, 19.75, 16.67,  #>     11.18, 18.29, 24, 17.56, 17.45, 24, 22.86, 13.68, 24, 24,  #>     17.46, 24, 24, 24, 24, 24, 13, 9.73, 15.65, 24, 3.53, 20.35,  #>     23.41, 16.47, 24, 24, 14.65, 17.81, 24, 21.83, 24, 24, 21.49,  #>     12.68, 24, 24, 24, 24, 10.07, 24, 24, 24, 8.37, 20.33, 24,  #>     24, 21.33, 12.63, 13.08, 24, 15.1, 20.14, 10.55, 24, 24,  #>     24, 24, 23.6, 24, 19.98, 15.55, 23.72, 22.41, 19.54, 16.57,  #>     24, 24, 24, 21.91, 24, 12.53, 24, 18.63, 14.82, 16.46, 24,  #>     9.24, 17.77, 24, 24, 9.92, 16.16, 10.51, 20.81, 24, 16.44,  #>     24, 22.4, 11.76, 24, 21.6, 24, 19.81, 24), label = \"Months to Death/Censor\")), class = c(\"tbl_df\",  #> \"tbl\", \"data.frame\"), row.names = c(NA, -200L))) #>  #> Coefficients: #> (Intercept)    trtDrug B       marker      stageT2      stageT3      stageT4   #>     45.9247      -0.4052      -0.1435       2.0519       2.4437      -3.1573   #>     gradeII     gradeIII     response        death      ttdeath   #>      0.1750       1.6855       4.9885       3.0775      -0.1394   #>  gtsummary::trial |>   default_parsing() |>   regression_model(     outcome.str = \"trt\",     auto.mode = FALSE,     fun = \"stats::glm\",     args.list = list(family = binomial(link = \"logit\"))   ) #>  #> Call:  (function (formula, family = gaussian, data, weights, subset,  #>     na.action, start = NULL, etastart, mustart, offset, control = list(...),  #>     model = TRUE, method = \"glm.fit\", x = FALSE, y = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, ...)  #> { #>     cal <- match.call() #>     if (is.character(family))  #>         family <- get(family, mode = \"function\", envir = parent.frame()) #>     if (is.function(family))  #>         family <- family() #>     if (is.null(family$family)) { #>         print(family) #>         stop(\"'family' not recognized\") #>     } #>     if (missing(data))  #>         data <- environment(formula) #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"etastart\", \"mustart\", \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (identical(method, \"model.frame\"))  #>         return(mf) #>     if (!is.character(method) && !is.function(method))  #>         stop(\"invalid 'method' argument\") #>     if (identical(method, \"glm.fit\"))  #>         control <- do.call(\"glm.control\", control) #>     mt <- attr(mf, \"terms\") #>     Y <- model.response(mf, \"any\") #>     if (length(dim(Y)) == 1L) { #>         nm <- rownames(Y) #>         dim(Y) <- NULL #>         if (!is.null(nm))  #>             names(Y) <- nm #>     } #>     X <- if (!is.empty.model(mt))  #>         model.matrix(mt, mf, contrasts) #>     else matrix(, NROW(Y), 0L) #>     weights <- as.vector(model.weights(mf)) #>     if (!is.null(weights) && !is.numeric(weights))  #>         stop(\"'weights' must be a numeric vector\") #>     if (!is.null(weights) && any(weights < 0))  #>         stop(\"negative weights not allowed\") #>     offset <- as.vector(model.offset(mf)) #>     if (!is.null(offset)) { #>         if (length(offset) != NROW(Y))  #>             stop(gettextf(\"number of offsets is %d should equal %d (number of observations)\",  #>                 length(offset), NROW(Y)), domain = NA) #>     } #>     mustart <- model.extract(mf, \"mustart\") #>     etastart <- model.extract(mf, \"etastart\") #>     fit <- eval(call(if (is.function(method)) \"method\" else method,  #>         x = X, y = Y, weights = weights, start = start, etastart = etastart,  #>         mustart = mustart, offset = offset, family = family,  #>         control = control, intercept = attr(mt, \"intercept\") >  #>             0L, singular.ok = singular.ok)) #>     if (length(offset) && attr(mt, \"intercept\") > 0L) { #>         fit2 <- eval(call(if (is.function(method)) \"method\" else method,  #>             x = X[, \"(Intercept)\", drop = FALSE], y = Y, mustart = fit$fitted.values,  #>             weights = weights, offset = offset, family = family,  #>             control = control, intercept = TRUE)) #>         if (!fit2$converged)  #>             warning(\"fitting to calculate the null deviance did not converge -- increase 'maxit'?\") #>         fit$null.deviance <- fit2$deviance #>     } #>     if (model)  #>         fit$model <- mf #>     fit$na.action <- attr(mf, \"na.action\") #>     if (x)  #>         fit$x <- X #>     if (!y)  #>         fit$y <- NULL #>     structure(c(fit, list(call = cal, formula = formula, terms = mt,  #>         data = data, offset = offset, control = control, method = method,  #>         contrasts = attr(X, \"contrasts\"), xlevels = .getXlevels(mt,  #>             mf))), class = c(fit$class, c(\"glm\", \"lm\"))) #> })(formula = trt ~ age + marker + stage + grade + response +  #>     death + ttdeath, family = structure(list(family = \"binomial\",  #>     link = \"logit\", linkfun = function (mu)  #>     .Call(C_logit_link, mu), linkinv = function (eta)  #>     .Call(C_logit_linkinv, eta), variance = function (mu)  #>     mu * (1 - mu), dev.resids = function (y, mu, wt)  #>     .Call(C_binomial_dev_resids, y, mu, wt), aic = function (y,  #>         n, mu, wt, dev)  #>     { #>         m <- if (any(n > 1))  #>             n #>         else wt #>         -2 * sum(ifelse(m > 0, (wt/m), 0) * dbinom(round(m *  #>             y), round(m), mu, log = TRUE)) #>     }, mu.eta = function (eta)  #>     .Call(C_logit_mu_eta, eta), initialize = { #>         if (NCOL(y) == 1) { #>             if (is.factor(y))  #>                 y <- y != levels(y)[1L] #>             n <- rep.int(1, nobs) #>             y[weights == 0] <- 0 #>             if (any(y < 0 | y > 1))  #>                 stop(\"y values must be 0 <= y <= 1\") #>             mustart <- (weights * y + 0.5)/(weights + 1) #>             m <- weights * y #>             if (\"binomial\" == \"binomial\" && any(abs(m - round(m)) >  #>                 0.001))  #>                 warning(gettextf(\"non-integer #successes in a %s glm!\",  #>                   \"binomial\"), domain = NA) #>         } #>         else if (NCOL(y) == 2) { #>             if (\"binomial\" == \"binomial\" && any(abs(y - round(y)) >  #>                 0.001))  #>                 warning(gettextf(\"non-integer counts in a %s glm!\",  #>                   \"binomial\"), domain = NA) #>             n <- (y1 <- y[, 1L]) + y[, 2L] #>             y <- y1/n #>             if (any(n0 <- n == 0))  #>                 y[n0] <- 0 #>             weights <- weights * n #>             mustart <- (n * y + 0.5)/(n + 1) #>         } #>         else stop(gettextf(\"for the '%s' family, y must be a vector of 0 and 1's\\nor a 2 column matrix where col 1 is no. successes and col 2 is no. failures\",  #>             \"binomial\"), domain = NA) #>     }, validmu = function (mu)  #>     all(is.finite(mu)) && all(mu > 0 & mu < 1), valideta = function (eta)  #>     TRUE, simulate = function (object, nsim)  #>     { #>         ftd <- fitted(object) #>         n <- length(ftd) #>         ntot <- n * nsim #>         wts <- object$prior.weights #>         if (any(wts%%1 != 0))  #>             stop(\"cannot simulate from non-integer prior.weights\") #>         if (!is.null(m <- object$model)) { #>             y <- model.response(m) #>             if (is.factor(y)) { #>                 yy <- factor(1 + rbinom(ntot, size = 1, prob = ftd),  #>                   labels = levels(y)) #>                 split(yy, rep(seq_len(nsim), each = n)) #>             } #>             else if (is.matrix(y) && ncol(y) == 2) { #>                 yy <- vector(\"list\", nsim) #>                 for (i in seq_len(nsim)) { #>                   Y <- rbinom(n, size = wts, prob = ftd) #>                   YY <- cbind(Y, wts - Y) #>                   colnames(YY) <- colnames(y) #>                   yy[[i]] <- YY #>                 } #>                 yy #>             } #>             else rbinom(ntot, size = wts, prob = ftd)/wts #>         } #>         else rbinom(ntot, size = wts, prob = ftd)/wts #>     }, dispersion = 1), class = \"family\"), data = structure(list( #>     trt = structure(c(1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L,  #>     2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,  #>     2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L,  #>     2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,  #>     2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L,  #>     1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L,  #>     1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L,  #>     2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 2L,  #>     2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L,  #>     1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L,  #>     2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L,  #>     2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L,  #>     1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L), levels = c(\"Drug A\",  #>     \"Drug B\"), class = \"factor\", label = \"Chemotherapy Treatment\"),  #>     age = structure(c(23, 9, 31, NA, 51, 39, 37, 32, 31, 34,  #>     42, 63, 54, 21, 48, 71, 38, 49, 57, 46, 47, 52, 61, 38, 34,  #>     49, 63, 67, 68, 78, 36, 37, 53, 36, 51, 48, 57, 31, 37, 28,  #>     40, 49, 61, 56, 54, 71, 38, 31, 48, NA, 83, 52, 32, 53, 69,  #>     60, 45, 39, NA, 38, 36, 71, 31, 43, 57, 53, 25, 44, 25, 30,  #>     51, 40, NA, 43, 21, 54, 67, 43, 54, 41, 34, 34, 6, 39, 36,  #>     58, 27, 47, NA, 50, 61, 47, 52, 51, 68, 33, 65, 34, 38, 60,  #>     10, 49, 56, 50, 60, 49, 54, 39, 48, 65, 47, 61, 34, NA, NA,  #>     58, 26, 44, 17, 68, 57, 66, 44, NA, 67, 48, 62, 35, 53, 53,  #>     66, 55, 57, 47, 58, 43, 45, 44, 63, 59, 44, 53, 51, 28, 65,  #>     63, 76, 61, 33, 48, 42, 36, 55, 20, 26, 50, 47, 74, 50, 31,  #>     45, 51, 66, 76, 47, 48, 56, 70, 46, 43, 41, 41, 19, 49, 43,  #>     43, 75, 52, 42, 37, 45, 35, 67, 38, 44, 45, 39, 46, NA, 42,  #>     60, 31, 45, 38, NA, 19, 69, 66, NA, 64), label = \"Age\"),  #>     marker = structure(c(0.16, 1.107, 0.277, 2.067, 2.767, 0.613,  #>     0.354, 1.739, 0.144, 0.205, 0.513, 0.06, 0.831, 0.258, 0.128,  #>     0.445, 2.083, 0.157, 0.066, 0.325, 0.266, 0.719, 1.713, 0.096,  #>     0.105, 0.043, 0.981, 1.156, 0.105, 0.175, 0.309, 1.869, 2.008,  #>     1.894, 0.16, 1.209, 0.108, 0.611, 0.222, 0.803, 0.37, NA,  #>     0.177, 1.479, 0.161, 0.737, 0.124, 0.092, 0.385, 0.21, 0.475,  #>     1.628, 0.583, NA, 0.702, 1.206, 2.213, 1.406, 0.101, 0.013,  #>     2.032, 1.046, 0.408, 2.636, 1.263, NA, 2.447, 1.041, 0.531,  #>     0.924, 1.087, 0.733, 2.157, 0.333, 1.527, 2.238, 0.153, 0.305,  #>     0.131, 0.386, 1.645, 1.321, 0.229, 0.615, 1.976, 1.941, 0.22,  #>     3.874, 0.982, 1.68, 1.091, 0.169, 0.511, 2.141, 0.599, NA,  #>     0.389, 0.005, 0.075, 1.491, 0.358, 1.709, 0.056, 1.354, 2.522,  #>     0.387, 0.592, 0.243, 0.215, 1.207, 0.29, 0.718, 0.589, 0.003,  #>     1.328, 0.308, 0.691, 3.249, 0.039, 1.804, 0.238, 2.702, 1.441,  #>     0.27, NA, NA, 0.062, 2.19, 0.976, 3.062, 0.124, 0.045, 1.892,  #>     0.711, 1.079, 1.061, 0.239, 0.361, 0.033, 1.133, 1.225, 1.418,  #>     3.751, 3.02, 0.086, 0.772, 1.882, 2.725, 2.41, 0.352, 0.895,  #>     0.215, 0.141, 2.288, 1.658, 1.255, 1.306, 0.081, 0.667, 0.046,  #>     0.662, 1.985, 1.063, 1.55, 0.015, 0.056, NA, 0.51, 0.929,  #>     2.345, 0.25, 0.816, 0.022, 0.16, 0.547, 3.642, 0.092, 1.2,  #>     1.512, 2.124, NA, 0.862, 0.182, 1.075, 0.021, 0.402, 0.063,  #>     1.129, 0.61, NA, 0.717, 0.205, 0.946, 0.386, 0.37, 1.148,  #>     NA, 0.136, 0.439, 1.148), label = \"Marker Level (ng/mL)\"),  #>     stage = structure(c(1L, 2L, 1L, 3L, 4L, 4L, 1L, 1L, 1L, 3L,  #>     1L, 3L, 4L, 4L, 1L, 4L, 4L, 2L, 1L, 1L, 2L, 2L, 4L, 4L, 4L,  #>     2L, 4L, 1L, 4L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 4L, 4L,  #>     3L, 1L, 4L, 3L, 4L, 1L, 1L, 2L, 1L, 4L, 1L, 2L, 2L, 3L, 3L,  #>     2L, 4L, 1L, 4L, 2L, 4L, 1L, 4L, 1L, 4L, 1L, 1L, 1L, 4L, 1L,  #>     2L, 2L, 2L, 1L, 4L, 4L, 2L, 2L, 4L, 4L, 3L, 2L, 4L, 3L, 2L,  #>     4L, 1L, 2L, 1L, 4L, 3L, 3L, 1L, 3L, 2L, 3L, 2L, 2L, 3L, 4L,  #>     4L, 3L, 3L, 2L, 3L, 2L, 2L, 3L, 2L, 1L, 1L, 3L, 4L, 1L, 4L,  #>     3L, 3L, 2L, 4L, 2L, 1L, 2L, 1L, 4L, 3L, 3L, 3L, 2L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 3L, 4L, 1L, 2L, 2L,  #>     1L, 3L, 4L, 2L, 4L, 2L, 1L, 2L, 3L, 1L, 3L, 4L, 2L, 2L, 1L,  #>     2L, 2L, 3L, 1L, 2L, 2L, 1L, 1L, 3L, 2L, 3L, 1L, 1L, 2L, 4L,  #>     2L, 4L, 4L, 2L, 3L, 4L, 3L, 4L, 4L, 1L, 1L, 4L, 4L, 4L, 1L,  #>     2L, 2L, 2L, 4L, 3L, 3L, 2L, 2L, 4L, 3L), levels = c(\"T1\",  #>     \"T2\", \"T3\", \"T4\"), class = \"factor\", label = \"T Stage\"),  #>     grade = structure(c(2L, 1L, 2L, 3L, 3L, 1L, 2L, 1L, 2L, 1L,  #>     3L, 1L, 3L, 1L, 1L, 3L, 3L, 2L, 3L, 2L, 1L, 2L, 1L, 1L, 2L,  #>     3L, 2L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 2L, 2L, 3L, 2L,  #>     2L, 3L, 3L, 1L, 3L, 1L, 3L, 2L, 2L, 2L, 3L, 3L, 3L, 2L, 3L,  #>     1L, 3L, 1L, 2L, 2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 3L, 2L,  #>     1L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L,  #>     3L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 1L,  #>     3L, 1L, 2L, 2L, 1L, 2L, 2L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 2L,  #>     3L, 3L, 2L, 1L, 3L, 2L, 1L, 2L, 2L, 2L, 1L, 3L, 3L, 2L, 3L,  #>     1L, 1L, 1L, 2L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L,  #>     2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, 2L, 1L, 2L, 1L, 2L, 3L, 2L,  #>     1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 2L, 1L,  #>     3L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L,  #>     3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 3L, 1L), levels = c(\"I\",  #>     \"II\", \"III\"), class = \"factor\", label = \"Grade\"), response = structure(c(1L,  #>     2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L,  #>     2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L,  #>     1L, 1L, 2L, 1L, NA, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L,  #>     2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 1L,  #>     1L, 1L, 1L, NA, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L,  #>     1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, NA, 1L, 1L, 2L,  #>     1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L,  #>     1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L,  #>     2L, 2L, NA, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, NA, 2L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L,  #>     1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, NA, 1L, 2L,  #>     1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, NA, 1L,  #>     2L, 2L, 1L, 1L), levels = c(\"0\", \"1\"), class = \"factor\", label = \"Tumor Response\"),  #>     death = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 2L,  #>     1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L,  #>     2L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L,  #>     2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 2L,  #>     2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 2L,  #>     1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L,  #>     2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 2L,  #>     2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 1L,  #>     1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L,  #>     1L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L,  #>     1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 1L,  #>     1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 2L,  #>     1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L,  #>     1L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L), levels = c(\"0\",  #>     \"1\"), class = \"factor\", label = \"Patient Died\"), ttdeath = structure(c(24,  #>     24, 24, 17.64, 16.43, 15.64, 24, 18.43, 24, 10.53, 24, 24,  #>     14.34, 12.89, 22.68, 8.71, 24, 15.21, 24, 24, 24, 24, 16.92,  #>     23.89, 6.32, 15.77, 24, 24, 15.45, 17.43, 24, 20.9, 24, 24,  #>     24, 21.19, 12.52, 24, 15.59, 18, 18.02, 12.43, 12.1, 24,  #>     17.42, 24, 24, 24, 12.19, 10.02, 18.23, 10.42, 24, 24, 19.34,  #>     12.21, 14.46, 19.34, 10.16, 13.15, 10.12, 24, 22.77, 24,  #>     24, 22.13, 24, 20.62, 23.23, 7.38, 24, 24, 24, 24, 24, 19.22,  #>     7.27, 23.88, 16.23, 24, 14.06, 24, 24, 24, 16.44, 23.81,  #>     24, 18.37, 11.44, 20.94, 5.33, 22.92, 10.33, 24, 24, 14.54,  #>     19.14, 24, 21.19, 16.07, 9.97, 24, 24, 24, 19.75, 16.67,  #>     11.18, 18.29, 24, 17.56, 17.45, 24, 22.86, 13.68, 24, 24,  #>     17.46, 24, 24, 24, 24, 24, 13, 9.73, 15.65, 24, 3.53, 20.35,  #>     23.41, 16.47, 24, 24, 14.65, 17.81, 24, 21.83, 24, 24, 21.49,  #>     12.68, 24, 24, 24, 24, 10.07, 24, 24, 24, 8.37, 20.33, 24,  #>     24, 21.33, 12.63, 13.08, 24, 15.1, 20.14, 10.55, 24, 24,  #>     24, 24, 23.6, 24, 19.98, 15.55, 23.72, 22.41, 19.54, 16.57,  #>     24, 24, 24, 21.91, 24, 12.53, 24, 18.63, 14.82, 16.46, 24,  #>     9.24, 17.77, 24, 24, 9.92, 16.16, 10.51, 20.81, 24, 16.44,  #>     24, 22.4, 11.76, 24, 21.6, 24, 19.81, 24), label = \"Months to Death/Censor\")), class = c(\"tbl_df\",  #> \"tbl\", \"data.frame\"), row.names = c(NA, -200L))) #>  #> Coefficients: #> (Intercept)          age       marker      stageT2      stageT3      stageT4   #>    1.652845    -0.002014    -0.259849     0.404341     0.117402    -0.002102   #>     gradeII     gradeIII    response1       death1      ttdeath   #>   -0.037012     0.022890     0.498952    -0.003916    -0.076073   #>  #> Degrees of Freedom: 172 Total (i.e. Null);  162 Residual #>   (27 observations deleted due to missingness) #> Null Deviance:\t    239.5  #> Residual Deviance: 230.9 \tAIC: 252.9 m <- mtcars |>   default_parsing() |>   regression_model(     outcome.str = \"mpg\",     auto.mode = FALSE,     fun = \"stats::lm\",     formula.str = \"{outcome.str}~{paste(vars,collapse='+')}\",     args.list = NULL,     vars = c(\"mpg\", \"cyl\")   )   broom::tidy(m) #> # A tibble: 3 × 5 #>   term        estimate std.error statistic  p.value #>   <chr>          <dbl>     <dbl>     <dbl>    <dbl> #> 1 (Intercept)    26.7      0.972     27.4  2.69e-22 #> 2 cyl6           -6.92     1.56      -4.44 1.19e- 4 #> 3 cyl8          -11.6      1.30      -8.90 8.57e-10 if (FALSE) { # \\dontrun{ gtsummary::trial |>   regression_model_uv(outcome.str = \"age\") gtsummary::trial |>   regression_model_uv(     outcome.str = \"age\",     fun = \"stats::lm\",     args.list = NULL   ) m <- gtsummary::trial |> regression_model_uv(   outcome.str = \"trt\",   fun = \"stats::glm\",   args.list = list(family = stats::binomial(link = \"logit\")) ) lapply(m,broom::tidy) |> dplyr::bind_rows() } # } if (FALSE) { # \\dontrun{ gtsummary::trial |>   regression_model(     outcome.str = \"age\",     fun = \"stats::lm\",     formula.str = \"{outcome.str}~.\",     args.list = NULL   ) ls <- regression_model_list(data = default_parsing(mtcars), outcome.str = \"cyl\", fun.descr = \"Ordinal logistic regression model\") summary(ls$model)  ls <- regression_model_list(data = default_parsing(gtsummary::trial), outcome.str = \"trt\", fun.descr = \"Logistic regression model\") tbl <- gtsummary::tbl_regression(ls$model, exponentiate = TRUE) m <- gtsummary::trial |>   default_parsing() |>   regression_model(     outcome.str = \"trt\",     fun = \"stats::glm\",     formula.str = \"{outcome.str}~.\",     args.list = list(family = stats::binomial(link = \"logit\"))   ) tbl2 <- gtsummary::tbl_regression(m, exponentiate = TRUE) broom::tidy(ls$model) broom::tidy(m) } # } if (FALSE) { # \\dontrun{ gtsummary::trial |> regression_model_uv(   outcome.str = \"trt\",   fun = \"stats::glm\",   args.list = list(family = stats::binomial(link = \"logit\")) ) |> lapply(broom::tidy) |> dplyr::bind_rows() ms <- regression_model_uv_list(data = default_parsing(mtcars), outcome.str = \"mpg\", fun.descr = \"Linear regression model\") lapply(ms$model,broom::tidy) |> dplyr::bind_rows() } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Create table of regression model — regression_table","title":"Create table of regression model — regression_table","text":"Create table regression model","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create table of regression model — regression_table","text":"","code":"regression_table(x, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create table of regression model — regression_table","text":"x regression model ... passed methods args.list list arguments passed 'fun'. fun function use table creation. Default \"gtsummary::tbl_regression\".","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create table of regression model — regression_table","text":"object standard class fun","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create table of regression model — regression_table","text":"","code":"if (FALSE) { # \\dontrun{ tbl <- gtsummary::trial |>   regression_model(     outcome.str = \"stage\",     fun = \"MASS::polr\"   ) |>   regression_table(args.list = list(\"exponentiate\" = TRUE)) gtsummary::trial |>   regression_model(     outcome.str = \"age\",     fun = \"stats::lm\",     formula.str = \"{outcome.str}~.\",     args.list = NULL   ) |>   regression_table() |> plot() gtsummary::trial |>   regression_model(     outcome.str = \"trt\",     fun = \"stats::glm\",     args.list = list(family = binomial(link = \"logit\"))   ) |>   regression_table() gtsummary::trial |>   regression_model_uv(     outcome.str = \"trt\",     fun = \"stats::glm\",     args.list = list(family = stats::binomial(link = \"logit\"))   ) |>   regression_table() gtsummary::trial |>   regression_model_uv(     outcome.str = \"stage\",     args.list = list(family = stats::binomial(link = \"logit\"))   ) |>   regression_table()  list(   \"Univariable\" = regression_model_uv,   \"Multivariable\" = regression_model ) |>   lapply(\\(.fun){     do.call(       .fun,       c(         list(data = gtsummary::trial),         list(outcome.str = \"stage\")       )     )   }) |>   purrr::map(regression_table) |>   tbl_merge()   } # } regression_table <- function(x, ...) {   UseMethod(\"regression_table\") }  #' @rdname regression_table #' @export regression_table.list <- function(x, ...) {   x |>     purrr::map(\\(.m){       regression_table(x = .m, ...) |>         gtsummary::add_n()     }) |>     gtsummary::tbl_stack() }  #' @rdname regression_table #' @export regression_table.default <- function(x, ..., args.list = NULL, fun = \"gtsummary::tbl_regression\") {   # Stripping custom class   class(x) <- class(x)[class(x) != \"freesearcher_model\"]    if (any(c(length(class(x)) != 1, class(x) != \"lm\"))) {     if (!\"exponentiate\" %in% names(args.list)) {       args.list <- c(args.list, list(exponentiate = TRUE))     }   }    out <- do.call(getfun(fun), c(list(x = x), args.list))   out |>     gtsummary::add_glance_source_note() # |>   # gtsummary::bold_p() }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Removes columns with completenes below cutoff — remove_empty_cols","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"Removes columns completenes cutoff","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"","code":"remove_empty_cols(data, cutoff = 0.7)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"data data frame cutoff numeric","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"data frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"","code":"data.frame(a=1:10,b=NA, c=c(2,NA)) |> remove_empty_cols(cutoff=.5) #>     a  c #> 1   1  2 #> 2   2 NA #> 3   3  2 #> 4   4 NA #> 5   5  2 #> 6   6 NA #> 7   7  2 #> 8   8 NA #> 9   9  2 #> 10 10 NA"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove NA labels — remove_na_attr","title":"Remove NA labels — remove_na_attr","text":"Remove NA labels","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove NA labels — remove_na_attr","text":"","code":"remove_na_attr(data, attr = \"label\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove NA labels — remove_na_attr","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove NA labels — remove_na_attr","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove NA labels — remove_na_attr","text":"","code":"ds <- mtcars |> lapply(\\(.x) REDCapCAST::set_attr(.x,label=NA,attr = \"label\")) ds |> remove_na_attr() |> str() #> tibble [32 × 11] (S3: tbl_df/tbl/data.frame) #>  $ mpg : num [1:32] 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : num [1:32] 6 6 4 6 8 6 8 4 4 6 ... #>  $ disp: num [1:32] 160 160 108 258 360 ... #>  $ hp  : num [1:32] 110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num [1:32] 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num [1:32] 2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num [1:32] 16.5 17 18.6 19.4 17 ... #>  $ vs  : num [1:32] 0 0 1 1 0 1 0 1 1 1 ... #>  $ am  : num [1:32] 1 1 1 0 0 0 0 0 0 0 ... #>  $ gear: num [1:32] 4 4 4 3 3 3 3 4 4 4 ... #>  $ carb: num [1:32] 4 4 1 1 2 1 4 2 2 4 ..."},{"path":"https://agdamsbo.github.io/freesearcheR/reference/repeated_instruments.html","id":null,"dir":"Reference","previous_headings":"","what":"Get names of repeated instruments — repeated_instruments","title":"Get names of repeated instruments — repeated_instruments","text":"Get names repeated instruments","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/repeated_instruments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get names of repeated instruments — repeated_instruments","text":"","code":"repeated_instruments(uri, token)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/repeated_instruments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get names of repeated instruments — repeated_instruments","text":"uri REDCap database uri token database token","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/repeated_instruments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get names of repeated instruments — repeated_instruments","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/selectInputIcon.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a select input control with icon(s) — selectInputIcon","title":"Create a select input control with icon(s) — selectInputIcon","text":"Extend form controls adding text icons , , sides classic selectInput.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/selectInputIcon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a select input control with icon(s) — selectInputIcon","text":"","code":"selectInputIcon(   inputId,   label,   choices,   selected = NULL,   multiple = FALSE,   selectize = TRUE,   size = NULL,   width = NULL,   icon = NULL )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/selectInputIcon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a select input control with icon(s) — selectInputIcon","text":"inputId input slot used access value. label Display label control, NULL label. choices List values select . elements list named, name — rather value — displayed user. also possible group related inputs providing named list whose elements (either named unnamed) lists, vectors, factors. case, outermost names used group labels (leveraging <optgroup> HTML tag) elements respective sublist. See example section small demo feature. selected initially selected value (multiple values multiple = TRUE). specified defaults first value single-select lists values multiple select lists. multiple selection multiple items allowed? selectize Whether use selectize.js . size Number items show selection box; larger number result taller box. compatible selectize=TRUE. Normally, multiple=FALSE, select input drop-list, size set, box instead. width width input, e.g. '400px', '100%'; see validateCssUnit().","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/selectInputIcon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a select input control with icon(s) — selectInputIcon","text":"numeric input control can added UI definition.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":null,"dir":"Reference","previous_headings":"","what":"Launch the freesearcheR tool locally — shiny_freesearcheR","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"data.frames global environment accessible app.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"","code":"shiny_freesearcheR(...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"... arguments passed shiny::runApp()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"shiny app","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"","code":"if (FALSE) { # \\dontrun{ data(mtcars) shiny_freesearcheR(launch.browser = TRUE) } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":null,"dir":"Reference","previous_headings":"","what":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"Specify format arguments include qmd header/frontmatter","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"","code":"specify_qmd_format(data, fileformat = c(\"docx\", \"odt\", \"pdf\", \"all\"))"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"data vector fileformat format include","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":null,"dir":"Reference","previous_headings":"","what":"Easily subset by data type function — subset_types","title":"Easily subset by data type function — subset_types","text":"Easily subset data type function","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Easily subset by data type function — subset_types","text":"","code":"subset_types(data, types, type.fun = outcome_type)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Easily subset by data type function — subset_types","text":"data data types desired types type.fun function get type. Default outcome_type","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Easily subset by data type function — subset_types","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Easily subset by data type function — subset_types","text":"","code":"default_parsing(mtcars) |> subset_types(\"ordinal\") #> # A tibble: 32 × 3 #>    cyl   gear  carb  #>    <fct> <fct> <fct> #>  1 6     4     4     #>  2 6     4     4     #>  3 4     4     1     #>  4 6     3     1     #>  5 8     3     2     #>  6 6     3     1     #>  7 8     3     4     #>  8 4     4     2     #>  9 4     4     2     #> 10 6     4     4     #> # ℹ 22 more rows default_parsing(mtcars) |> subset_types(c(\"dichotomous\", \"ordinal\")) #> # A tibble: 32 × 5 #>    cyl   vs    am    gear  carb  #>    <fct> <fct> <fct> <fct> <fct> #>  1 6     0     1     4     4     #>  2 6     0     1     4     4     #>  3 4     1     1     4     1     #>  4 6     1     0     3     1     #>  5 8     0     0     3     2     #>  6 6     1     0     3     1     #>  7 8     0     0     3     4     #>  8 4     1     0     4     2     #>  9 4     1     0     4     2     #> 10 6     1     0     4     4     #> # ℹ 22 more rows #' default_parsing(mtcars) |> subset_types(\"factor\",class)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Implemented functions — supported_functions","title":"Implemented functions — supported_functions","text":"Library supported functions. list name \"descr\" element unique element list.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Implemented functions — supported_functions","text":"","code":"supported_functions()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Implemented functions — supported_functions","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Implemented functions — supported_functions","text":"","code":"supported_functions() #> $lm #> $lm$descr #> [1] \"Linear regression model\" #>  #> $lm$design #> [1] \"cross-sectional\" #>  #> $lm$out.type #> [1] \"continuous\" #>  #> $lm$fun #> [1] \"stats::lm\" #>  #> $lm$args.list #> NULL #>  #> $lm$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $lm$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $lm$table.args.list #> $lm$table.args.list$exponentiate #> [1] FALSE #>  #>  #>  #> $glm #> $glm$descr #> [1] \"Logistic regression model\" #>  #> $glm$design #> [1] \"cross-sectional\" #>  #> $glm$out.type #> [1] \"dichotomous\" #>  #> $glm$fun #> [1] \"stats::glm\" #>  #> $glm$args.list #> $glm$args.list$family #>  #> Family: binomial  #> Link function: logit  #>  #>  #>  #> $glm$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $glm$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $glm$table.args.list #> list() #>  #>  #> $polr #> $polr$descr #> [1] \"Ordinal logistic regression model\" #>  #> $polr$design #> [1] \"cross-sectional\" #>  #> $polr$out.type #> [1] \"ordinal\" #>  #> $polr$fun #> [1] \"MASS::polr\" #>  #> $polr$args.list #> $polr$args.list$Hess #> [1] TRUE #>  #> $polr$args.list$method #> [1] \"logistic\" #>  #>  #> $polr$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $polr$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $polr$table.args.list #> list() #>  #>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Implemented functions — supported_plots","title":"Implemented functions — supported_plots","text":"Library supported functions. list name \"descr\" element unique element list. descr: Plot description primary.type: Primary variable data type (continuous, dichotomous ordinal) secondary.type: Secondary variable data type (continuous, dichotomous ordinal) secondary.extra: \"none\" NULL option choose none. tertiary.type: Tertiary variable data type (continuous, dichotomous ordinal)","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Implemented functions — supported_plots","text":"","code":"supported_plots()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Implemented functions — supported_plots","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Implemented functions — supported_plots","text":"","code":"supported_plots() |> str() #> List of 5 #>  $ plot_hbars  :List of 8 #>   ..$ fun            : chr \"plot_hbars\" #>   ..$ descr          : chr \"Stacked horizontal bars\" #>   ..$ note           : chr \"A classical way of visualising the distribution of an ordinal scale like the modified Ranking Scale and known as Grotta bars\" #>   ..$ primary.type   : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.type : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.multi: logi FALSE #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: chr \"none\" #>  $ plot_violin :List of 8 #>   ..$ fun            : chr \"plot_violin\" #>   ..$ descr          : chr \"Violin plot\" #>   ..$ note           : chr \"A modern alternative to the classic boxplot to visualise data distribution\" #>   ..$ primary.type   : chr [1:3] \"continuous\" \"dichotomous\" \"ordinal\" #>   ..$ secondary.type : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.multi: logi FALSE #>   ..$ secondary.extra: chr \"none\" #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>  $ plot_sankey :List of 8 #>   ..$ fun            : chr \"plot_sankey\" #>   ..$ descr          : chr \"Sankey plot\" #>   ..$ note           : chr \"A way of visualising change between groups\" #>   ..$ primary.type   : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.type : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.multi: logi FALSE #>   ..$ secondary.extra: NULL #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>  $ plot_scatter:List of 8 #>   ..$ fun            : chr \"plot_scatter\" #>   ..$ descr          : chr \"Scatter plot\" #>   ..$ note           : chr \"A classic way of showing the association between to variables\" #>   ..$ primary.type   : chr \"continuous\" #>   ..$ secondary.type : chr [1:2] \"continuous\" \"ordinal\" #>   ..$ secondary.multi: logi FALSE #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: NULL #>  $ plot_euler  :List of 9 #>   ..$ fun            : chr \"plot_euler\" #>   ..$ descr          : chr \"Euler diagram\" #>   ..$ note           : chr \"Generate area-proportional Euler diagrams to display set relationships\" #>   ..$ primary.type   : chr \"dichotomous\" #>   ..$ secondary.type : chr \"dichotomous\" #>   ..$ secondary.multi: logi TRUE #>   ..$ secondary.max  : num 4 #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: NULL"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/tbl_merge.html","id":null,"dir":"Reference","previous_headings":"","what":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","title":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","text":"substitue gtsummary::tbl_merge, use list names tab spanner names.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/tbl_merge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","text":"","code":"tbl_merge(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/tbl_merge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","text":"data gtsummary list object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/tbl_merge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","text":"gt summary list object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-factor.html","id":null,"dir":"Reference","previous_headings":"","what":"Module to Reorder the Levels of a Factor Variable — update-factor","title":"Module to Reorder the Levels of a Factor Variable — update-factor","text":"module contain interface reorder levels factor variable.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-factor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module to Reorder the Levels of a Factor Variable — update-factor","text":"","code":"update_factor_ui(id)  update_factor_server(id, data_r = reactive(NULL))  modal_update_factor(   id,   title = i18n(\"Update levels of a factor\"),   easyClose = TRUE,   size = \"l\",   footer = NULL )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-factor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module to Reorder the Levels of a Factor Variable — update-factor","text":"id Module ID. data_r shiny::reactive() function returning data.frame. title optional title dialog. easyClose TRUE, modal dialog can dismissed clicking outside dialog box, pressing Escape key. FALSE (default), modal dialog dismissed ways; instead must dismissed clicking modalButton(), call removeModal() server. size One \"s\" small, \"m\" (default) medium, \"l\" large, \"xl\" extra large. Note \"xl\" works Bootstrap 4 (opt-Bootstrap 4+, pass bslib::bs_theme() theme argument page container like fluidPage()). footer UI footer. Use NULL footer.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-factor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module to Reorder the Levels of a Factor Variable — update-factor","text":"shiny::reactive() function returning data.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-variables.html","id":null,"dir":"Reference","previous_headings":"","what":"Select, rename and convert variables — update-variables","title":"Select, rename and convert variables — update-variables","text":"Select, rename convert variables","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-variables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Select, rename and convert variables — update-variables","text":"","code":"update_variables_ui(id, title = \"\")  update_variables_server(   id,   data,   height = NULL,   return_data_on_init = FALSE,   try_silent = FALSE )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-variables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Select, rename and convert variables — update-variables","text":"id Module's ID title Module's title, TRUE use default title, use NULL title shiny.tag custom one. data data.frame reactive function returning data.frame. height Height table. return_data_on_init Return initial data module called. try_silent logical: report error messages suppressed?","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-variables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Select, rename and convert variables — update-variables","text":"shiny::reactive() function returning updated data.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update_variables_datagrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Modified from the datamods pacakge — update_variables_datagrid","title":"Modified from the datamods pacakge — update_variables_datagrid","text":"Modified datamods pacakge","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update_variables_datagrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modified from the datamods pacakge — update_variables_datagrid","text":"","code":"update_variables_datagrid(   data,   height = NULL,   selectionId = NULL,   buttonId = NULL )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update_variables_datagrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modified from the datamods pacakge — update_variables_datagrid","text":"data data height height selectionId selectionId buttonId buttonId","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update_variables_datagrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Modified from the datamods pacakge — update_variables_datagrid","text":"","code":"mtcars |>   summary_vars() |>   update_variables_datagrid() #> Error in update_variables_datagrid(summary_vars(mtcars)): could not find function \"update_variables_datagrid\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vectorSelectInput.html","id":null,"dir":"Reference","previous_headings":"","what":"A selectizeInput customized for named vectors — vectorSelectInput","title":"A selectizeInput customized for named vectors — vectorSelectInput","text":"selectizeInput customized named vectors","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vectorSelectInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A selectizeInput customized for named vectors — vectorSelectInput","text":"","code":"vectorSelectInput(   inputId,   label,   choices,   selected = \"\",   ...,   placeholder = \"\",   onInitialize )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vectorSelectInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A selectizeInput customized for named vectors — vectorSelectInput","text":"inputId passed selectizeInput label passed selectizeInput choices named vector fields populated selected default selection ... passed selectizeInput placeholder passed selectizeInput options onInitialize passed selectizeInput options","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vectorSelectInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A selectizeInput customized for named vectors — vectorSelectInput","text":"selectizeInput dropdown element","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vectorSelectInput.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A selectizeInput customized for named vectors — vectorSelectInput","text":"","code":"if (shiny::interactive()) { shinyApp(   ui = fluidPage(     shiny::uiOutput(\"select\"),     tableOutput(\"data\")   ),   server = function(input, output) {     output$select <- shiny::renderUI({       vectorSelectInput(         inputId = \"variable\", label = \"Variable:\",         data = c(           \"Cylinders\" = \"cyl\",           \"Transmission\" = \"am\",           \"Gears\" = \"gear\"         )       )     })      output$data <- renderTable(       {         mtcars[, c(\"mpg\", input$variable), drop = FALSE]       },       rownames = TRUE     )   } ) } #> Error: 'interactive' is not an exported object from 'namespace:shiny'"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vertical_stacked_bars.html","id":null,"dir":"Reference","previous_headings":"","what":"Vertical stacked bar plot wrapper — vertical_stacked_bars","title":"Vertical stacked bar plot wrapper — vertical_stacked_bars","text":"Vertical stacked bar plot wrapper","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vertical_stacked_bars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vertical stacked bar plot wrapper — vertical_stacked_bars","text":"","code":"vertical_stacked_bars(   data,   score = \"full_score\",   group = \"pase_0_q\",   strata = NULL,   t.size = 10,   l.color = \"black\",   l.size = 0.5,   draw.lines = TRUE )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vertical_stacked_bars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vertical stacked bar plot wrapper — vertical_stacked_bars","text":"data data.frame score outcome variable group grouping variable strata stratifying variable t.size text size","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vertical_stacked_bars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Vertical stacked bar plot wrapper — vertical_stacked_bars","text":"ggplot2 object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/wide2long.html","id":null,"dir":"Reference","previous_headings":"","what":"Alternative pivoting method for easily pivoting based on name pattern — wide2long","title":"Alternative pivoting method for easily pivoting based on name pattern — wide2long","text":"function requires assumes systematic naming variables. now supports one level pivoting. Adding levels require added \"ignore\" string pattern similarly. Example 2.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/wide2long.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Alternative pivoting method for easily pivoting based on name pattern — wide2long","text":"","code":"wide2long(   data,   pattern,   type = c(\"prefix\", \"infix\", \"suffix\"),   id.col = 1,   instance.name = \"instance\" )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/wide2long.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Alternative pivoting method for easily pivoting based on name pattern — wide2long","text":"data data pattern pattern(s) match. Character vector length 1 . type type match. can one \"prefix\",\"infix\" \"suffix\". id.col ID column. fill ID . Column name numeric index. Default \"1\", first column. instance.name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/wide2long.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Alternative pivoting method for easily pivoting based on name pattern — wide2long","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/wide2long.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Alternative pivoting method for easily pivoting based on name pattern — wide2long","text":"","code":"data.frame(   1:20, sample(70:80, 20, TRUE),   sample(70:100, 20, TRUE),   sample(70:100, 20, TRUE),   sample(170:200, 20, TRUE) ) |>   setNames(c(\"id\", \"age\", \"weight_0\", \"weight_1\", \"height_1\")) |>   wide2long(pattern = c(\"_0\", \"_1\"), type = \"suffix\") #>    id age instance weight height #> 1   1  71        0     95     NA #> 2   1  NA        1     98    179 #> 3   2  72        0     77     NA #> 4   2  NA        1     98    182 #> 5   3  70        0     85     NA #> 6   3  NA        1     74    197 #> 7   4  71        0     83     NA #> 8   4  NA        1     82    199 #> 9   5  72        0     90     NA #> 10  5  NA        1     88    179 #> 11  6  75        0     94     NA #> 12  6  NA        1     94    175 #> 13  7  74        0     75     NA #> 14  7  NA        1    100    179 #> 15  8  71        0     91     NA #> 16  8  NA        1     83    195 #> 17  9  78        0     77     NA #> 18  9  NA        1     96    176 #> 19 10  79        0     90     NA #> 20 10  NA        1     92    187 #> 21 11  78        0     93     NA #> 22 11  NA        1     96    188 #> 23 12  71        0     72     NA #> 24 12  NA        1     73    193 #> 25 13  71        0     77     NA #> 26 13  NA        1     89    187 #> 27 14  76        0     74     NA #> 28 14  NA        1    100    192 #> 29 15  73        0     83     NA #> 30 15  NA        1     96    190 #> 31 16  75        0     96     NA #> 32 16  NA        1     82    183 #> 33 17  71        0     82     NA #> 34 17  NA        1     72    192 #> 35 18  76        0     88     NA #> 36 18  NA        1     77    195 #> 37 19  78        0     72     NA #> 38 19  NA        1     93    184 #> 39 20  75        0     97     NA #> 40 20  NA        1     98    198 data.frame(   1:20, sample(70:80, 20, TRUE),   sample(70:100, 20, TRUE),   sample(70:100, 20, TRUE),   sample(170:200, 20, TRUE) ) |>   setNames(c(\"id\", \"age\", \"weight_0\", \"weight_a_1\", \"height_b_1\")) |>   wide2long(pattern = c(\"_0\", \"_1\"), type = \"suffix\") #>    id age instance weight weight_a height_b #> 1   1  79        0     75       NA       NA #> 2   1  NA        1     NA       71      171 #> 3   2  74        0     93       NA       NA #> 4   2  NA        1     NA       97      199 #> 5   3  75        0     95       NA       NA #> 6   3  NA        1     NA       81      192 #> 7   4  70        0     97       NA       NA #> 8   4  NA        1     NA       75      195 #> 9   5  70        0     77       NA       NA #> 10  5  NA        1     NA       83      191 #> 11  6  75        0     90       NA       NA #> 12  6  NA        1     NA       95      178 #> 13  7  75        0     76       NA       NA #> 14  7  NA        1     NA       78      200 #> 15  8  79        0     72       NA       NA #> 16  8  NA        1     NA       76      185 #> 17  9  75        0     79       NA       NA #> 18  9  NA        1     NA       88      195 #> 19 10  78        0     70       NA       NA #> 20 10  NA        1     NA       74      199 #> 21 11  70        0     99       NA       NA #> 22 11  NA        1     NA       86      176 #> 23 12  77        0     74       NA       NA #> 24 12  NA        1     NA       78      174 #> 25 13  75        0     74       NA       NA #> 26 13  NA        1     NA       91      192 #> 27 14  70        0     73       NA       NA #> 28 14  NA        1     NA       81      176 #> 29 15  79        0     80       NA       NA #> 30 15  NA        1     NA       91      176 #> 31 16  72        0     78       NA       NA #> 32 16  NA        1     NA       94      181 #> 33 17  77        0     71       NA       NA #> 34 17  NA        1     NA       82      181 #> 35 18  80        0     97       NA       NA #> 36 18  NA        1     NA       81      200 #> 37 19  80        0     79       NA       NA #> 38 19  NA        1     NA       72      195 #> 39 20  74        0     71       NA       NA #> 40 20  NA        1     NA       77      171 # Optional filling of missing values by last observation carried forward # Needed for mmrm analyses long_missings |>   # Fills record ID assuming none are missing   tidyr::fill(record_id) |>   # Grouping by ID for the last step   dplyr::group_by(record_id) |>   # Filling missing data by ID   tidyr::fill(names(long_missings)[!names(long_missings) %in% new_names]) |>   # Remove grouping   dplyr::ungroup() #> Error: object 'long_missings' not found"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/write_quarto.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to save data in RDS, load into specified qmd and render — write_quarto","title":"Wrapper to save data in RDS, load into specified qmd and render — write_quarto","text":"Wrapper save data RDS, load specified qmd render","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/write_quarto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to save data in RDS, load into specified qmd and render — write_quarto","text":"","code":"write_quarto(data, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/write_quarto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to save data in RDS, load into specified qmd and render — write_quarto","text":"data list pass qmd ... Passed quarto::quarto_render()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/write_quarto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper to save data in RDS, load into specified qmd and render — write_quarto","text":"output file name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/news/index.html","id":"freesearcher-2532","dir":"Changelog","previous_headings":"","what":"freesearcheR 25.3.2","title":"freesearcheR 25.3.2","text":"Focus polish improved ui/ux. First steps towards updated name (FreesearchR), renamed repository. Also, repo move organisation (named FreesearchR). Testing file upload conducted improved. Working omproving code export.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/news/index.html","id":"freesearcher-2531","dir":"Changelog","previous_headings":"","what":"freesearcheR 25.3.1","title":"freesearcheR 25.3.1","text":"First steps towards focused simplified interface. Focus ease use, handling basic functionality data inspection descriptive analyses. Inspired Stroke Center implementation guidelines WSO, apply similar approach project order keep interface simple robust. Basic functions descriptive analyses data browsing basics. advanced features like regression analyses added learning purposes, really done one self software like R ensure learning reproducibility. Teal dependencies removed. teal framework really seems powerful promising, also mean less control clutter. May come later. main components implemented: Data import different sources Data management (variable creation, re-classing, naming, labelling ) Basic data comparisons descriptive analyses Basic data visualisations select set plot types great publication purposes Regression analysis basic clinical cross-sectional data (mixed models repeated measures survival analyses table) Export outputs (descriptive analyses regression) well modified dataset (code also showed, working ) Next steps : Polished code export Improved workflow descriptive text well thorough step-wise guide/documentation (possibly small videos) Implement clinical projects Implement data analysis courses Extensive testing bug squashing","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/news/index.html","id":"freesearcher-2511","dir":"Changelog","previous_headings":"","what":"freesearcheR 25.1.1","title":"freesearcheR 25.1.1","text":"UI tweaks. NEW: Option set class hms using hms package. NEW: summary grid sparklines. Speed improvements better regression analysis handling. Preparations extending analysis options study designs.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/news/index.html","id":"freesearcher-24121","dir":"Changelog","previous_headings":"","what":"freesearcheR 24.12.1","title":"freesearcheR 24.12.1","text":"Initial release Zenodo.","code":""}]
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Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement agdamsbo@clin.au.dk. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. 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Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired [Mozilla’s code conduct enforcement ladder][https://github.com/mozilla/inclusion]. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU Affero General Public License","title":"GNU Affero General Public License","text":"Version 3, 19 November 2007 Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU Affero General Public License","text":"GNU Affero General Public License free, copyleft license software kinds works, specifically designed ensure cooperation community case network server software. licenses software practical works designed take away freedom share change works. contrast, General Public Licenses intended guarantee freedom share change versions program–make sure remains free software users. speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. Developers use General Public Licenses protect rights two steps: (1) assert copyright software, (2) offer License gives legal permission copy, distribute /modify software. secondary benefit defending users’ freedom improvements made alternate versions program, receive widespread use, become available developers incorporate. Many developers free software heartened encouraged resulting cooperation. However, case software used network servers, result may fail come . GNU General Public License permits making modified version letting public access server without ever releasing source code public. GNU Affero General Public License designed specifically ensure , cases, modified source code becomes available community. requires operator network server provide source code modified version running users server. Therefore, public use modified version, publicly accessible server, gives public access source code modified version. older license, called Affero General Public License published Affero, designed accomplish similar goals. different license, version Affero GPL, Affero released new version Affero GPL permits relicensing license. precise terms conditions copying, distribution modification follow.","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_0-definitions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"0. Definitions.","title":"GNU Affero General Public License","text":"“License” refers version 3 GNU Affero General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. 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License explicitly affirms unlimited permission run unmodified Program. output running covered work covered License output, given content, constitutes covered work. License acknowledges rights fair use equivalent, provided copyright law. may make, run propagate covered works convey, without conditions long license otherwise remains force. may convey covered works others sole purpose make modifications exclusively , provide facilities running works, provided comply terms License conveying material control copyright. thus making running covered works must exclusively behalf, direction control, terms prohibit making copies copyrighted material outside relationship . Conveying circumstances permitted solely conditions stated . Sublicensing allowed; section 10 makes unnecessary.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_3-protecting-users-legal-rights-from-anti-circumvention-law","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"3. Protecting Users’ Legal Rights From Anti-Circumvention Law.","title":"GNU Affero General Public License","text":"covered work shall deemed part effective technological measure applicable law fulfilling obligations article 11 WIPO copyright treaty adopted 20 December 1996, similar laws prohibiting restricting circumvention measures. convey covered work, waive legal power forbid circumvention technological measures extent circumvention effected exercising rights License respect covered work, disclaim intention limit operation modification work means enforcing, work’s users, third parties’ legal rights forbid circumvention technological measures.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_4-conveying-verbatim-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"4. Conveying Verbatim Copies.","title":"GNU Affero General Public License","text":"may convey verbatim copies Program’s source code receive , medium, provided conspicuously appropriately publish copy appropriate copyright notice; keep intact notices stating License non-permissive terms added accord section 7 apply code; keep intact notices absence warranty; give recipients copy License along Program. may charge price price copy convey, may offer support warranty protection fee.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_5-conveying-modified-source-versions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"5. Conveying Modified Source Versions.","title":"GNU Affero General Public License","text":"may convey work based Program, modifications produce Program, form source code terms section 4, provided also meet conditions: work must carry prominent notices stating modified , giving relevant date. work must carry prominent notices stating released License conditions added section 7. requirement modifies requirement section 4 “keep intact notices”. must license entire work, whole, License anyone comes possession copy. License therefore apply, along applicable section 7 additional terms, whole work, parts, regardless packaged. 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Conveying Non-Source Forms.","title":"GNU Affero General Public License","text":"may convey covered work object code form terms sections 4 5, provided also convey machine-readable Corresponding Source terms License, one ways: Convey object code , embodied , physical product (including physical distribution medium), accompanied Corresponding Source fixed durable physical medium customarily used software interchange. Convey object code , embodied , physical product (including physical distribution medium), accompanied written offer, valid least three years valid long offer spare parts customer support product model, give anyone possesses object code either (1) copy Corresponding Source software product covered License, durable physical medium customarily used software interchange, price reasonable cost physically performing conveying source, (2) access copy Corresponding Source network server charge. 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Access network may denied modification materially adversely affects operation network violates rules protocols communication across network. Corresponding Source conveyed, Installation Information provided, accord section must format publicly documented (implementation available public source code form), must require special password key unpacking, reading copying.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_7-additional-terms","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"7. Additional Terms.","title":"GNU Affero General Public License","text":"“Additional permissions” terms supplement terms License making exceptions one conditions. Additional permissions applicable entire Program shall treated though included License, extent valid applicable law. additional permissions apply part Program, part may used separately permissions, entire Program remains governed License without regard additional permissions. convey copy covered work, may option remove additional permissions copy, part . (Additional permissions may written require removal certain cases modify work.) may place additional permissions material, added covered work, can give appropriate copyright permission. 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Termination.","title":"GNU Affero General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. Termination rights section terminate licenses parties received copies rights License. rights terminated permanently reinstated, qualify receive new licenses material section 10.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_9-acceptance-not-required-for-having-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"9. Acceptance Not Required for Having Copies.","title":"GNU Affero General Public License","text":"required accept License order receive run copy Program. Ancillary propagation covered work occurring solely consequence using peer--peer transmission receive copy likewise require acceptance. However, nothing License grants permission propagate modify covered work. actions infringe copyright accept License. Therefore, modifying propagating covered work, indicate acceptance License .","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_10-automatic-licensing-of-downstream-recipients","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"10. Automatic Licensing of Downstream Recipients.","title":"GNU Affero General Public License","text":"time convey covered work, recipient automatically receives license original licensors, run, modify propagate work, subject License. responsible enforcing compliance third parties License. “entity transaction” transaction transferring control organization, substantially assets one, subdividing organization, merging organizations. propagation covered work results entity transaction, party transaction receives copy work also receives whatever licenses work party’s predecessor interest give previous paragraph, plus right possession Corresponding Source work predecessor interest, predecessor can get reasonable efforts. may impose restrictions exercise rights granted affirmed License. example, may impose license fee, royalty, charge exercise rights granted License, may initiate litigation (including cross-claim counterclaim lawsuit) alleging patent claim infringed making, using, selling, offering sale, importing Program portion .","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_11-patents","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"11. Patents.","title":"GNU Affero General Public License","text":"“contributor” copyright holder authorizes use License Program work Program based. work thus licensed called contributor’s “contributor version”. contributor’s “essential patent claims” patent claims owned controlled contributor, whether already acquired hereafter acquired, infringed manner, permitted License, making, using, selling contributor version, include claims infringed consequence modification contributor version. purposes definition, “control” includes right grant patent sublicenses manner consistent requirements License. contributor grants non-exclusive, worldwide, royalty-free patent license contributor’s essential patent claims, make, use, sell, offer sale, import otherwise run, modify propagate contents contributor version. following three paragraphs, “patent license” express agreement commitment, however denominated, enforce patent (express permission practice patent covenant sue patent infringement). “grant” patent license party means make agreement commitment enforce patent party. convey covered work, knowingly relying patent license, Corresponding Source work available anyone copy, free charge terms License, publicly available network server readily accessible means, must either (1) cause Corresponding Source available, (2) arrange deprive benefit patent license particular work, (3) arrange, manner consistent requirements License, extend patent license downstream recipients. “Knowingly relying” means actual knowledge , patent license, conveying covered work country, recipient’s use covered work country, infringe one identifiable patents country reason believe valid. , pursuant connection single transaction arrangement, convey, propagate procuring conveyance , covered work, grant patent license parties receiving covered work authorizing use, propagate, modify convey specific copy covered work, patent license grant automatically extended recipients covered work works based . patent license “discriminatory” include within scope coverage, prohibits exercise , conditioned non-exercise one rights specifically granted License. may convey covered work party arrangement third party business distributing software, make payment third party based extent activity conveying work, third party grants, parties receive covered work , discriminatory patent license () connection copies covered work conveyed (copies made copies), (b) primarily connection specific products compilations contain covered work, unless entered arrangement, patent license granted, prior 28 March 2007. Nothing License shall construed excluding limiting implied license defenses infringement may otherwise available applicable patent law.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_12-no-surrender-of-others-freedom","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"12. No Surrender of Others’ Freedom.","title":"GNU Affero General Public License","text":"conditions imposed (whether court order, agreement otherwise) contradict conditions License, excuse conditions License. convey covered work satisfy simultaneously obligations License pertinent obligations, consequence may convey . example, agree terms obligate collect royalty conveying convey Program, way satisfy terms License refrain entirely conveying Program.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_13-remote-network-interaction-use-with-the-gnu-general-public-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"13. Remote Network Interaction; Use with the GNU General Public License.","title":"GNU Affero General Public License","text":"Notwithstanding provision License, modify Program, modified version must prominently offer users interacting remotely computer network (version supports interaction) opportunity receive Corresponding Source version providing access Corresponding Source network server charge, standard customary means facilitating copying software. Corresponding Source shall include Corresponding Source work covered version 3 GNU General Public License incorporated pursuant following paragraph. Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU General Public License single combined work, convey resulting work. terms License continue apply part covered work, work combined remain governed version 3 GNU General Public License.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License.","title":"GNU Affero General Public License","text":"Free Software Foundation may publish revised /new versions GNU Affero General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU Affero General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU Affero General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU Affero General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty.","title":"GNU Affero General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_16-limitation-of-liability","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"16. Limitation of Liability.","title":"GNU Affero General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16.","title":"GNU Affero General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU Affero General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. software can interact users remotely computer network, also make sure provides way users get source. example, program web application, interface display “Source” link leads users archive code. many ways offer source, different solutions better different programs; see section 13 specific requirements. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU AGPL, see https://www.gnu.org/licenses/.","code":"<one line to give the program's name and a brief idea of what it does.>     Copyright (C) <year>  <name of author>      This program is free software: you can redistribute it and/or modify     it under the terms of the GNU Affero General Public License as     published by the Free Software Foundation, either version 3 of the     License, or (at your option) any later version.      This program is distributed in the hope that it will be useful,     but WITHOUT ANY WARRANTY; without even the implied warranty of     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the     GNU Affero General Public License for more details.      You should have received a copy of the GNU Affero General Public License     along with this program.  If not, see <https://www.gnu.org/licenses/>."},{"path":"https://agdamsbo.github.io/freesearcheR/QA.html","id":null,"dir":"","previous_headings":"","what":"Questions and answers","title":"Questions and answers","text":"complete instructions set available, collection questions answers project use app.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/QA.html","id":"are-you-keeping-the-uploaded-data","dir":"","previous_headings":"","what":"Are you keeping the uploaded data?","title":"Questions and answers","text":"! uploaded data deleted session ends, stored analyses immediately deleted.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/QA.html","id":"how-do-i-merge-multiple-datasets","dir":"","previous_headings":"","what":"How do I merge multiple datasets?","title":"Questions and answers","text":"can merge multiple sheets ods xls(x) files import common key variable present selected sheets. Multiple file upload/merge currently supported.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/ROADMAP.html","id":null,"dir":"","previous_headings":"","what":"Project roadmap","title":"Project roadmap","text":"current state app considered experimental, lot things still changing. , however, usable state, basic functions available user. (actual list quite long growing) planned features improvements: Stratified analyses Additional study designs: Cross-sectional data analyses Longitudinal data analyses Survival analysis detailed variable browser Add histograms data distribution. 2025-01-16 Option edit labels. 2025-01-16 output controls Theming output tables Select analyses include report Export modified data. 2025-01-16 Include reproducible code steps (maybe , steps, final dataset can exported) Modify factor levels Factor level modifications possible converting factors numeric > cutting numeric desired fixed values. 2024-12-12 options date/datetime/time grouping/factoring. Included weekday month-options. 2024-12-12 Graphs plots Correlation matrix plot data exploration 2025-2-20 Grotta bars ordianl outcomes (sankey) 2025-3-17 Coefficient plotting regression analyses (forest plot) 2025-2-20","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/articles/freesearcheR.html","id":"getting-started-with-freesearcher","dir":"Articles","previous_headings":"","what":"Getting started with freesearcheR","title":"freesearcheR","text":"simple walk-trough basic instructions functions freesearcheR app.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/articles/freesearcheR.html","id":"launching","dir":"Articles","previous_headings":"Getting started with freesearcheR","what":"Launching","title":"freesearcheR","text":"easiest way get started launch hosted version app shinyapps.io (click link). Additionally option run app locally access data current working environment. , open R (RStudio similar), run following code install latest version freesearcheR launch app: small note, standalone Windows app version drawing board well, time frame available.","code":"require(\"pak\") pak::pak(\"agdamsbo/freesearcheR\") library(freesearcheR) freesearcheR::launch_freesearcheR()"},{"path":"https://agdamsbo.github.io/freesearcheR/articles/freesearcheR.html","id":"importing-data","dir":"Articles","previous_headings":"Getting started with freesearcheR","what":"Importing data","title":"freesearcheR","text":"app “Import”, three options available importing data: file upload, REDCap server export local sample data. choosing data source, can set threshold filter data completenes manually specify variables include analyses.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/articles/freesearcheR.html","id":"file-upload","dir":"Articles","previous_headings":"Getting started with freesearcheR > Importing data","what":"File upload","title":"freesearcheR","text":"Currently several data file formats supported easy import (csv, txt, xls(x), ods, rds, dta). importing workbooks (xls(x) ods), prompted specify sheet(s) import. choosing multiple sheets, automatically merged common variable(s), please make sure key variables correctly named identically.","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://agdamsbo.github.io/freesearcheR/articles/freesearcheR.html","id":"visualise","dir":"Articles","previous_headings":"Getting started with freesearcheR","what":"Visualise","title":"freesearcheR","text":"nice table possible plots, description data options","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://agdamsbo.github.io/freesearcheR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Andreas Gammelgaard Damsbo. Author, maintainer.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Damsbo (2025). freesearcheR: Browser Based Data Analysis. R package version 25.3.2, https://agdamsbo.github.io/freesearcheR/, https://github.com/agdamsbo/freesearcheR.","code":"@Manual{,   title = {freesearcheR: Browser Based Data Analysis},   author = {Andreas Gammelgaard Damsbo},   year = {2025},   note = {R package version 25.3.2, https://agdamsbo.github.io/freesearcheR/},   url = {https://github.com/agdamsbo/freesearcheR}, }"},{"path":"https://agdamsbo.github.io/freesearcheR/index.html","id":"freesearcher","dir":"","previous_headings":"","what":"Browser Based Data Analysis","title":"Browser Based Data Analysis","text":"package backbone freesearcheR, free open-source browser based data exploration analysis tool clinicians researchers publication ready output. package freesearcheR-tool part larger initiative democratize health data analysis remove barriers clinicians engage health research. freesearcheR-tool online accessible : link app freely hosted shinyapps.io. feedback welcome can shared GitHub issue. Initiatives funding continued development tool surrounding initiatives ongoing.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/index.html","id":"install-locally","dir":"","previous_headings":"","what":"Install locally","title":"Browser Based Data Analysis","text":"freesearcheR-tool can also launched locally. data.frame available global environment accessible interface.","code":"require(\"devtools\") devtools::install_github(\"agdamsbo/freesearcheR\") library(freesearcheR) # By loading mtcars to the environment, it will be available # in the interface like any other data.frame data(mtcars) shiny_freesearcheR()"},{"path":"https://agdamsbo.github.io/freesearcheR/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Browser Based Data Analysis","text":"Please note freesearcheR project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert class grid column to icon — add_class_icon","title":"Convert class grid column to icon — add_class_icon","text":"Convert class grid column icon","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert class grid column to icon — add_class_icon","text":"","code":"add_class_icon(grid, column = \"class\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert class grid column to icon — add_class_icon","text":"grid grid column column","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert class grid column to icon — add_class_icon","text":"datagrid","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert class grid column to icon — add_class_icon","text":"","code":"mtcars |>   overview_vars() |>   toastui::datagrid() |>   add_class_icon()      {\"x\":{\"nrow\":11,\"ncol\":7,\"data\":[[\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\"],[\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\"],[\"mpg\",\"cyl\",\"disp\",\"hp\",\"drat\",\"wt\",\"qsec\",\"vs\",\"am\",\"gear\",\"carb\"],[0,0,0,0,0,0,0,0,0,0,0],[1,1,1,1,1,1,1,1,1,1,1],[25,3,27,22,22,29,30,2,2,3,6],[[21,21,22.8,21.4,18.7,18.1,14.3,24.4,22.8,19.2,17.8,16.4,17.3,15.2,10.4,10.4,14.7,32.4,30.4,33.9,21.5,15.5,15.2,13.3,19.2,27.3,26,30.4,15.8,19.7,15,21.4],[6,6,4,6,8,6,8,4,4,6,6,8,8,8,8,8,8,4,4,4,4,8,8,8,8,4,4,4,8,6,8,4],[160,160,108,258,360,225,360,146.7,140.8,167.6,167.6,275.8,275.8,275.8,472,460,440,78.7,75.7,71.09999999999999,120.1,318,304,350,400,79,120.3,95.09999999999999,351,145,301,121],[110,110,93,110,175,105,245,62,95,123,123,180,180,180,205,215,230,66,52,65,97,150,150,245,175,66,91,113,264,175,335,109],[3.9,3.9,3.85,3.08,3.15,2.76,3.21,3.69,3.92,3.92,3.92,3.07,3.07,3.07,2.93,3,3.23,4.08,4.93,4.22,3.7,2.76,3.15,3.73,3.08,4.08,4.43,3.77,4.22,3.62,3.54,4.11],[2.62,2.875,2.32,3.215,3.44,3.46,3.57,3.19,3.15,3.44,3.44,4.07,3.73,3.78,5.25,5.424,5.345,2.2,1.615,1.835,2.465,3.52,3.435,3.84,3.845,1.935,2.14,1.513,3.17,2.77,3.57,2.78],[16.46,17.02,18.61,19.44,17.02,20.22,15.84,20,22.9,18.3,18.9,17.4,17.6,18,17.98,17.82,17.42,19.47,18.52,19.9,20.01,16.87,17.3,15.41,17.05,18.9,16.7,16.9,14.5,15.5,14.6,18.6],[0,0,1,1,0,1,0,1,1,1,1,0,0,0,0,0,0,1,1,1,1,0,0,0,0,1,0,1,0,0,0,1],[1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,1,1,1,1,1],[4,4,4,3,3,3,3,4,4,4,4,3,3,3,3,3,3,4,4,4,3,3,3,3,3,4,5,5,5,5,5,4],[4,4,1,1,2,1,4,2,2,4,4,3,3,3,4,4,4,1,2,1,1,2,2,4,2,1,2,2,4,6,8,2]]],\"colnames\":[\"class\",\"type\",\"name\",\"n_missing\",\"p_complete\",\"n_unique\",\"vals\"],\"options\":{\"columns\":[{\"header\":\"class\",\"name\":\"class\",\"sortable\":true,\"align\":\"left\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"},\"type\":\"datagrid.renderer.format\",\"options\":{\"formatted\":[\"<i 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{\"x\":{\"nrow\":11,\"ncol\":7,\"data\":[[\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\"],[\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\"],[\"mpg\",\"cyl\",\"disp\",\"hp\",\"drat\",\"wt\",\"qsec\",\"vs\",\"am\",\"gear\",\"carb\"],[0,0,0,0,0,0,0,0,0,0,0],[1,1,1,1,1,1,1,1,1,1,1],[25,3,27,22,22,29,30,2,2,3,6],[[21,21,22.8,21.4,18.7,18.1,14.3,24.4,22.8,19.2,17.8,16.4,17.3,15.2,10.4,10.4,14.7,32.4,30.4,33.9,21.5,15.5,15.2,13.3,19.2,27.3,26,30.4,15.8,19.7,15,21.4],[6,6,4,6,8,6,8,4,4,6,6,8,8,8,8,8,8,4,4,4,4,8,8,8,8,4,4,4,8,6,8,4],[160,160,108,258,360,225,360,146.7,140.8,167.6,167.6,275.8,275.8,275.8,472,460,440,78.7,75.7,71.09999999999999,120.1,318,304,350,400,79,120.3,95.09999999999999,351,145,301,121],[110,110,93,110,175,105,245,62,95,123,123,180,180,180,205,215,230,66,52,65,97,150,150,245,175,66,91,113,264,175,335,109],[3.9,3.9,3.85,3.08,3.15,2.76,3.21,3.69,3.92,3.92,3.92,3.07,3.07,3.07,2.93,3,3.23,4.08,4.93,4.22,3.7,2.76,3.15,3.73,3.08,4.08,4.43,3.77,4.22,3.62,3.54,4.11],[2.62,2.875,2.32,3.215,3.44,3.46,3.57,3.19,3.15,3.44,3.44,4.07,3.73,3.78,5.25,5.424,5.345,2.2,1.615,1.835,2.465,3.52,3.435,3.84,3.845,1.935,2.14,1.513,3.17,2.77,3.57,2.78],[16.46,17.02,18.61,19.44,17.02,20.22,15.84,20,22.9,18.3,18.9,17.4,17.6,18,17.98,17.82,17.42,19.47,18.52,19.9,20.01,16.87,17.3,15.41,17.05,18.9,16.7,16.9,14.5,15.5,14.6,18.6],[0,0,1,1,0,1,0,1,1,1,1,0,0,0,0,0,0,1,1,1,1,0,0,0,0,1,0,1,0,0,0,1],[1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,1,1,1,1,1],[4,4,4,3,3,3,3,4,4,4,4,3,3,3,3,3,3,4,4,4,3,3,3,3,3,4,5,5,5,5,5,4],[4,4,1,1,2,1,4,2,2,4,4,3,3,3,4,4,4,1,2,1,1,2,2,4,2,1,2,2,4,6,8,2]]],\"colnames\":[\"class\",\"type\",\"name\",\"n_missing\",\"p_complete\",\"n_unique\",\"vals\"],\"options\":{\"columns\":[{\"header\":\" 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theme based on unity — custom_theme","title":"Custom theme based on unity — custom_theme","text":"Custom theme based unity","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/custom_theme.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom theme based on unity — custom_theme","text":"","code":"custom_theme(   ...,   version = 5,   primary = \"#1E4A8F\",   secondary = \"#FF6F61\",   bootswatch = \"united\",   base_font = bslib::font_google(\"Montserrat\"),   heading_font = bslib::font_google(\"Public Sans\", wght = \"700\"),   code_font = bslib::font_google(\"Open Sans\") )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/custom_theme.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom theme based on unity — custom_theme","text":"... everything passed bslib::bs_theme()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/custom_theme.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom theme based on unity — custom_theme","text":"theme list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut-variable.html","id":null,"dir":"Reference","previous_headings":"","what":"Module to Convert Numeric to Factor — cut-variable","title":"Module to Convert Numeric to Factor — cut-variable","text":"module contain interface cut numeric several intervals.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut-variable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module to Convert Numeric to Factor — cut-variable","text":"","code":"cut_variable_ui(id)  cut_variable_server(id, data_r = reactive(NULL))  modal_cut_variable(   id,   title = i18n(\"Convert Numeric to Factor\"),   easyClose = TRUE,   size = \"l\",   footer = NULL )  winbox_cut_variable(   id,   title = i18n(\"Convert Numeric to Factor\"),   options = shinyWidgets::wbOptions(),   controls = shinyWidgets::wbControls() )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut-variable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module to Convert Numeric to Factor — cut-variable","text":"id Module ID. data_r shiny::reactive() function returning data.frame. title optional title dialog. easyClose TRUE, modal dialog can dismissed clicking outside dialog box, pressing Escape key. FALSE (default), modal dialog dismissed ways; instead must dismissed clicking modalButton(), call removeModal() server. size One \"s\" small, \"m\" (default) medium, \"l\" large, \"xl\" extra large. Note \"xl\" works Bootstrap 4 (opt-Bootstrap 4+, pass bslib::bs_theme() theme argument page container like fluidPage()). footer UI footer. Use NULL footer. options List options, see wbOptions(). controls List controls, see wbControls().","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut-variable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module to Convert Numeric to Factor — cut-variable","text":"shiny::reactive() function returning data.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut.html","id":null,"dir":"Reference","previous_headings":"","what":"Extended cutting function — cut.hms","title":"Extended cutting function — cut.hms","text":"Extended cutting function","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extended cutting function — cut.hms","text":"","code":"# S3 method for class 'hms' cut(x, breaks, ...)  # S3 method for class 'POSIXt' cut(   x,   breaks,   right = FALSE,   include.lowest = TRUE,   start.on.monday = TRUE,   ... )  # S3 method for class 'POSIXct' cut(   x,   breaks,   right = FALSE,   include.lowest = TRUE,   start.on.monday = TRUE,   ... )  # S3 method for class 'Date' cut(x, breaks, start.on.monday = TRUE, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extended cutting function — cut.hms","text":"x object inheriting class \"POSIXct\" ... passed ","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extended cutting function — cut.hms","text":"factor","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extended cutting function — cut.hms","text":"","code":"readr::parse_time(c(\"01:00:20\", \"03:00:20\", \"01:20:20\", \"08:20:20\", \"21:20:20\", \"03:02:20\")) |> cut(2) #> [1] 01:00:20 01:00:20 01:00:20 03:01:20 <NA>     03:01:20 #> attr(,\"brks\") #> 01:00:20 #> 03:01:20 #> 21:20:20 #> Levels: 01:00:20 03:01:20 readr::parse_time(c(\"01:00:20\", \"03:00:20\", \"01:20:20\", \"08:20:20\", \"21:20:20\", \"03:02:20\")) |> cut(\"min\") #> [1] 01:00:00 03:00:00 01:20:00 08:20:00 21:20:00 03:02:00 #> attr(,\"brks\") #> 01:00:00 #> 01:20:00 #> 03:00:00 #> 03:02:00 #> 08:20:00 #> 21:20:00 #> 21:20:20 #> Levels: 01:00:00 01:20:00 03:00:00 03:02:00 08:20:00 21:20:00 readr::parse_time(c(\"01:00:20\", \"03:00:20\", \"01:20:20\", \"08:20:20\", \"21:20:20\", \"03:02:20\")) |> cut(breaks = \"hour\") #> [1] 01:00:00 03:00:00 01:00:00 08:00:00 21:00:00 03:00:00 #> attr(,\"brks\") #> 01:00:00 #> 03:00:00 #> 08:00:00 #> 21:00:00 #> 21:20:20 #> Levels: 01:00:00 03:00:00 08:00:00 21:00:00 readr::parse_time(c(\"01:00:20\", \"03:00:20\", \"01:20:20\", \"08:20:20\", \"21:20:20\", \"03:02:20\")) |> cut(breaks = hms::as_hms(c(\"01:00:00\", \"03:01:20\", \"9:20:20\"))) #> [1] 01:00:00 01:00:00 01:00:00 03:01:20 <NA>     03:01:20 #> attr(,\"brks\") #> 01:00:00 #> 03:01:20 #> 09:20:20 #> Levels: 01:00:00 03:01:20 d_t <- readr::parse_time(c(\"01:00:20\", \"03:00:20\", \"01:20:20\", \"03:02:20\", NA)) f <- d_t |> cut(2) readr::parse_time(c(\"01:00:20\", \"03:00:20\", \"01:20:20\", \"03:02:20\", NA)) |> cut(breaks = lubridate::as_datetime(c(hms::as_hms(levels(f)), hms::as_hms(max(d_t, na.rm = TRUE) + 1))), right = FALSE) #> Warning: tz(): Don't know how to compute timezone for object of class hms/difftime; returning \"UTC\". #> [1] 01:00:20 02:10:20 01:00:20 02:10:20 <NA>     #> attr(,\"brks\") #> 01:00:20 #> 02:10:20 #> 03:02:21 #> Levels: 01:00:20 02:10:20 readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(2) #> [1] 1992-02-01 01:00:20 1992-02-01 01:00:20 1992-02-01 01:00:20 #> [4] 1992-02-01 01:00:20 1999-02-01 21:20:20 1992-02-01 01:00:20 #> Levels: 1992-02-01 01:00:20 1999-02-01 21:20:20 readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(breaks=\"weekday\") #> Error in cut.POSIXt(readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\",     \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\",     \"1992-12-01 03:02:20\")), breaks = \"weekday\"): invalid specification of 'breaks' readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(breaks=\"month_only\") #> Error in cut.POSIXt(readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\",     \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\",     \"1992-12-01 03:02:20\")), breaks = \"month_only\"): invalid specification of 'breaks' as.Date(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(2) #> [1] 1992-02-01 1992-02-01 1992-02-01 1992-02-01 1999-02-01 1992-02-01 #> Levels: 1992-02-01 1999-02-01 as.Date(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(breaks=\"weekday\") #> Error in cut.Date(as.Date(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\",     \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\",     \"1992-12-01 03:02:20\")), breaks = \"weekday\"): invalid specification of 'breaks'"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":null,"dir":"Reference","previous_headings":"","what":"Data correlations evaluation module — data-correlations","title":"Data correlations evaluation module — data-correlations","text":"Data correlations evaluation module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data correlations evaluation module — data-correlations","text":"","code":"data_correlations_ui(id, ...)  data_correlations_server(id, data, include.class = NULL, cutoff = 0.7, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data correlations evaluation module — data-correlations","text":"id Module id. (Use 'ns(\"id\")') ... arguments passed toastui::datagrid data data color.main main color color.sec secondary color","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data correlations evaluation module — data-correlations","text":"Shiny ui module shiny server module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-import.html","id":null,"dir":"Reference","previous_headings":"","what":"Test app for the data-import module — data_import_demo_app","title":"Test app for the data-import module — data_import_demo_app","text":"Test app data-import module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-import.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test app for the data-import module — data_import_demo_app","text":"","code":"data_import_demo_app()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-import.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test app for the data-import module — data_import_demo_app","text":"","code":"if (FALSE) { # \\dontrun{ data_import_demo_app() } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Data correlations evaluation module — data-plots","title":"Data correlations evaluation module — data-plots","text":"Data correlations evaluation module Wrapper create plot based provided type Nice horizontal stacked bars (Grotta bars) Plot nice ridge plot Readying data sankey plot Beautiful sankey plot option split tertiary group Beautiful violin plot Beatiful violin plot","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data correlations evaluation module — data-plots","text":"","code":"data_visuals_ui(id, tab_title = \"Plots\", ...)  data_visuals_server(id, data, ...)  create_plot(data, type, x, y, z = NULL, ...)  plot_hbars(data, x, y, z = NULL)  plot_ridge(data, x, y, z = NULL, ...)  sankey_ready(data, x, y, numbers = \"count\", ...)  plot_sankey(data, x, y, z = NULL, color.group = \"x\", colors = NULL)  plot_scatter(data, x, y, z = NULL)  plot_violin(data, x, y, z = NULL)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data correlations evaluation module — data-plots","text":"id Module id. (Use 'ns(\"id\")') ... ignored now data data.frame type plot type (derived possible_plots() matches custom function) x primary variable y secondary variable z tertiary variable","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data correlations evaluation module — data-plots","text":"Shiny ui module shiny server module ggplot2 object ggplot2 object ggplot2 object data.frame ggplot2 object ggplot2 object ggplot2 object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data correlations evaluation module — data-plots","text":"","code":"create_plot(mtcars, \"plot_violin\", \"mpg\", \"cyl\") #> Error in if (!z %in% names(data)) {    z <- NULL}: argument is of length zero mtcars |> plot_hbars(x = \"carb\", y = \"cyl\") #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale.  mtcars |> plot_hbars(x = \"carb\", y = NULL) #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale.  mtcars |>   default_parsing() |>   plot_ridge(x = \"mpg\", y = \"cyl\") #> Picking joint bandwidth of 1.38  mtcars |> plot_ridge(x = \"mpg\", y = \"cyl\", z = \"gear\") #> Picking joint bandwidth of 1.52 #> Warning: The following aesthetics were dropped during statistical transformation: y and #> fill. #> ℹ This can happen when ggplot fails to infer the correct grouping structure in #>   the data. #> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical #>   variable into a factor? #> Error in ggridges::geom_density_ridges(): Problem while setting up geom. #> ℹ Error occurred in the 1st layer. #> Caused by error in `compute_geom_1()`: #> ! `geom_density_ridges()` requires the following missing aesthetics: y. ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = sample(c(letters[1:4], NA), 100, TRUE, prob = c(rep(.23, 4), .08))) ds |> sankey_ready(\"first\", \"last\") #> # A tibble: 19 × 7 #>    first last      n gx.sum gy.sum lx          ly          #>    <fct> <fct> <int>  <int>  <int> <fct>       <fct>       #>  1 c     c         5     28     15 \"c\\n(n=28)\" \"c\\n(n=15)\" #>  2 c     a         7     28     32 \"c\\n(n=28)\" \"a\\n(n=32)\" #>  3 c     b         6     28     26 \"c\\n(n=28)\" \"b\\n(n=26)\" #>  4 c     d         6     28     17 \"c\\n(n=28)\" \"d\\n(n=17)\" #>  5 c     NA        4     28     10 \"c\\n(n=28)\"  NA         #>  6 a     c         6     24     15 \"a\\n(n=24)\" \"c\\n(n=15)\" #>  7 a     a         9     24     32 \"a\\n(n=24)\" \"a\\n(n=32)\" #>  8 a     b         6     24     26 \"a\\n(n=24)\" \"b\\n(n=26)\" #>  9 a     d         1     24     17 \"a\\n(n=24)\" \"d\\n(n=17)\" #> 10 a     NA        2     24     10 \"a\\n(n=24)\"  NA         #> 11 b     c         4     20     15 \"b\\n(n=20)\" \"c\\n(n=15)\" #> 12 b     a         8     20     32 \"b\\n(n=20)\" \"a\\n(n=32)\" #> 13 b     b         5     20     26 \"b\\n(n=20)\" \"b\\n(n=26)\" #> 14 b     d         2     20     17 \"b\\n(n=20)\" \"d\\n(n=17)\" #> 15 b     NA        1     20     10 \"b\\n(n=20)\"  NA         #> 16 d     a         8     28     32 \"d\\n(n=28)\" \"a\\n(n=32)\" #> 17 d     b         9     28     26 \"d\\n(n=28)\" \"b\\n(n=26)\" #> 18 d     d         8     28     17 \"d\\n(n=28)\" \"d\\n(n=17)\" #> 19 d     NA        3     28     10 \"d\\n(n=28)\"  NA         ds |> sankey_ready(\"first\", \"last\", numbers = \"percentage\") #> # A tibble: 19 × 7 #>    first last      n gx.sum gy.sum lx         ly         #>    <fct> <fct> <int>  <int>  <int> <fct>      <fct>      #>  1 c     c         5     28     15 \"c\\n(28%)\" \"c\\n(15%)\" #>  2 c     a         7     28     32 \"c\\n(28%)\" \"a\\n(32%)\" #>  3 c     b         6     28     26 \"c\\n(28%)\" \"b\\n(26%)\" #>  4 c     d         6     28     17 \"c\\n(28%)\" \"d\\n(17%)\" #>  5 c     NA        4     28     10 \"c\\n(28%)\"  NA        #>  6 a     c         6     24     15 \"a\\n(24%)\" \"c\\n(15%)\" #>  7 a     a         9     24     32 \"a\\n(24%)\" \"a\\n(32%)\" #>  8 a     b         6     24     26 \"a\\n(24%)\" \"b\\n(26%)\" #>  9 a     d         1     24     17 \"a\\n(24%)\" \"d\\n(17%)\" #> 10 a     NA        2     24     10 \"a\\n(24%)\"  NA        #> 11 b     c         4     20     15 \"b\\n(20%)\" \"c\\n(15%)\" #> 12 b     a         8     20     32 \"b\\n(20%)\" \"a\\n(32%)\" #> 13 b     b         5     20     26 \"b\\n(20%)\" \"b\\n(26%)\" #> 14 b     d         2     20     17 \"b\\n(20%)\" \"d\\n(17%)\" #> 15 b     NA        1     20     10 \"b\\n(20%)\"  NA        #> 16 d     a         8     28     32 \"d\\n(28%)\" \"a\\n(32%)\" #> 17 d     b         9     28     26 \"d\\n(28%)\" \"b\\n(26%)\" #> 18 d     d         8     28     17 \"d\\n(28%)\" \"d\\n(17%)\" #> 19 d     NA        3     28     10 \"d\\n(28%)\"  NA        data.frame(   g = sample(LETTERS[1:2], 100, TRUE),   first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)),   last = sample(c(TRUE, FALSE, FALSE), 100, TRUE) ) |>   sankey_ready(\"first\", \"last\") #> # A tibble: 8 × 7 #>   first last      n gx.sum gy.sum lx          ly              #>   <fct> <fct> <int>  <int>  <int> <fct>       <fct>           #> 1 a     FALSE    21     29     61 \"a\\n(n=29)\" \"FALSE\\n(n=61)\" #> 2 a     TRUE      8     29     39 \"a\\n(n=29)\" \"TRUE\\n(n=39)\"  #> 3 d     FALSE    12     22     61 \"d\\n(n=22)\" \"FALSE\\n(n=61)\" #> 4 d     TRUE     10     22     39 \"d\\n(n=22)\" \"TRUE\\n(n=39)\"  #> 5 b     FALSE    13     26     61 \"b\\n(n=26)\" \"FALSE\\n(n=61)\" #> 6 b     TRUE     13     26     39 \"b\\n(n=26)\" \"TRUE\\n(n=39)\"  #> 7 c     FALSE    15     23     61 \"c\\n(n=23)\" \"FALSE\\n(n=61)\" #> 8 c     TRUE      8     23     39 \"c\\n(n=23)\" \"TRUE\\n(n=39)\"  ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE))) ds |> plot_sankey(\"first\", \"last\") #> Loading required package: ggplot2  ds |> plot_sankey(\"first\", \"last\", color.group = \"y\")  ds |> plot_sankey(\"first\", \"last\", z = \"g\", color.group = \"y\")  mtcars |> plot_scatter(x = \"mpg\", y = \"wt\")  mtcars |> plot_violin(x = \"mpg\", y = \"cyl\", z = \"gear\") #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 1: `cyl = 4`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 1: `cyl = 4`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 2: `cyl = 6`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 2: `cyl = 6`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: Groups with fewer than two datapoints have been dropped. #> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes. #> Warning: Groups with fewer than two datapoints have been dropped. #> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes. #> Warning: Groups with fewer than two datapoints have been dropped. #> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes. #> Warning: Groups with fewer than two datapoints have been dropped. #> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes. #> Warning: Removed 2 rows containing non-finite outside the scale range #> (`stat_ydensity()`). #> Warning: Groups with fewer than two datapoints have been dropped. #> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes. #> Warning: Removed 1 row containing missing values or values outside the scale range #> (`geom_point()`). #> Warning: Removed 4 rows containing non-finite outside the scale range #> (`stat_ydensity()`). #> Warning: Removed 1 row containing missing values or values outside the scale range #> (`geom_point()`). #> Warning: Removed 1 row containing non-finite outside the scale range #> (`stat_ydensity()`). #> Warning: Removed 1 row containing missing values or values outside the scale range #> (`geom_point()`)."},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Data summary module — data-summary","title":"Data summary module — data-summary","text":"Data summary module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data summary module — data-summary","text":"","code":"data_summary_ui(id)  data_summary_server(id, data, color.main, color.sec, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data summary module — data-summary","text":"id Module id. (Use 'ns(\"id\")') data data color.main main color color.sec secondary color ... arguments passed toastui::datagrid","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data summary module — data-summary","text":"Shiny ui module shiny server module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_format_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Defaults qmd formats — default_format_arguments","title":"Defaults qmd formats — default_format_arguments","text":"Defaults qmd formats","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_format_arguments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Defaults qmd formats — default_format_arguments","text":"","code":"default_format_arguments()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_format_arguments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Defaults qmd formats — default_format_arguments","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":null,"dir":"Reference","previous_headings":"","what":"Default data parsing — default_parsing","title":"Default data parsing — default_parsing","text":"Default data parsing","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Default data parsing — default_parsing","text":"","code":"default_parsing(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Default data parsing — default_parsing","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Default data parsing — default_parsing","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Default data parsing — default_parsing","text":"","code":"mtcars |> str() #> 'data.frame':\t32 obs. of  11 variables: #>  $ mpg : num  21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : num  6 6 4 6 8 6 8 4 4 6 ... #>  $ disp: num  160 160 108 258 360 ... #>  $ hp  : num  110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num  3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num  2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num  16.5 17 18.6 19.4 17 ... #>  $ vs  : num  0 0 1 1 0 1 0 1 1 1 ... #>  $ am  : num  1 1 1 0 0 0 0 0 0 0 ... #>  $ gear: num  4 4 4 3 3 3 3 4 4 4 ... #>  $ carb: num  4 4 1 1 2 1 4 2 2 4 ... mtcars |>   default_parsing() |>   str() #> tibble [32 × 11] (S3: tbl_df/tbl/data.frame) #>  $ mpg : num [1:32] 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : Factor w/ 3 levels \"4\",\"6\",\"8\": 2 2 1 2 3 2 3 1 1 2 ... #>  $ disp: num [1:32] 160 160 108 258 360 ... #>  $ hp  : num [1:32] 110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num [1:32] 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num [1:32] 2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num [1:32] 16.5 17 18.6 19.4 17 ... #>  $ vs  : Factor w/ 2 levels \"0\",\"1\": 1 1 2 2 1 2 1 2 2 2 ... #>  $ am  : Factor w/ 2 levels \"0\",\"1\": 2 2 2 1 1 1 1 1 1 1 ... #>  $ gear: Factor w/ 3 levels \"3\",\"4\",\"5\": 2 2 2 1 1 1 1 2 2 2 ... #>  $ carb: Factor w/ 6 levels \"1\",\"2\",\"3\",\"4\",..: 4 4 1 1 2 1 4 2 2 4 ..."},{"path":"https://agdamsbo.github.io/freesearcheR/reference/drop_empty_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Drop empty events from REDCap export — drop_empty_event","title":"Drop empty events from REDCap export — drop_empty_event","text":"Drop empty events REDCap export","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/drop_empty_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Drop empty events from REDCap export — drop_empty_event","text":"","code":"drop_empty_event(data, event = \"redcap_event_name\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/drop_empty_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Drop empty events from REDCap export — drop_empty_event","text":"data data event \"redcap_event_name\", \"redcap_repeat_instrument\" \"redcap_repeat_instance\"","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/drop_empty_event.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Drop empty events from REDCap export — drop_empty_event","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":null,"dir":"Reference","previous_headings":"","what":"Factorize variables in data.frame — factorize","title":"Factorize variables in data.frame — factorize","text":"Factorize variables data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Factorize variables in data.frame — factorize","text":"","code":"factorize(data, vars)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Factorize variables in data.frame — factorize","text":"data data.frame vars variables force factorize","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Factorize variables in data.frame — factorize","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":null,"dir":"Reference","previous_headings":"","what":"Title — file_export","title":"Title — file_export","text":"Title","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title — file_export","text":"","code":"file_export(data, output.format = c(\"df\", \"teal\", \"list\"), filename, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title — file_export","text":"data data output.format output filename filename ... passed ","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title — file_export","text":"data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":null,"dir":"Reference","previous_headings":"","what":"Merges list of named arguments for qmd header generation — format_writer","title":"Merges list of named arguments for qmd header generation — format_writer","text":"Merges list named arguments qmd header generation","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Merges list of named arguments for qmd header generation — format_writer","text":"","code":"format_writer(data, name)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Merges list of named arguments for qmd header generation — format_writer","text":"data vector name name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Merges list of named arguments for qmd header generation — format_writer","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the function options based on the selected function description — get_fun_options","title":"Get the function options based on the selected function description — get_fun_options","text":"Get function options based selected function description","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the function options based on the selected function description — get_fun_options","text":"","code":"get_fun_options(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the function options based on the selected function description — get_fun_options","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the function options based on the selected function description — get_fun_options","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the function options based on the selected function description — get_fun_options","text":"","code":"mtcars |>   default_parsing() |>   dplyr::pull(mpg) |>   possible_functions(design = \"cross-sectional\") |>   (\\(.x){     .x[[1]]   })() |>   get_fun_options() #> $lm #> $lm$descr #> [1] \"Linear regression model\" #>  #> $lm$design #> [1] \"cross-sectional\" #>  #> $lm$out.type #> [1] \"continuous\" #>  #> $lm$fun #> [1] \"stats::lm\" #>  #> $lm$args.list #> NULL #>  #> $lm$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $lm$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $lm$table.args.list #> $lm$table.args.list$exponentiate #> [1] FALSE #>  #>  #>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Print label, and if missing print variable name — get_label","title":"Print label, and if missing print variable name — get_label","text":"Print label, missing print variable name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print label, and if missing print variable name — get_label","text":"","code":"get_label(data, var = NULL)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print label, and if missing print variable name — get_label","text":"data vector data frame var variable name. Optional.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print label, and if missing print variable name — get_label","text":"character string","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Print label, and if missing print variable name — get_label","text":"","code":"mtcars |> get_label(var = \"mpg\") #> [1] \"mpg\" mtcars |> get_label() #> [1] \"mtcars\" mtcars$mpg |> get_label() #> [1] \"mtcars$mpg\" gtsummary::trial |> get_label(var = \"trt\") #> [1] \"Chemotherapy Treatment\" 1:10 |> get_label() #> [1] \"1:10\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the function options based on the selected function description — get_plot_options","title":"Get the function options based on the selected function description — get_plot_options","text":"Get function options based selected function description","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the function options based on the selected function description — get_plot_options","text":"","code":"get_plot_options(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the function options based on the selected function description — get_plot_options","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the function options based on the selected function description — get_plot_options","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the function options based on the selected function description — get_plot_options","text":"","code":"ls <- mtcars |>   default_parsing() |>   dplyr::pull(mpg) |>   possible_plots() |>   (\\(.x){     .x[[1]]   })() |>   get_plot_options()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"function follows idea comment: https://stackoverflow.com/questions/38983179/-call--function--r-without-loading--package","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"","code":"getfun(x)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"x function function name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"function character vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"","code":"getfun(\"stats::lm\") #> function (formula, data, subset, weights, na.action, method = \"qr\",  #>     model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, offset, ...)  #> { #>     ret.x <- x #>     ret.y <- y #>     cl <- match.call() #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (method == \"model.frame\")  #>         return(mf) #>     else if (method != \"qr\")  #>         warning(gettextf(\"method = '%s' is not supported. Using 'qr'\",  #>             method), domain = NA) #>     mt <- attr(mf, \"terms\") #>     y <- model.response(mf, \"numeric\") #>     w <- as.vector(model.weights(mf)) #>     if (!is.null(w) && !is.numeric(w))  #>         stop(\"'weights' must be a numeric vector\") #>     offset <- model.offset(mf) #>     mlm <- is.matrix(y) #>     ny <- if (mlm)  #>         nrow(y) #>     else length(y) #>     if (!is.null(offset)) { #>         if (!mlm)  #>             offset <- as.vector(offset) #>         if (NROW(offset) != ny)  #>             stop(gettextf(\"number of offsets is %d, should equal %d (number of observations)\",  #>                 NROW(offset), ny), domain = NA) #>     } #>     if (is.empty.model(mt)) { #>         x <- NULL #>         z <- list(coefficients = if (mlm) matrix(NA_real_, 0,  #>             ncol(y)) else numeric(), residuals = y, fitted.values = 0 *  #>             y, weights = w, rank = 0L, df.residual = if (!is.null(w)) sum(w !=  #>             0) else ny) #>         if (!is.null(offset)) { #>             z$fitted.values <- offset #>             z$residuals <- y - offset #>         } #>     } #>     else { #>         x <- model.matrix(mt, mf, contrasts) #>         z <- if (is.null(w))  #>             lm.fit(x, y, offset = offset, singular.ok = singular.ok,  #>                 ...) #>         else lm.wfit(x, y, w, offset = offset, singular.ok = singular.ok,  #>             ...) #>     } #>     class(z) <- c(if (mlm) \"mlm\", \"lm\") #>     z$na.action <- attr(mf, \"na.action\") #>     z$offset <- offset #>     z$contrasts <- attr(x, \"contrasts\") #>     z$xlevels <- .getXlevels(mt, mf) #>     z$call <- cl #>     z$terms <- mt #>     if (model)  #>         z$model <- mf #>     if (ret.x)  #>         z$x <- x #>     if (ret.y)  #>         z$y <- y #>     if (!qr)  #>         z$qr <- NULL #>     z #> } #> <bytecode: 0x5629d0813b78> #> <environment: namespace:stats>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_export.html","id":null,"dir":"Reference","previous_headings":"","what":"GGplot default theme for plotting export objects — gg_theme_export","title":"GGplot default theme for plotting export objects — gg_theme_export","text":"GGplot default theme plotting export objects","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_export.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GGplot default theme for plotting export objects — gg_theme_export","text":"","code":"gg_theme_export()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_export.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GGplot default theme for plotting export objects — gg_theme_export","text":"data ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_export.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"GGplot default theme for plotting export objects — gg_theme_export","text":"ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_shiny.html","id":null,"dir":"Reference","previous_headings":"","what":"GGplot default theme for plotting in Shiny — gg_theme_shiny","title":"GGplot default theme for plotting in Shiny — gg_theme_shiny","text":"GGplot default theme plotting Shiny","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_shiny.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GGplot default theme for plotting in Shiny — gg_theme_shiny","text":"","code":"gg_theme_shiny()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_shiny.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GGplot default theme for plotting in Shiny — gg_theme_shiny","text":"data ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_shiny.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"GGplot default theme for plotting in Shiny — gg_theme_shiny","text":"ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/ggeulerr.html","id":null,"dir":"Reference","previous_headings":"","what":"Area proportional venn diagrams — ggeulerr","title":"Area proportional venn diagrams — ggeulerr","text":"slightly modified https://gist.github.com/danlooo/d23d8bcf8856c7dd8e86266097404ded functions uses eulerr::euler plot area proportional venn diagramms plots using ggplot2","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/ggeulerr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Area proportional venn diagrams — ggeulerr","text":"","code":"ggeulerr(combinations, show_quantities = TRUE, show_labels = TRUE, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/ggeulerr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Area proportional venn diagrams — ggeulerr","text":"combinations set relationships named numeric vector, matrix, data.frame(See eulerr::euler) show_quantities whether show number intersecting elements show_labels whether show set names ... arguments passed eulerr::euler","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/grepl_fix.html","id":null,"dir":"Reference","previous_headings":"","what":"Matches pattern to vector based on match type — grepl_fix","title":"Matches pattern to vector based on match type — grepl_fix","text":"Matches pattern vector based match type","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/grepl_fix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Matches pattern to vector based on match type — grepl_fix","text":"","code":"grepl_fix(data, pattern, type = c(\"prefix\", \"infix\", \"suffix\"))"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/grepl_fix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Matches pattern to vector based on match type — grepl_fix","text":"data vector pattern pattern(s) match. Character vector length 1 . type type match. can one \"prefix\",\"infix\" \"suffix\".","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/grepl_fix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Matches pattern to vector based on match type — grepl_fix","text":"logical vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/grepl_fix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Matches pattern to vector based on match type — grepl_fix","text":"","code":"c(\"id\", \"age\", \"weight_0\", \"weight_1\") |> grepl_fix(pattern = c(\"_0\", \"_1\"), type = \"suffix\") #> [1] FALSE FALSE  TRUE  TRUE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file-type.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to ease data file import — import-file-type","title":"Wrapper to ease data file import — import-file-type","text":"Wrapper ease data file import","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file-type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to ease data file import — import-file-type","text":"","code":"import_delim(file, skip, encoding, na.strings)  import_xls(file, sheet, skip, na.strings)  import_ods(file, sheet, skip, na.strings)  import_dta(file)  import_rds(file)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file-type.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to ease data file import — import-file-type","text":"file path file skip number row skip encoding file encoding na.strings character(s) interpret missing values. sheet Excel files, sheet read","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file-type.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper to ease data file import — import-file-type","text":"data.frame data.frame data.frame data.frame data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file.html","id":null,"dir":"Reference","previous_headings":"","what":"Import data from a file — import-file","title":"Import data from a file — import-file","text":"Let user upload file import data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Import data from a file — import-file","text":"","code":"import_file_ui(   id,   title = \"\",   preview_data = TRUE,   file_extensions = c(\".csv\", \".txt\", \".xls\", \".xlsx\", \".rds\", \".fst\", \".sas7bdat\",     \".sav\"),   layout_params = c(\"dropdown\", \"inline\") )  import_file_server(   id,   btn_show_data = TRUE,   show_data_in = c(\"popup\", \"modal\"),   trigger_return = c(\"button\", \"change\"),   return_class = c(\"data.frame\", \"data.table\", \"tbl_df\", \"raw\"),   reset = reactive(NULL) )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Import data from a file — import-file","text":"preview_data Show preview data file input. file_extensions File extensions accepted shiny::fileInput(), can also MIME type. layout_params display import parameters : dropdown button inline file input.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file_module.html","id":null,"dir":"Reference","previous_headings":"","what":"Test app for the import_file module — import_file_demo_app","title":"Test app for the import_file module — import_file_demo_app","text":"Test app import_file module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file_module.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test app for the import_file module — import_file_demo_app","text":"","code":"import_file_demo_app()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/import-file_module.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test app for the import_file module — import_file_demo_app","text":"","code":"if (FALSE) { # \\dontrun{ import_file_demo_app() } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/index_embed.html","id":null,"dir":"Reference","previous_headings":"","what":"Split vector by an index and embed addition — index_embed","title":"Split vector by an index and embed addition — index_embed","text":"Split vector index embed addition","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/index_embed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split vector by an index and embed addition — index_embed","text":"","code":"index_embed(data, index, add = NULL)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/index_embed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split vector by an index and embed addition — index_embed","text":"data vector index split index add addition","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/index_embed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split vector by an index and embed addition — index_embed","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":null,"dir":"Reference","previous_headings":"","what":"Test class — is_any_class","title":"Test class — is_any_class","text":"Test class","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test class — is_any_class","text":"","code":"is_any_class(data, class.vec)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test class — is_any_class","text":"data data class.vec vector class names test","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test class — is_any_class","text":"factor","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test class — is_any_class","text":"","code":"if (FALSE) { # \\dontrun{ vapply(REDCapCAST::redcapcast_data, \\(.x){   is_any_class(.x, c(\"hms\", \"Date\", \"POSIXct\", \"POSIXt\")) }, logical(1)) } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"Checks elements vector equally spaced indication ID","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"","code":"is_consecutive(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"logical","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"","code":"1:10 |> is_consecutive() #> [1] TRUE sample(1:100,40) |> is_consecutive() #> [1] FALSE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":null,"dir":"Reference","previous_headings":"","what":"Test is date/datetime/time — is_datetime","title":"Test is date/datetime/time — is_datetime","text":"Test date/datetime/time","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test is date/datetime/time — is_datetime","text":"","code":"is_datetime(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test is date/datetime/time — is_datetime","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test is date/datetime/time — is_datetime","text":"factor","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test is date/datetime/time — is_datetime","text":"","code":"vapply(REDCapCAST::redcapcast_data, is_datetime, logical(1)) #>                    record_id            redcap_event_name  #>                        FALSE                        FALSE  #>     redcap_repeat_instrument       redcap_repeat_instance  #>                        FALSE                        FALSE  #>                          cpr                    inclusion  #>                        FALSE                         TRUE  #>               inclusion_time                          dob  #>                         TRUE                         TRUE  #>                          age                  age_integer  #>                        FALSE                        FALSE  #>                          sex                 cohabitation  #>                        FALSE                        FALSE  #>                 hypertension                     diabetes  #>                        FALSE                        FALSE  #>                       region baseline_data_start_complete  #>                        FALSE                        FALSE  #>                 mrs_assessed                     mrs_date  #>                        FALSE                         TRUE  #>                    mrs_score                 mrs_complete  #>                        FALSE                        FALSE  #>                      con_mrs                     con_calc  #>                        FALSE                        FALSE  #>           consensus_complete               event_datetime  #>                        FALSE                         TRUE  #>                    event_age                   event_type  #>                        FALSE                        FALSE  #>           new_event_complete  #>                        FALSE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if url is valid format for REDCap API — is_valid_redcap_url","title":"Test if url is valid format for REDCap API — is_valid_redcap_url","text":"Test url valid format REDCap API","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if url is valid format for REDCap API — is_valid_redcap_url","text":"","code":"is_valid_redcap_url(url)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if url is valid format for REDCap API — is_valid_redcap_url","text":"url url","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test if url is valid format for REDCap API — is_valid_redcap_url","text":"logical","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test if url is valid format for REDCap API — is_valid_redcap_url","text":"","code":"url <- c(   \"www.example.com\",   \"redcap.your.inst/api/\",   \"https://redcap.your.inst/api/\",   \"https://your.inst/redcap/api/\",   \"https://www.your.inst/redcap/api/\" ) is_valid_redcap_url(url) #> [1] FALSE FALSE  TRUE  TRUE  TRUE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate REDCap token — is_valid_token","title":"Validate REDCap token — is_valid_token","text":"Validate REDCap token","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate REDCap token — is_valid_token","text":"","code":"is_valid_token(token, pattern_env = NULL, nchar = 32)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate REDCap token — is_valid_token","text":"token token pattern_env pattern","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate REDCap token — is_valid_token","text":"logical","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate REDCap token — is_valid_token","text":"","code":"token <- paste(sample(c(1:9, LETTERS[1:6]), 32, TRUE), collapse = \"\") is_valid_token(token) #> [1] TRUE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":null,"dir":"Reference","previous_headings":"","what":"Easily launch the freesearcheR app — launch_freesearcheR","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"Easily launch freesearcheR app","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"","code":"launch_freesearcheR(...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"... passed shiny::runApp()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"shiny app","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":null,"dir":"Reference","previous_headings":"","what":"Line breaking at given number of characters for nicely plotting labels — line_break","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"Line breaking given number characters nicely plotting labels","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"","code":"line_break(data, lineLength = 20, fixed = FALSE)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"data string lineLength maximum line length fixed flag force split exactly value given lineLength. Default FALSE, splitting spaces.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"character string","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"","code":"\"Lorem ipsum... you know the routine\" |> line_break() #> [1] \"Lorem ipsum... you\\nknow the routine\" paste(sample(letters[1:10], 100, TRUE), collapse = \"\") |> line_break(fixed = TRUE) #> [1] \"jdhegaaegchcffhcedhcgghhdifbfjheabacfibfhecjigehjdgdjfaffbfhfcghgefddidiihdhbgedgdgaahcjicggefhgfjhb\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":null,"dir":"Reference","previous_headings":"","what":"Shiny UI module to load a data file — m_datafileUI","title":"Shiny UI module to load a data file — m_datafileUI","text":"Shiny UI module load data file","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shiny UI module to load a data file — m_datafileUI","text":"","code":"m_datafileUI(id)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shiny UI module to load a data file — m_datafileUI","text":"id id","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shiny UI module to load a data file — m_datafileUI","text":"shiny UI","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"Wrapper pivot gtsummary table data long plotting","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"","code":"merge_long(list, model.names)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"list custom regression models list model.names names models include","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/missing_fraction.html","id":null,"dir":"Reference","previous_headings":"","what":"Get missingsness fraction — missing_fraction","title":"Get missingsness fraction — missing_fraction","text":"Get missingsness fraction","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/missing_fraction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get missingsness fraction — missing_fraction","text":"","code":"missing_fraction(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/missing_fraction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get missingsness fraction — missing_fraction","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/missing_fraction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get missingsness fraction — missing_fraction","text":"numeric vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/missing_fraction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get missingsness fraction — missing_fraction","text":"","code":"c(NA,1:10,rep(NA,3)) |> missing_fraction() #> [1] 0.2857143"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to modify quarto file to render specific formats — modify_qmd","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"Wrapper modify quarto file render specific formats","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"","code":"modify_qmd(file, format)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"file filename format desired output","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"none","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":null,"dir":"Reference","previous_headings":"","what":"Outcome data type assessment — outcome_type","title":"Outcome data type assessment — outcome_type","text":"Outcome data type assessment","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Outcome data type assessment — outcome_type","text":"","code":"outcome_type(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Outcome data type assessment — outcome_type","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Outcome data type assessment — outcome_type","text":"outcome type","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Outcome data type assessment — outcome_type","text":"","code":"mtcars |>   default_parsing() |>   lapply(outcome_type) #> $mpg #> [1] \"continuous\" #>  #> $cyl #> [1] \"ordinal\" #>  #> $disp #> [1] \"continuous\" #>  #> $hp #> [1] \"continuous\" #>  #> $drat #> [1] \"continuous\" #>  #> $wt #> [1] \"continuous\" #>  #> $qsec #> [1] \"continuous\" #>  #> $vs #> [1] \"dichotomous\" #>  #> $am #> [1] \"dichotomous\" #>  #> $gear #> [1] \"ordinal\" #>  #> $carb #> [1] \"ordinal\" #>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a data overview data.frame ready for sparklines — overview_vars","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"Create data overview data.frame ready sparklines","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"","code":"overview_vars(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"","code":"mtcars |> overview_vars() #> # A tibble: 11 × 7 #>    class   type    name  n_missing p_complete n_unique vals         #>    <chr>   <chr>   <chr>     <dbl>      <dbl>    <int> <named list> #>  1 numeric numeric mpg           0          1       25 <dbl [32]>   #>  2 numeric numeric cyl           0          1        3 <dbl [32]>   #>  3 numeric numeric disp          0          1       27 <dbl [32]>   #>  4 numeric numeric hp            0          1       22 <dbl [32]>   #>  5 numeric numeric drat          0          1       22 <dbl [32]>   #>  6 numeric numeric wt            0          1       29 <dbl [32]>   #>  7 numeric numeric qsec          0          1       30 <dbl [32]>   #>  8 numeric numeric vs            0          1        2 <dbl [32]>   #>  9 numeric numeric am            0          1        2 <dbl [32]>   #> 10 numeric numeric gear          0          1        3 <dbl [32]>   #> 11 numeric numeric carb          0          1        6 <dbl [32]>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"Regression coef plot gtsummary. Slightly modified pass arguments","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"","code":"# S3 method for class 'tbl_regression' plot(x, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"x (tbl_regression, tbl_uvregression) 'tbl_regression' 'tbl_uvregression' object ... arguments passed ggstats::ggcoef_plot(...)","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"","code":"if (FALSE) { # \\dontrun{ mod <- lm(mpg ~ ., mtcars) p <- mod |>   gtsummary::tbl_regression() |>   plot(colour = \"variable\") } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler.html","id":null,"dir":"Reference","previous_headings":"","what":"Easily plot euler diagrams — plot_euler","title":"Easily plot euler diagrams — plot_euler","text":"Easily plot euler diagrams","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Easily plot euler diagrams — plot_euler","text":"","code":"plot_euler(data, x, y, z = NULL, seed = 2103)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Easily plot euler diagrams — plot_euler","text":"data data x name main variable y name secondary variables z grouping variable seed seed","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Easily plot euler diagrams — plot_euler","text":"patchwork object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Easily plot euler diagrams — plot_euler","text":"","code":"data.frame(   A = sample(c(TRUE, TRUE, FALSE), 50, TRUE),   B = sample(c(\"A\", \"C\"), 50, TRUE),   C = sample(c(TRUE, FALSE, FALSE, FALSE), 50, TRUE),   D = sample(c(TRUE, FALSE, FALSE, FALSE), 50, TRUE) ) |> plot_euler(\"A\", c(\"B\", \"C\"), \"D\", seed = 4)  mtcars |> plot_euler(\"vs\", \"am\", seed = 1) #> [[1]]  #>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler_single.html","id":null,"dir":"Reference","previous_headings":"","what":"Easily plot single euler diagrams — plot_euler_single","title":"Easily plot single euler diagrams — plot_euler_single","text":"Easily plot single euler diagrams","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler_single.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Easily plot single euler diagrams — plot_euler_single","text":"","code":"plot_euler_single(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler_single.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Easily plot single euler diagrams — plot_euler_single","text":"ggplot2 object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_euler_single.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Easily plot single euler diagrams — plot_euler_single","text":"","code":"data.frame(   A = sample(c(TRUE, TRUE, FALSE), 50, TRUE),   B = sample(c(\"A\", \"C\"), 50, TRUE),   C = sample(c(TRUE, FALSE, FALSE, FALSE), 50, TRUE),   D = sample(c(TRUE, FALSE, FALSE, FALSE), 50, TRUE) ) |> plot_euler_single()  mtcars[c(\"vs\", \"am\")] |> plot_euler_single()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":null,"dir":"Reference","previous_headings":"","what":"Beautiful sankey plot — plot_sankey_single","title":"Beautiful sankey plot — plot_sankey_single","text":"Beautiful sankey plot","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Beautiful sankey plot — plot_sankey_single","text":"","code":"plot_sankey_single(data, x, y, color.group = c(\"x\", \"y\"), colors = NULL, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Beautiful sankey plot — plot_sankey_single","text":"color.group set group colour . \"x\" \"y\". colors optinally specify colors. Give NA color, color level primary group color level secondary group. ... passed sankey_ready()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Beautiful sankey plot — plot_sankey_single","text":"ggplot2 object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Beautiful sankey plot — plot_sankey_single","text":"","code":"ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE))) ds |> plot_sankey_single(\"first\", \"last\") #> Warning: Some strata appear at multiple axes. #> Warning: Some strata appear at multiple axes. #> Warning: Some strata appear at multiple axes.  ds |> plot_sankey_single(\"first\", \"last\", color.group = \"y\") #> Warning: Some strata appear at multiple axes. #> Warning: Some strata appear at multiple axes. #> Warning: Some strata appear at multiple axes.  data.frame(   g = sample(LETTERS[1:2], 100, TRUE),   first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)),   last = sample(c(TRUE, FALSE, FALSE), 100, TRUE) ) |>   plot_sankey_single(\"first\", \"last\", color.group = \"x\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Get possible regression models — possible_functions","title":"Get possible regression models — possible_functions","text":"Get possible regression models","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get possible regression models — possible_functions","text":"","code":"possible_functions(data, design = c(\"cross-sectional\"))"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get possible regression models — possible_functions","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get possible regression models — possible_functions","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get possible regression models — possible_functions","text":"","code":"mtcars |>   default_parsing() |>   dplyr::pull(\"cyl\") |>   possible_functions(design = \"cross-sectional\") #> [1] \"Ordinal logistic regression model\"  mtcars |>   default_parsing() |>   dplyr::select(\"cyl\") |>   possible_functions(design = \"cross-sectional\") #> [1] \"Ordinal logistic regression model\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Get possible regression models — possible_plots","title":"Get possible regression models — possible_plots","text":"Get possible regression models","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get possible regression models — possible_plots","text":"","code":"possible_plots(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get possible regression models — possible_plots","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get possible regression models — possible_plots","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get possible regression models — possible_plots","text":"","code":"mtcars |>   default_parsing() |>   dplyr::pull(\"cyl\") |>   possible_plots() #> [1] \"Stacked horizontal bars\" \"Violin plot\"             #> [3] \"Sankey plot\"              mtcars |>   default_parsing() |>   dplyr::select(\"mpg\") |>   possible_plots() #> [1] \"Violin plot\"  \"Scatter plot\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Flexible file import based on extension — read_input","title":"Flexible file import based on extension — read_input","text":"Flexible file import based extension","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Flexible file import based on extension — read_input","text":"","code":"read_input(file, consider.na = c(\"NA\", \"\\\"\\\"\", \"\"))"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Flexible file import based on extension — read_input","text":"file file name consider.na character vector strings consider NAs","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Flexible file import based on extension — read_input","text":"tibble","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Flexible file import based on extension — read_input","text":"","code":"read_input(\"https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv\") #> Rows: 28 Columns: 8 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> dbl (8): id, ab, age, imm, vis, ver, att, del #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> # A tibble: 28 × 8 #>       id    ab   age   imm   vis   ver   att   del #>    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1     1     1    74    38    35    30    29    35 #>  2     1     2    69    36    36    21    27    37 #>  3     2     1    63    32    31    26    34    38 #>  4     2     2    64    37    34    26    36    46 #>  5     3     1    69    39    33    31    47    29 #>  6     3     2    70    40    36    31    46    25 #>  7     4     1    79    44    37    20    37    36 #>  8     4     2    81    35    36    31    37    40 #>  9     5     1    77    35    26    17    20    36 #> 10     5     2    80    29    34    18    23    36 #> # ℹ 18 more rows"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":null,"dir":"Reference","previous_headings":"","what":"Shiny module to browser and export REDCap data — m_redcap_readUI","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"Shiny module browser export REDCap data Test app redcap_read_shiny_module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"","code":"m_redcap_readUI(id, title = TRUE)  m_redcap_readServer(id)  redcap_demo_app()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"id Namespace id include_title logical include title","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"shiny ui element shiny server module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"","code":"if (FALSE) { # \\dontrun{ redcap_demo_app() } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a regression model programatically — regression_model","title":"Create a regression model programatically — regression_model","text":"Output concatenated list model information model","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a regression model programatically — regression_model","text":"","code":"regression_model(   data,   outcome.str,   auto.mode = FALSE,   formula.str = NULL,   args.list = NULL,   fun = NULL,   vars = NULL,   ... )  regression_model_uv(   data,   outcome.str,   args.list = NULL,   fun = NULL,   vars = NULL,   ... )  regression_model_list(   data,   outcome.str,   fun.descr,   fun = NULL,   formula.str = NULL,   args.list = NULL,   vars = NULL,   ... )  regression_model_uv_list(   data,   outcome.str,   fun.descr,   fun = NULL,   formula.str = NULL,   args.list = NULL,   vars = NULL,   ... )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a regression model programatically — regression_model","text":"data data outcome.str name outcome variable auto.mode Make assumptions function dependent outcome data format. Overwrites arguments. formula.str custom formula glue string. Default NULL. args.list custom character string converted using argsstring2list() list arguments. Default NULL. fun name custom function. Default NULL. vars character vector variables include ... ignored fun.descr Description chosen function matching description \"supported_functions()\"","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a regression model programatically — regression_model","text":"object standard class fun object standard class fun list list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a regression model programatically — regression_model","text":"","code":"gtsummary::trial |>   regression_model(outcome.str = \"age\") #>  #> Call: #> (function (formula, data, subset, weights, na.action, method = \"qr\",  #>     model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, offset, ...)  #> { #>     ret.x <- x #>     ret.y <- y #>     cl <- match.call() #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (method == \"model.frame\")  #>         return(mf) #>     else if (method != \"qr\")  #>         warning(gettextf(\"method = '%s' is not supported. Using 'qr'\",  #>             method), domain = NA) #>     mt <- attr(mf, \"terms\") #>     y <- model.response(mf, \"numeric\") #>     w <- as.vector(model.weights(mf)) #>     if (!is.null(w) && !is.numeric(w))  #>         stop(\"'weights' must be a numeric vector\") #>     offset <- model.offset(mf) #>     mlm <- is.matrix(y) #>     ny <- if (mlm)  #>         nrow(y) #>     else length(y) #>     if (!is.null(offset)) { #>         if (!mlm)  #>             offset <- as.vector(offset) #>         if (NROW(offset) != ny)  #>             stop(gettextf(\"number of offsets is %d, should equal %d (number of observations)\",  #>                 NROW(offset), ny), domain = NA) #>     } #>     if (is.empty.model(mt)) { #>         x <- NULL #>         z <- list(coefficients = if (mlm) matrix(NA_real_, 0,  #>             ncol(y)) else numeric(), residuals = y, fitted.values = 0 *  #>             y, weights = w, rank = 0L, df.residual = if (!is.null(w)) sum(w !=  #>             0) else ny) #>         if (!is.null(offset)) { #>             z$fitted.values <- offset #>             z$residuals <- y - offset #>         } #>     } #>     else { #>         x <- model.matrix(mt, mf, contrasts) #>         z <- if (is.null(w))  #>             lm.fit(x, y, offset = offset, singular.ok = singular.ok,  #>                 ...) #>         else lm.wfit(x, y, w, offset = offset, singular.ok = singular.ok,  #>             ...) #>     } #>     class(z) <- c(if (mlm) \"mlm\", \"lm\") #>     z$na.action <- attr(mf, \"na.action\") #>     z$offset <- offset #>     z$contrasts <- attr(x, \"contrasts\") #>     z$xlevels <- .getXlevels(mt, mf) #>     z$call <- cl #>     z$terms <- mt #>     if (model)  #>         z$model <- mf #>     if (ret.x)  #>         z$x <- x #>     if (ret.y)  #>         z$y <- y #>     if (!qr)  #>         z$qr <- NULL #>     z #> })(formula = age ~ trt + marker + stage + grade + response +  #>     death + ttdeath, data = structure(list(trt = structure(c(1L,  #> 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L,  #> 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L,  #> 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L,  #> 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L,  #> 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L,  #> 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L,  #> 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L,  #> 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L,  #> 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,  #> 2L, 1L, 2L, 1L, 1L, 1L, 1L), levels = c(\"Drug A\", \"Drug B\"), class = \"factor\", label = \"Chemotherapy Treatment\"),  #>     age = structure(c(23, 9, 31, NA, 51, 39, 37, 32, 31, 34,  #>     42, 63, 54, 21, 48, 71, 38, 49, 57, 46, 47, 52, 61, 38, 34,  #>     49, 63, 67, 68, 78, 36, 37, 53, 36, 51, 48, 57, 31, 37, 28,  #>     40, 49, 61, 56, 54, 71, 38, 31, 48, NA, 83, 52, 32, 53, 69,  #>     60, 45, 39, NA, 38, 36, 71, 31, 43, 57, 53, 25, 44, 25, 30,  #>     51, 40, NA, 43, 21, 54, 67, 43, 54, 41, 34, 34, 6, 39, 36,  #>     58, 27, 47, NA, 50, 61, 47, 52, 51, 68, 33, 65, 34, 38, 60,  #>     10, 49, 56, 50, 60, 49, 54, 39, 48, 65, 47, 61, 34, NA, NA,  #>     58, 26, 44, 17, 68, 57, 66, 44, NA, 67, 48, 62, 35, 53, 53,  #>     66, 55, 57, 47, 58, 43, 45, 44, 63, 59, 44, 53, 51, 28, 65,  #>     63, 76, 61, 33, 48, 42, 36, 55, 20, 26, 50, 47, 74, 50, 31,  #>     45, 51, 66, 76, 47, 48, 56, 70, 46, 43, 41, 41, 19, 49, 43,  #>     43, 75, 52, 42, 37, 45, 35, 67, 38, 44, 45, 39, 46, NA, 42,  #>     60, 31, 45, 38, NA, 19, 69, 66, NA, 64), label = \"Age\"),  #>     marker = structure(c(0.16, 1.107, 0.277, 2.067, 2.767, 0.613,  #>     0.354, 1.739, 0.144, 0.205, 0.513, 0.06, 0.831, 0.258, 0.128,  #>     0.445, 2.083, 0.157, 0.066, 0.325, 0.266, 0.719, 1.713, 0.096,  #>     0.105, 0.043, 0.981, 1.156, 0.105, 0.175, 0.309, 1.869, 2.008,  #>     1.894, 0.16, 1.209, 0.108, 0.611, 0.222, 0.803, 0.37, NA,  #>     0.177, 1.479, 0.161, 0.737, 0.124, 0.092, 0.385, 0.21, 0.475,  #>     1.628, 0.583, NA, 0.702, 1.206, 2.213, 1.406, 0.101, 0.013,  #>     2.032, 1.046, 0.408, 2.636, 1.263, NA, 2.447, 1.041, 0.531,  #>     0.924, 1.087, 0.733, 2.157, 0.333, 1.527, 2.238, 0.153, 0.305,  #>     0.131, 0.386, 1.645, 1.321, 0.229, 0.615, 1.976, 1.941, 0.22,  #>     3.874, 0.982, 1.68, 1.091, 0.169, 0.511, 2.141, 0.599, NA,  #>     0.389, 0.005, 0.075, 1.491, 0.358, 1.709, 0.056, 1.354, 2.522,  #>     0.387, 0.592, 0.243, 0.215, 1.207, 0.29, 0.718, 0.589, 0.003,  #>     1.328, 0.308, 0.691, 3.249, 0.039, 1.804, 0.238, 2.702, 1.441,  #>     0.27, NA, NA, 0.062, 2.19, 0.976, 3.062, 0.124, 0.045, 1.892,  #>     0.711, 1.079, 1.061, 0.239, 0.361, 0.033, 1.133, 1.225, 1.418,  #>     3.751, 3.02, 0.086, 0.772, 1.882, 2.725, 2.41, 0.352, 0.895,  #>     0.215, 0.141, 2.288, 1.658, 1.255, 1.306, 0.081, 0.667, 0.046,  #>     0.662, 1.985, 1.063, 1.55, 0.015, 0.056, NA, 0.51, 0.929,  #>     2.345, 0.25, 0.816, 0.022, 0.16, 0.547, 3.642, 0.092, 1.2,  #>     1.512, 2.124, NA, 0.862, 0.182, 1.075, 0.021, 0.402, 0.063,  #>     1.129, 0.61, NA, 0.717, 0.205, 0.946, 0.386, 0.37, 1.148,  #>     NA, 0.136, 0.439, 1.148), label = \"Marker Level (ng/mL)\"),  #>     stage = structure(c(1L, 2L, 1L, 3L, 4L, 4L, 1L, 1L, 1L, 3L,  #>     1L, 3L, 4L, 4L, 1L, 4L, 4L, 2L, 1L, 1L, 2L, 2L, 4L, 4L, 4L,  #>     2L, 4L, 1L, 4L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 4L, 4L,  #>     3L, 1L, 4L, 3L, 4L, 1L, 1L, 2L, 1L, 4L, 1L, 2L, 2L, 3L, 3L,  #>     2L, 4L, 1L, 4L, 2L, 4L, 1L, 4L, 1L, 4L, 1L, 1L, 1L, 4L, 1L,  #>     2L, 2L, 2L, 1L, 4L, 4L, 2L, 2L, 4L, 4L, 3L, 2L, 4L, 3L, 2L,  #>     4L, 1L, 2L, 1L, 4L, 3L, 3L, 1L, 3L, 2L, 3L, 2L, 2L, 3L, 4L,  #>     4L, 3L, 3L, 2L, 3L, 2L, 2L, 3L, 2L, 1L, 1L, 3L, 4L, 1L, 4L,  #>     3L, 3L, 2L, 4L, 2L, 1L, 2L, 1L, 4L, 3L, 3L, 3L, 2L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 3L, 4L, 1L, 2L, 2L,  #>     1L, 3L, 4L, 2L, 4L, 2L, 1L, 2L, 3L, 1L, 3L, 4L, 2L, 2L, 1L,  #>     2L, 2L, 3L, 1L, 2L, 2L, 1L, 1L, 3L, 2L, 3L, 1L, 1L, 2L, 4L,  #>     2L, 4L, 4L, 2L, 3L, 4L, 3L, 4L, 4L, 1L, 1L, 4L, 4L, 4L, 1L,  #>     2L, 2L, 2L, 4L, 3L, 3L, 2L, 2L, 4L, 3L), levels = c(\"T1\",  #>     \"T2\", \"T3\", \"T4\"), class = \"factor\", label = \"T Stage\"),  #>     grade = structure(c(2L, 1L, 2L, 3L, 3L, 1L, 2L, 1L, 2L, 1L,  #>     3L, 1L, 3L, 1L, 1L, 3L, 3L, 2L, 3L, 2L, 1L, 2L, 1L, 1L, 2L,  #>     3L, 2L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 2L, 2L, 3L, 2L,  #>     2L, 3L, 3L, 1L, 3L, 1L, 3L, 2L, 2L, 2L, 3L, 3L, 3L, 2L, 3L,  #>     1L, 3L, 1L, 2L, 2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 3L, 2L,  #>     1L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L,  #>     3L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 1L,  #>     3L, 1L, 2L, 2L, 1L, 2L, 2L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 2L,  #>     3L, 3L, 2L, 1L, 3L, 2L, 1L, 2L, 2L, 2L, 1L, 3L, 3L, 2L, 3L,  #>     1L, 1L, 1L, 2L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L,  #>     2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, 2L, 1L, 2L, 1L, 2L, 3L, 2L,  #>     1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 2L, 1L,  #>     3L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L,  #>     3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 3L, 1L), levels = c(\"I\",  #>     \"II\", \"III\"), class = \"factor\", label = \"Grade\"), response = structure(c(0L,  #>     1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L,  #>     0L, 0L, 1L, 0L, NA, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     0L, 0L, 0L, NA, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     1L, 1L, NA, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, NA, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 0L, 0L,  #>     0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, NA, 0L, 1L,  #>     0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L,  #>     1L, 1L, 0L, 0L), label = \"Tumor Response\"), death = structure(c(0L,  #>     0L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L,  #>     0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 1L,  #>     1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L,  #>     1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L,  #>     1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L,  #>     0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     0L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 1L, 0L), label = \"Patient Died\"), ttdeath = structure(c(24,  #>     24, 24, 17.64, 16.43, 15.64, 24, 18.43, 24, 10.53, 24, 24,  #>     14.34, 12.89, 22.68, 8.71, 24, 15.21, 24, 24, 24, 24, 16.92,  #>     23.89, 6.32, 15.77, 24, 24, 15.45, 17.43, 24, 20.9, 24, 24,  #>     24, 21.19, 12.52, 24, 15.59, 18, 18.02, 12.43, 12.1, 24,  #>     17.42, 24, 24, 24, 12.19, 10.02, 18.23, 10.42, 24, 24, 19.34,  #>     12.21, 14.46, 19.34, 10.16, 13.15, 10.12, 24, 22.77, 24,  #>     24, 22.13, 24, 20.62, 23.23, 7.38, 24, 24, 24, 24, 24, 19.22,  #>     7.27, 23.88, 16.23, 24, 14.06, 24, 24, 24, 16.44, 23.81,  #>     24, 18.37, 11.44, 20.94, 5.33, 22.92, 10.33, 24, 24, 14.54,  #>     19.14, 24, 21.19, 16.07, 9.97, 24, 24, 24, 19.75, 16.67,  #>     11.18, 18.29, 24, 17.56, 17.45, 24, 22.86, 13.68, 24, 24,  #>     17.46, 24, 24, 24, 24, 24, 13, 9.73, 15.65, 24, 3.53, 20.35,  #>     23.41, 16.47, 24, 24, 14.65, 17.81, 24, 21.83, 24, 24, 21.49,  #>     12.68, 24, 24, 24, 24, 10.07, 24, 24, 24, 8.37, 20.33, 24,  #>     24, 21.33, 12.63, 13.08, 24, 15.1, 20.14, 10.55, 24, 24,  #>     24, 24, 23.6, 24, 19.98, 15.55, 23.72, 22.41, 19.54, 16.57,  #>     24, 24, 24, 21.91, 24, 12.53, 24, 18.63, 14.82, 16.46, 24,  #>     9.24, 17.77, 24, 24, 9.92, 16.16, 10.51, 20.81, 24, 16.44,  #>     24, 22.4, 11.76, 24, 21.6, 24, 19.81, 24), label = \"Months to Death/Censor\")), class = c(\"tbl_df\",  #> \"tbl\", \"data.frame\"), row.names = c(NA, -200L))) #>  #> Coefficients: #> (Intercept)    trtDrug B       marker      stageT2      stageT3      stageT4   #>     45.9247      -0.4052      -0.1435       2.0519       2.4437      -3.1573   #>     gradeII     gradeIII     response        death      ttdeath   #>      0.1750       1.6855       4.9885       3.0775      -0.1394   #>  gtsummary::trial |>   regression_model(     outcome.str = \"age\",     auto.mode = FALSE,     fun = \"stats::lm\",     formula.str = \"{outcome.str}~.\",     args.list = NULL   ) #>  #> Call: #> (function (formula, data, subset, weights, na.action, method = \"qr\",  #>     model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, offset, ...)  #> { #>     ret.x <- x #>     ret.y <- y #>     cl <- match.call() #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (method == \"model.frame\")  #>         return(mf) #>     else if (method != \"qr\")  #>         warning(gettextf(\"method = '%s' is not supported. Using 'qr'\",  #>             method), domain = NA) #>     mt <- attr(mf, \"terms\") #>     y <- model.response(mf, \"numeric\") #>     w <- as.vector(model.weights(mf)) #>     if (!is.null(w) && !is.numeric(w))  #>         stop(\"'weights' must be a numeric vector\") #>     offset <- model.offset(mf) #>     mlm <- is.matrix(y) #>     ny <- if (mlm)  #>         nrow(y) #>     else length(y) #>     if (!is.null(offset)) { #>         if (!mlm)  #>             offset <- as.vector(offset) #>         if (NROW(offset) != ny)  #>             stop(gettextf(\"number of offsets is %d, should equal %d (number of observations)\",  #>                 NROW(offset), ny), domain = NA) #>     } #>     if (is.empty.model(mt)) { #>         x <- NULL #>         z <- list(coefficients = if (mlm) matrix(NA_real_, 0,  #>             ncol(y)) else numeric(), residuals = y, fitted.values = 0 *  #>             y, weights = w, rank = 0L, df.residual = if (!is.null(w)) sum(w !=  #>             0) else ny) #>         if (!is.null(offset)) { #>             z$fitted.values <- offset #>             z$residuals <- y - offset #>         } #>     } #>     else { #>         x <- model.matrix(mt, mf, contrasts) #>         z <- if (is.null(w))  #>             lm.fit(x, y, offset = offset, singular.ok = singular.ok,  #>                 ...) #>         else lm.wfit(x, y, w, offset = offset, singular.ok = singular.ok,  #>             ...) #>     } #>     class(z) <- c(if (mlm) \"mlm\", \"lm\") #>     z$na.action <- attr(mf, \"na.action\") #>     z$offset <- offset #>     z$contrasts <- attr(x, \"contrasts\") #>     z$xlevels <- .getXlevels(mt, mf) #>     z$call <- cl #>     z$terms <- mt #>     if (model)  #>         z$model <- mf #>     if (ret.x)  #>         z$x <- x #>     if (ret.y)  #>         z$y <- y #>     if (!qr)  #>         z$qr <- NULL #>     z #> })(formula = age ~ ., data = structure(list(trt = structure(c(1L,  #> 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L,  #> 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L,  #> 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L,  #> 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L,  #> 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L,  #> 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L,  #> 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L,  #> 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L,  #> 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,  #> 2L, 1L, 2L, 1L, 1L, 1L, 1L), levels = c(\"Drug A\", \"Drug B\"), class = \"factor\", label = \"Chemotherapy Treatment\"),  #>     age = structure(c(23, 9, 31, NA, 51, 39, 37, 32, 31, 34,  #>     42, 63, 54, 21, 48, 71, 38, 49, 57, 46, 47, 52, 61, 38, 34,  #>     49, 63, 67, 68, 78, 36, 37, 53, 36, 51, 48, 57, 31, 37, 28,  #>     40, 49, 61, 56, 54, 71, 38, 31, 48, NA, 83, 52, 32, 53, 69,  #>     60, 45, 39, NA, 38, 36, 71, 31, 43, 57, 53, 25, 44, 25, 30,  #>     51, 40, NA, 43, 21, 54, 67, 43, 54, 41, 34, 34, 6, 39, 36,  #>     58, 27, 47, NA, 50, 61, 47, 52, 51, 68, 33, 65, 34, 38, 60,  #>     10, 49, 56, 50, 60, 49, 54, 39, 48, 65, 47, 61, 34, NA, NA,  #>     58, 26, 44, 17, 68, 57, 66, 44, NA, 67, 48, 62, 35, 53, 53,  #>     66, 55, 57, 47, 58, 43, 45, 44, 63, 59, 44, 53, 51, 28, 65,  #>     63, 76, 61, 33, 48, 42, 36, 55, 20, 26, 50, 47, 74, 50, 31,  #>     45, 51, 66, 76, 47, 48, 56, 70, 46, 43, 41, 41, 19, 49, 43,  #>     43, 75, 52, 42, 37, 45, 35, 67, 38, 44, 45, 39, 46, NA, 42,  #>     60, 31, 45, 38, NA, 19, 69, 66, NA, 64), label = \"Age\"),  #>     marker = structure(c(0.16, 1.107, 0.277, 2.067, 2.767, 0.613,  #>     0.354, 1.739, 0.144, 0.205, 0.513, 0.06, 0.831, 0.258, 0.128,  #>     0.445, 2.083, 0.157, 0.066, 0.325, 0.266, 0.719, 1.713, 0.096,  #>     0.105, 0.043, 0.981, 1.156, 0.105, 0.175, 0.309, 1.869, 2.008,  #>     1.894, 0.16, 1.209, 0.108, 0.611, 0.222, 0.803, 0.37, NA,  #>     0.177, 1.479, 0.161, 0.737, 0.124, 0.092, 0.385, 0.21, 0.475,  #>     1.628, 0.583, NA, 0.702, 1.206, 2.213, 1.406, 0.101, 0.013,  #>     2.032, 1.046, 0.408, 2.636, 1.263, NA, 2.447, 1.041, 0.531,  #>     0.924, 1.087, 0.733, 2.157, 0.333, 1.527, 2.238, 0.153, 0.305,  #>     0.131, 0.386, 1.645, 1.321, 0.229, 0.615, 1.976, 1.941, 0.22,  #>     3.874, 0.982, 1.68, 1.091, 0.169, 0.511, 2.141, 0.599, NA,  #>     0.389, 0.005, 0.075, 1.491, 0.358, 1.709, 0.056, 1.354, 2.522,  #>     0.387, 0.592, 0.243, 0.215, 1.207, 0.29, 0.718, 0.589, 0.003,  #>     1.328, 0.308, 0.691, 3.249, 0.039, 1.804, 0.238, 2.702, 1.441,  #>     0.27, NA, NA, 0.062, 2.19, 0.976, 3.062, 0.124, 0.045, 1.892,  #>     0.711, 1.079, 1.061, 0.239, 0.361, 0.033, 1.133, 1.225, 1.418,  #>     3.751, 3.02, 0.086, 0.772, 1.882, 2.725, 2.41, 0.352, 0.895,  #>     0.215, 0.141, 2.288, 1.658, 1.255, 1.306, 0.081, 0.667, 0.046,  #>     0.662, 1.985, 1.063, 1.55, 0.015, 0.056, NA, 0.51, 0.929,  #>     2.345, 0.25, 0.816, 0.022, 0.16, 0.547, 3.642, 0.092, 1.2,  #>     1.512, 2.124, NA, 0.862, 0.182, 1.075, 0.021, 0.402, 0.063,  #>     1.129, 0.61, NA, 0.717, 0.205, 0.946, 0.386, 0.37, 1.148,  #>     NA, 0.136, 0.439, 1.148), label = \"Marker Level (ng/mL)\"),  #>     stage = structure(c(1L, 2L, 1L, 3L, 4L, 4L, 1L, 1L, 1L, 3L,  #>     1L, 3L, 4L, 4L, 1L, 4L, 4L, 2L, 1L, 1L, 2L, 2L, 4L, 4L, 4L,  #>     2L, 4L, 1L, 4L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 4L, 4L,  #>     3L, 1L, 4L, 3L, 4L, 1L, 1L, 2L, 1L, 4L, 1L, 2L, 2L, 3L, 3L,  #>     2L, 4L, 1L, 4L, 2L, 4L, 1L, 4L, 1L, 4L, 1L, 1L, 1L, 4L, 1L,  #>     2L, 2L, 2L, 1L, 4L, 4L, 2L, 2L, 4L, 4L, 3L, 2L, 4L, 3L, 2L,  #>     4L, 1L, 2L, 1L, 4L, 3L, 3L, 1L, 3L, 2L, 3L, 2L, 2L, 3L, 4L,  #>     4L, 3L, 3L, 2L, 3L, 2L, 2L, 3L, 2L, 1L, 1L, 3L, 4L, 1L, 4L,  #>     3L, 3L, 2L, 4L, 2L, 1L, 2L, 1L, 4L, 3L, 3L, 3L, 2L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 3L, 4L, 1L, 2L, 2L,  #>     1L, 3L, 4L, 2L, 4L, 2L, 1L, 2L, 3L, 1L, 3L, 4L, 2L, 2L, 1L,  #>     2L, 2L, 3L, 1L, 2L, 2L, 1L, 1L, 3L, 2L, 3L, 1L, 1L, 2L, 4L,  #>     2L, 4L, 4L, 2L, 3L, 4L, 3L, 4L, 4L, 1L, 1L, 4L, 4L, 4L, 1L,  #>     2L, 2L, 2L, 4L, 3L, 3L, 2L, 2L, 4L, 3L), levels = c(\"T1\",  #>     \"T2\", \"T3\", \"T4\"), class = \"factor\", label = \"T Stage\"),  #>     grade = structure(c(2L, 1L, 2L, 3L, 3L, 1L, 2L, 1L, 2L, 1L,  #>     3L, 1L, 3L, 1L, 1L, 3L, 3L, 2L, 3L, 2L, 1L, 2L, 1L, 1L, 2L,  #>     3L, 2L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 2L, 2L, 3L, 2L,  #>     2L, 3L, 3L, 1L, 3L, 1L, 3L, 2L, 2L, 2L, 3L, 3L, 3L, 2L, 3L,  #>     1L, 3L, 1L, 2L, 2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 3L, 2L,  #>     1L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L,  #>     3L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 1L,  #>     3L, 1L, 2L, 2L, 1L, 2L, 2L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 2L,  #>     3L, 3L, 2L, 1L, 3L, 2L, 1L, 2L, 2L, 2L, 1L, 3L, 3L, 2L, 3L,  #>     1L, 1L, 1L, 2L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L,  #>     2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, 2L, 1L, 2L, 1L, 2L, 3L, 2L,  #>     1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 2L, 1L,  #>     3L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L,  #>     3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 3L, 1L), levels = c(\"I\",  #>     \"II\", \"III\"), class = \"factor\", label = \"Grade\"), response = structure(c(0L,  #>     1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L,  #>     0L, 0L, 1L, 0L, NA, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     0L, 0L, 0L, NA, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     1L, 1L, NA, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, NA, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 0L, 0L,  #>     0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, NA, 0L, 1L,  #>     0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L,  #>     1L, 1L, 0L, 0L), label = \"Tumor Response\"), death = structure(c(0L,  #>     0L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L,  #>     0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 1L,  #>     1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L,  #>     1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L,  #>     1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L,  #>     0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     0L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 1L, 0L), label = \"Patient Died\"), ttdeath = structure(c(24,  #>     24, 24, 17.64, 16.43, 15.64, 24, 18.43, 24, 10.53, 24, 24,  #>     14.34, 12.89, 22.68, 8.71, 24, 15.21, 24, 24, 24, 24, 16.92,  #>     23.89, 6.32, 15.77, 24, 24, 15.45, 17.43, 24, 20.9, 24, 24,  #>     24, 21.19, 12.52, 24, 15.59, 18, 18.02, 12.43, 12.1, 24,  #>     17.42, 24, 24, 24, 12.19, 10.02, 18.23, 10.42, 24, 24, 19.34,  #>     12.21, 14.46, 19.34, 10.16, 13.15, 10.12, 24, 22.77, 24,  #>     24, 22.13, 24, 20.62, 23.23, 7.38, 24, 24, 24, 24, 24, 19.22,  #>     7.27, 23.88, 16.23, 24, 14.06, 24, 24, 24, 16.44, 23.81,  #>     24, 18.37, 11.44, 20.94, 5.33, 22.92, 10.33, 24, 24, 14.54,  #>     19.14, 24, 21.19, 16.07, 9.97, 24, 24, 24, 19.75, 16.67,  #>     11.18, 18.29, 24, 17.56, 17.45, 24, 22.86, 13.68, 24, 24,  #>     17.46, 24, 24, 24, 24, 24, 13, 9.73, 15.65, 24, 3.53, 20.35,  #>     23.41, 16.47, 24, 24, 14.65, 17.81, 24, 21.83, 24, 24, 21.49,  #>     12.68, 24, 24, 24, 24, 10.07, 24, 24, 24, 8.37, 20.33, 24,  #>     24, 21.33, 12.63, 13.08, 24, 15.1, 20.14, 10.55, 24, 24,  #>     24, 24, 23.6, 24, 19.98, 15.55, 23.72, 22.41, 19.54, 16.57,  #>     24, 24, 24, 21.91, 24, 12.53, 24, 18.63, 14.82, 16.46, 24,  #>     9.24, 17.77, 24, 24, 9.92, 16.16, 10.51, 20.81, 24, 16.44,  #>     24, 22.4, 11.76, 24, 21.6, 24, 19.81, 24), label = \"Months to Death/Censor\")), class = c(\"tbl_df\",  #> \"tbl\", \"data.frame\"), row.names = c(NA, -200L))) #>  #> Coefficients: #> (Intercept)    trtDrug B       marker      stageT2      stageT3      stageT4   #>     45.9247      -0.4052      -0.1435       2.0519       2.4437      -3.1573   #>     gradeII     gradeIII     response        death      ttdeath   #>      0.1750       1.6855       4.9885       3.0775      -0.1394   #>  gtsummary::trial |>   default_parsing() |>   regression_model(     outcome.str = \"trt\",     auto.mode = FALSE,     fun = \"stats::glm\",     args.list = list(family = binomial(link = \"logit\"))   ) #>  #> Call:  (function (formula, family = gaussian, data, weights, subset,  #>     na.action, start = NULL, etastart, mustart, offset, control = list(...),  #>     model = TRUE, method = \"glm.fit\", x = FALSE, y = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, ...)  #> { #>     cal <- match.call() #>     if (is.character(family))  #>         family <- get(family, mode = \"function\", envir = parent.frame()) #>     if (is.function(family))  #>         family <- family() #>     if (is.null(family$family)) { #>         print(family) #>         stop(\"'family' not recognized\") #>     } #>     if (missing(data))  #>         data <- environment(formula) #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"etastart\", \"mustart\", \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (identical(method, \"model.frame\"))  #>         return(mf) #>     if (!is.character(method) && !is.function(method))  #>         stop(\"invalid 'method' argument\") #>     if (identical(method, \"glm.fit\"))  #>         control <- do.call(\"glm.control\", control) #>     mt <- attr(mf, \"terms\") #>     Y <- model.response(mf, \"any\") #>     if (length(dim(Y)) == 1L) { #>         nm <- rownames(Y) #>         dim(Y) <- NULL #>         if (!is.null(nm))  #>             names(Y) <- nm #>     } #>     X <- if (!is.empty.model(mt))  #>         model.matrix(mt, mf, contrasts) #>     else matrix(, NROW(Y), 0L) #>     weights <- as.vector(model.weights(mf)) #>     if (!is.null(weights) && !is.numeric(weights))  #>         stop(\"'weights' must be a numeric vector\") #>     if (!is.null(weights) && any(weights < 0))  #>         stop(\"negative weights not allowed\") #>     offset <- as.vector(model.offset(mf)) #>     if (!is.null(offset)) { #>         if (length(offset) != NROW(Y))  #>             stop(gettextf(\"number of offsets is %d should equal %d (number of observations)\",  #>                 length(offset), NROW(Y)), domain = NA) #>     } #>     mustart <- model.extract(mf, \"mustart\") #>     etastart <- model.extract(mf, \"etastart\") #>     fit <- eval(call(if (is.function(method)) \"method\" else method,  #>         x = X, y = Y, weights = weights, start = start, etastart = etastart,  #>         mustart = mustart, offset = offset, family = family,  #>         control = control, intercept = attr(mt, \"intercept\") >  #>             0L, singular.ok = singular.ok)) #>     if (length(offset) && attr(mt, \"intercept\") > 0L) { #>         fit2 <- eval(call(if (is.function(method)) \"method\" else method,  #>             x = X[, \"(Intercept)\", drop = FALSE], y = Y, mustart = fit$fitted.values,  #>             weights = weights, offset = offset, family = family,  #>             control = control, intercept = TRUE)) #>         if (!fit2$converged)  #>             warning(\"fitting to calculate the null deviance did not converge -- increase 'maxit'?\") #>         fit$null.deviance <- fit2$deviance #>     } #>     if (model)  #>         fit$model <- mf #>     fit$na.action <- attr(mf, \"na.action\") #>     if (x)  #>         fit$x <- X #>     if (!y)  #>         fit$y <- NULL #>     structure(c(fit, list(call = cal, formula = formula, terms = mt,  #>         data = data, offset = offset, control = control, method = method,  #>         contrasts = attr(X, \"contrasts\"), xlevels = .getXlevels(mt,  #>             mf))), class = c(fit$class, c(\"glm\", \"lm\"))) #> })(formula = trt ~ age + marker + stage + grade + response +  #>     death + ttdeath, family = structure(list(family = \"binomial\",  #>     link = \"logit\", linkfun = function (mu)  #>     .Call(C_logit_link, mu), linkinv = function (eta)  #>     .Call(C_logit_linkinv, eta), variance = function (mu)  #>     mu * (1 - mu), dev.resids = function (y, mu, wt)  #>     .Call(C_binomial_dev_resids, y, mu, wt), aic = function (y,  #>         n, mu, wt, dev)  #>     { #>         m <- if (any(n > 1))  #>             n #>         else wt #>         -2 * sum(ifelse(m > 0, (wt/m), 0) * dbinom(round(m *  #>             y), round(m), mu, log = TRUE)) #>     }, mu.eta = function (eta)  #>     .Call(C_logit_mu_eta, eta), initialize = { #>         if (NCOL(y) == 1) { #>             if (is.factor(y))  #>                 y <- y != levels(y)[1L] #>             n <- rep.int(1, nobs) #>             y[weights == 0] <- 0 #>             if (any(y < 0 | y > 1))  #>                 stop(\"y values must be 0 <= y <= 1\") #>             mustart <- (weights * y + 0.5)/(weights + 1) #>             m <- weights * y #>             if (\"binomial\" == \"binomial\" && any(abs(m - round(m)) >  #>                 0.001))  #>                 warning(gettextf(\"non-integer #successes in a %s glm!\",  #>                   \"binomial\"), domain = NA) #>         } #>         else if (NCOL(y) == 2) { #>             if (\"binomial\" == \"binomial\" && any(abs(y - round(y)) >  #>                 0.001))  #>                 warning(gettextf(\"non-integer counts in a %s glm!\",  #>                   \"binomial\"), domain = NA) #>             n <- (y1 <- y[, 1L]) + y[, 2L] #>             y <- y1/n #>             if (any(n0 <- n == 0))  #>                 y[n0] <- 0 #>             weights <- weights * n #>             mustart <- (n * y + 0.5)/(n + 1) #>         } #>         else stop(gettextf(\"for the '%s' family, y must be a vector of 0 and 1's\\nor a 2 column matrix where col 1 is no. successes and col 2 is no. failures\",  #>             \"binomial\"), domain = NA) #>     }, validmu = function (mu)  #>     all(is.finite(mu)) && all(mu > 0 & mu < 1), valideta = function (eta)  #>     TRUE, simulate = function (object, nsim)  #>     { #>         ftd <- fitted(object) #>         n <- length(ftd) #>         ntot <- n * nsim #>         wts <- object$prior.weights #>         if (any(wts%%1 != 0))  #>             stop(\"cannot simulate from non-integer prior.weights\") #>         if (!is.null(m <- object$model)) { #>             y <- model.response(m) #>             if (is.factor(y)) { #>                 yy <- factor(1 + rbinom(ntot, size = 1, prob = ftd),  #>                   labels = levels(y)) #>                 split(yy, rep(seq_len(nsim), each = n)) #>             } #>             else if (is.matrix(y) && ncol(y) == 2) { #>                 yy <- vector(\"list\", nsim) #>                 for (i in seq_len(nsim)) { #>                   Y <- rbinom(n, size = wts, prob = ftd) #>                   YY <- cbind(Y, wts - Y) #>                   colnames(YY) <- colnames(y) #>                   yy[[i]] <- YY #>                 } #>                 yy #>             } #>             else rbinom(ntot, size = wts, prob = ftd)/wts #>         } #>         else rbinom(ntot, size = wts, prob = ftd)/wts #>     }, dispersion = 1), class = \"family\"), data = structure(list( #>     trt = structure(c(1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L,  #>     2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,  #>     2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L,  #>     2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,  #>     2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L,  #>     1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L,  #>     1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L,  #>     2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 2L,  #>     2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L,  #>     1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L,  #>     2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L,  #>     2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L,  #>     1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L), levels = c(\"Drug A\",  #>     \"Drug B\"), class = \"factor\", label = \"Chemotherapy Treatment\"),  #>     age = structure(c(23, 9, 31, NA, 51, 39, 37, 32, 31, 34,  #>     42, 63, 54, 21, 48, 71, 38, 49, 57, 46, 47, 52, 61, 38, 34,  #>     49, 63, 67, 68, 78, 36, 37, 53, 36, 51, 48, 57, 31, 37, 28,  #>     40, 49, 61, 56, 54, 71, 38, 31, 48, NA, 83, 52, 32, 53, 69,  #>     60, 45, 39, NA, 38, 36, 71, 31, 43, 57, 53, 25, 44, 25, 30,  #>     51, 40, NA, 43, 21, 54, 67, 43, 54, 41, 34, 34, 6, 39, 36,  #>     58, 27, 47, NA, 50, 61, 47, 52, 51, 68, 33, 65, 34, 38, 60,  #>     10, 49, 56, 50, 60, 49, 54, 39, 48, 65, 47, 61, 34, NA, NA,  #>     58, 26, 44, 17, 68, 57, 66, 44, NA, 67, 48, 62, 35, 53, 53,  #>     66, 55, 57, 47, 58, 43, 45, 44, 63, 59, 44, 53, 51, 28, 65,  #>     63, 76, 61, 33, 48, 42, 36, 55, 20, 26, 50, 47, 74, 50, 31,  #>     45, 51, 66, 76, 47, 48, 56, 70, 46, 43, 41, 41, 19, 49, 43,  #>     43, 75, 52, 42, 37, 45, 35, 67, 38, 44, 45, 39, 46, NA, 42,  #>     60, 31, 45, 38, NA, 19, 69, 66, NA, 64), label = \"Age\"),  #>     marker = structure(c(0.16, 1.107, 0.277, 2.067, 2.767, 0.613,  #>     0.354, 1.739, 0.144, 0.205, 0.513, 0.06, 0.831, 0.258, 0.128,  #>     0.445, 2.083, 0.157, 0.066, 0.325, 0.266, 0.719, 1.713, 0.096,  #>     0.105, 0.043, 0.981, 1.156, 0.105, 0.175, 0.309, 1.869, 2.008,  #>     1.894, 0.16, 1.209, 0.108, 0.611, 0.222, 0.803, 0.37, NA,  #>     0.177, 1.479, 0.161, 0.737, 0.124, 0.092, 0.385, 0.21, 0.475,  #>     1.628, 0.583, NA, 0.702, 1.206, 2.213, 1.406, 0.101, 0.013,  #>     2.032, 1.046, 0.408, 2.636, 1.263, NA, 2.447, 1.041, 0.531,  #>     0.924, 1.087, 0.733, 2.157, 0.333, 1.527, 2.238, 0.153, 0.305,  #>     0.131, 0.386, 1.645, 1.321, 0.229, 0.615, 1.976, 1.941, 0.22,  #>     3.874, 0.982, 1.68, 1.091, 0.169, 0.511, 2.141, 0.599, NA,  #>     0.389, 0.005, 0.075, 1.491, 0.358, 1.709, 0.056, 1.354, 2.522,  #>     0.387, 0.592, 0.243, 0.215, 1.207, 0.29, 0.718, 0.589, 0.003,  #>     1.328, 0.308, 0.691, 3.249, 0.039, 1.804, 0.238, 2.702, 1.441,  #>     0.27, NA, NA, 0.062, 2.19, 0.976, 3.062, 0.124, 0.045, 1.892,  #>     0.711, 1.079, 1.061, 0.239, 0.361, 0.033, 1.133, 1.225, 1.418,  #>     3.751, 3.02, 0.086, 0.772, 1.882, 2.725, 2.41, 0.352, 0.895,  #>     0.215, 0.141, 2.288, 1.658, 1.255, 1.306, 0.081, 0.667, 0.046,  #>     0.662, 1.985, 1.063, 1.55, 0.015, 0.056, NA, 0.51, 0.929,  #>     2.345, 0.25, 0.816, 0.022, 0.16, 0.547, 3.642, 0.092, 1.2,  #>     1.512, 2.124, NA, 0.862, 0.182, 1.075, 0.021, 0.402, 0.063,  #>     1.129, 0.61, NA, 0.717, 0.205, 0.946, 0.386, 0.37, 1.148,  #>     NA, 0.136, 0.439, 1.148), label = \"Marker Level (ng/mL)\"),  #>     stage = structure(c(1L, 2L, 1L, 3L, 4L, 4L, 1L, 1L, 1L, 3L,  #>     1L, 3L, 4L, 4L, 1L, 4L, 4L, 2L, 1L, 1L, 2L, 2L, 4L, 4L, 4L,  #>     2L, 4L, 1L, 4L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 4L, 4L,  #>     3L, 1L, 4L, 3L, 4L, 1L, 1L, 2L, 1L, 4L, 1L, 2L, 2L, 3L, 3L,  #>     2L, 4L, 1L, 4L, 2L, 4L, 1L, 4L, 1L, 4L, 1L, 1L, 1L, 4L, 1L,  #>     2L, 2L, 2L, 1L, 4L, 4L, 2L, 2L, 4L, 4L, 3L, 2L, 4L, 3L, 2L,  #>     4L, 1L, 2L, 1L, 4L, 3L, 3L, 1L, 3L, 2L, 3L, 2L, 2L, 3L, 4L,  #>     4L, 3L, 3L, 2L, 3L, 2L, 2L, 3L, 2L, 1L, 1L, 3L, 4L, 1L, 4L,  #>     3L, 3L, 2L, 4L, 2L, 1L, 2L, 1L, 4L, 3L, 3L, 3L, 2L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 3L, 4L, 1L, 2L, 2L,  #>     1L, 3L, 4L, 2L, 4L, 2L, 1L, 2L, 3L, 1L, 3L, 4L, 2L, 2L, 1L,  #>     2L, 2L, 3L, 1L, 2L, 2L, 1L, 1L, 3L, 2L, 3L, 1L, 1L, 2L, 4L,  #>     2L, 4L, 4L, 2L, 3L, 4L, 3L, 4L, 4L, 1L, 1L, 4L, 4L, 4L, 1L,  #>     2L, 2L, 2L, 4L, 3L, 3L, 2L, 2L, 4L, 3L), levels = c(\"T1\",  #>     \"T2\", \"T3\", \"T4\"), class = \"factor\", label = \"T Stage\"),  #>     grade = structure(c(2L, 1L, 2L, 3L, 3L, 1L, 2L, 1L, 2L, 1L,  #>     3L, 1L, 3L, 1L, 1L, 3L, 3L, 2L, 3L, 2L, 1L, 2L, 1L, 1L, 2L,  #>     3L, 2L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 2L, 2L, 3L, 2L,  #>     2L, 3L, 3L, 1L, 3L, 1L, 3L, 2L, 2L, 2L, 3L, 3L, 3L, 2L, 3L,  #>     1L, 3L, 1L, 2L, 2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 3L, 2L,  #>     1L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L,  #>     3L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 1L,  #>     3L, 1L, 2L, 2L, 1L, 2L, 2L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 2L,  #>     3L, 3L, 2L, 1L, 3L, 2L, 1L, 2L, 2L, 2L, 1L, 3L, 3L, 2L, 3L,  #>     1L, 1L, 1L, 2L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L,  #>     2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, 2L, 1L, 2L, 1L, 2L, 3L, 2L,  #>     1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 2L, 1L,  #>     3L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L,  #>     3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 3L, 1L), levels = c(\"I\",  #>     \"II\", \"III\"), class = \"factor\", label = \"Grade\"), response = structure(c(1L,  #>     2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L,  #>     2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L,  #>     1L, 1L, 2L, 1L, NA, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L,  #>     2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 1L,  #>     1L, 1L, 1L, NA, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L,  #>     1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, NA, 1L, 1L, 2L,  #>     1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L,  #>     1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L,  #>     2L, 2L, NA, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, NA, 2L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L,  #>     1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, NA, 1L, 2L,  #>     1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, NA, 1L,  #>     2L, 2L, 1L, 1L), levels = c(\"0\", \"1\"), class = \"factor\", label = \"Tumor Response\"),  #>     death = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 2L,  #>     1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L,  #>     2L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L,  #>     2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 2L,  #>     2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 2L,  #>     1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L,  #>     2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 2L,  #>     2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 1L,  #>     1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L,  #>     1L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L,  #>     1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 1L,  #>     1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 2L,  #>     1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L,  #>     1L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L), levels = c(\"0\",  #>     \"1\"), class = \"factor\", label = \"Patient Died\"), ttdeath = structure(c(24,  #>     24, 24, 17.64, 16.43, 15.64, 24, 18.43, 24, 10.53, 24, 24,  #>     14.34, 12.89, 22.68, 8.71, 24, 15.21, 24, 24, 24, 24, 16.92,  #>     23.89, 6.32, 15.77, 24, 24, 15.45, 17.43, 24, 20.9, 24, 24,  #>     24, 21.19, 12.52, 24, 15.59, 18, 18.02, 12.43, 12.1, 24,  #>     17.42, 24, 24, 24, 12.19, 10.02, 18.23, 10.42, 24, 24, 19.34,  #>     12.21, 14.46, 19.34, 10.16, 13.15, 10.12, 24, 22.77, 24,  #>     24, 22.13, 24, 20.62, 23.23, 7.38, 24, 24, 24, 24, 24, 19.22,  #>     7.27, 23.88, 16.23, 24, 14.06, 24, 24, 24, 16.44, 23.81,  #>     24, 18.37, 11.44, 20.94, 5.33, 22.92, 10.33, 24, 24, 14.54,  #>     19.14, 24, 21.19, 16.07, 9.97, 24, 24, 24, 19.75, 16.67,  #>     11.18, 18.29, 24, 17.56, 17.45, 24, 22.86, 13.68, 24, 24,  #>     17.46, 24, 24, 24, 24, 24, 13, 9.73, 15.65, 24, 3.53, 20.35,  #>     23.41, 16.47, 24, 24, 14.65, 17.81, 24, 21.83, 24, 24, 21.49,  #>     12.68, 24, 24, 24, 24, 10.07, 24, 24, 24, 8.37, 20.33, 24,  #>     24, 21.33, 12.63, 13.08, 24, 15.1, 20.14, 10.55, 24, 24,  #>     24, 24, 23.6, 24, 19.98, 15.55, 23.72, 22.41, 19.54, 16.57,  #>     24, 24, 24, 21.91, 24, 12.53, 24, 18.63, 14.82, 16.46, 24,  #>     9.24, 17.77, 24, 24, 9.92, 16.16, 10.51, 20.81, 24, 16.44,  #>     24, 22.4, 11.76, 24, 21.6, 24, 19.81, 24), label = \"Months to Death/Censor\")), class = c(\"tbl_df\",  #> \"tbl\", \"data.frame\"), row.names = c(NA, -200L))) #>  #> Coefficients: #> (Intercept)          age       marker      stageT2      stageT3      stageT4   #>    1.652845    -0.002014    -0.259849     0.404341     0.117402    -0.002102   #>     gradeII     gradeIII    response1       death1      ttdeath   #>   -0.037012     0.022890     0.498952    -0.003916    -0.076073   #>  #> Degrees of Freedom: 172 Total (i.e. Null);  162 Residual #>   (27 observations deleted due to missingness) #> Null Deviance:\t    239.5  #> Residual Deviance: 230.9 \tAIC: 252.9 m <- mtcars |>   default_parsing() |>   regression_model(     outcome.str = \"mpg\",     auto.mode = FALSE,     fun = \"stats::lm\",     formula.str = \"{outcome.str}~{paste(vars,collapse='+')}\",     args.list = NULL,     vars = c(\"mpg\", \"cyl\")   )   broom::tidy(m) #> # A tibble: 3 × 5 #>   term        estimate std.error statistic  p.value #>   <chr>          <dbl>     <dbl>     <dbl>    <dbl> #> 1 (Intercept)    26.7      0.972     27.4  2.69e-22 #> 2 cyl6           -6.92     1.56      -4.44 1.19e- 4 #> 3 cyl8          -11.6      1.30      -8.90 8.57e-10 if (FALSE) { # \\dontrun{ gtsummary::trial |>   regression_model_uv(outcome.str = \"age\") gtsummary::trial |>   regression_model_uv(     outcome.str = \"age\",     fun = \"stats::lm\",     args.list = NULL   ) m <- gtsummary::trial |> regression_model_uv(   outcome.str = \"trt\",   fun = \"stats::glm\",   args.list = list(family = stats::binomial(link = \"logit\")) ) lapply(m,broom::tidy) |> dplyr::bind_rows() } # } if (FALSE) { # \\dontrun{ gtsummary::trial |>   regression_model(     outcome.str = \"age\",     fun = \"stats::lm\",     formula.str = \"{outcome.str}~.\",     args.list = NULL   ) ls <- regression_model_list(data = default_parsing(mtcars), outcome.str = \"cyl\", fun.descr = \"Ordinal logistic regression model\") summary(ls$model)  ls <- regression_model_list(data = default_parsing(gtsummary::trial), outcome.str = \"trt\", fun.descr = \"Logistic regression model\") tbl <- gtsummary::tbl_regression(ls$model, exponentiate = TRUE) m <- gtsummary::trial |>   default_parsing() |>   regression_model(     outcome.str = \"trt\",     fun = \"stats::glm\",     formula.str = \"{outcome.str}~.\",     args.list = list(family = stats::binomial(link = \"logit\"))   ) tbl2 <- gtsummary::tbl_regression(m, exponentiate = TRUE) broom::tidy(ls$model) broom::tidy(m) } # } if (FALSE) { # \\dontrun{ gtsummary::trial |> regression_model_uv(   outcome.str = \"trt\",   fun = \"stats::glm\",   args.list = list(family = stats::binomial(link = \"logit\")) ) |> lapply(broom::tidy) |> dplyr::bind_rows() ms <- regression_model_uv_list(data = default_parsing(mtcars), outcome.str = \"mpg\", fun.descr = \"Linear regression model\") lapply(ms$model,broom::tidy) |> dplyr::bind_rows() } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Create table of regression model — regression_table","title":"Create table of regression model — regression_table","text":"Create table regression model","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create table of regression model — regression_table","text":"","code":"regression_table(x, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create table of regression model — regression_table","text":"x regression model ... passed methods args.list list arguments passed 'fun'. fun function use table creation. Default \"gtsummary::tbl_regression\".","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create table of regression model — regression_table","text":"object standard class fun","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create table of regression model — regression_table","text":"","code":"if (FALSE) { # \\dontrun{ tbl <- gtsummary::trial |>   regression_model(     outcome.str = \"stage\",     fun = \"MASS::polr\"   ) |>   regression_table(args.list = list(\"exponentiate\" = TRUE)) gtsummary::trial |>   regression_model(     outcome.str = \"age\",     fun = \"stats::lm\",     formula.str = \"{outcome.str}~.\",     args.list = NULL   ) |>   regression_table() |> plot() gtsummary::trial |>   regression_model(     outcome.str = \"trt\",     fun = \"stats::glm\",     args.list = list(family = binomial(link = \"logit\"))   ) |>   regression_table() gtsummary::trial |>   regression_model_uv(     outcome.str = \"trt\",     fun = \"stats::glm\",     args.list = list(family = stats::binomial(link = \"logit\"))   ) |>   regression_table() gtsummary::trial |>   regression_model_uv(     outcome.str = \"stage\",     args.list = list(family = stats::binomial(link = \"logit\"))   ) |>   regression_table()  list(   \"Univariable\" = regression_model_uv,   \"Multivariable\" = regression_model ) |>   lapply(\\(.fun){     do.call(       .fun,       c(         list(data = gtsummary::trial),         list(outcome.str = \"stage\")       )     )   }) |>   purrr::map(regression_table) |>   tbl_merge()   } # } regression_table <- function(x, ...) {   UseMethod(\"regression_table\") }  #' @rdname regression_table #' @export regression_table.list <- function(x, ...) {   x |>     purrr::map(\\(.m){       regression_table(x = .m, ...) |>         gtsummary::add_n()     }) |>     gtsummary::tbl_stack() }  #' @rdname regression_table #' @export regression_table.default <- function(x, ..., args.list = NULL, fun = \"gtsummary::tbl_regression\") {   # Stripping custom class   class(x) <- class(x)[class(x) != \"freesearcher_model\"]    if (any(c(length(class(x)) != 1, class(x) != \"lm\"))) {     if (!\"exponentiate\" %in% names(args.list)) {       args.list <- c(args.list, list(exponentiate = TRUE))     }   }    out <- do.call(getfun(fun), c(list(x = x), args.list))   out |>     gtsummary::add_glance_source_note() # |>   # gtsummary::bold_p() }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Removes columns with completenes below cutoff — remove_empty_cols","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"Removes columns completenes cutoff","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"","code":"remove_empty_cols(data, cutoff = 0.7)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"data data frame cutoff numeric","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"data frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"","code":"data.frame(a=1:10,b=NA, c=c(2,NA)) |> remove_empty_cols(cutoff=.5) #>     a  c #> 1   1  2 #> 2   2 NA #> 3   3  2 #> 4   4 NA #> 5   5  2 #> 6   6 NA #> 7   7  2 #> 8   8 NA #> 9   9  2 #> 10 10 NA"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove NA labels — remove_na_attr","title":"Remove NA labels — remove_na_attr","text":"Remove NA labels","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove NA labels — remove_na_attr","text":"","code":"remove_na_attr(data, attr = \"label\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove NA labels — remove_na_attr","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove NA labels — remove_na_attr","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove NA labels — remove_na_attr","text":"","code":"ds <- mtcars |> lapply(\\(.x) REDCapCAST::set_attr(.x,label=NA,attr = \"label\")) ds |> remove_na_attr() |> str() #> tibble [32 × 11] (S3: tbl_df/tbl/data.frame) #>  $ mpg : num [1:32] 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : num [1:32] 6 6 4 6 8 6 8 4 4 6 ... #>  $ disp: num [1:32] 160 160 108 258 360 ... #>  $ hp  : num [1:32] 110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num [1:32] 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num [1:32] 2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num [1:32] 16.5 17 18.6 19.4 17 ... #>  $ vs  : num [1:32] 0 0 1 1 0 1 0 1 1 1 ... #>  $ am  : num [1:32] 1 1 1 0 0 0 0 0 0 0 ... #>  $ gear: num [1:32] 4 4 4 3 3 3 3 4 4 4 ... #>  $ carb: num [1:32] 4 4 1 1 2 1 4 2 2 4 ..."},{"path":"https://agdamsbo.github.io/freesearcheR/reference/repeated_instruments.html","id":null,"dir":"Reference","previous_headings":"","what":"Get names of repeated instruments — repeated_instruments","title":"Get names of repeated instruments — repeated_instruments","text":"Get names repeated instruments","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/repeated_instruments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get names of repeated instruments — repeated_instruments","text":"","code":"repeated_instruments(uri, token)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/repeated_instruments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get names of repeated instruments — repeated_instruments","text":"uri REDCap database uri token database token","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/repeated_instruments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get names of repeated instruments — repeated_instruments","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/selectInputIcon.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a select input control with icon(s) — selectInputIcon","title":"Create a select input control with icon(s) — selectInputIcon","text":"Extend form controls adding text icons , , sides classic selectInput.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/selectInputIcon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a select input control with icon(s) — selectInputIcon","text":"","code":"selectInputIcon(   inputId,   label,   choices,   selected = NULL,   multiple = FALSE,   selectize = TRUE,   size = NULL,   width = NULL,   icon = NULL )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/selectInputIcon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a select input control with icon(s) — selectInputIcon","text":"inputId input slot used access value. label Display label control, NULL label. choices List values select . elements list named, name — rather value — displayed user. also possible group related inputs providing named list whose elements (either named unnamed) lists, vectors, factors. case, outermost names used group labels (leveraging <optgroup> HTML tag) elements respective sublist. See example section small demo feature. selected initially selected value (multiple values multiple = TRUE). specified defaults first value single-select lists values multiple select lists. multiple selection multiple items allowed? selectize Whether use selectize.js . size Number items show selection box; larger number result taller box. compatible selectize=TRUE. Normally, multiple=FALSE, select input drop-list, size set, box instead. width width input, e.g. '400px', '100%'; see validateCssUnit().","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/selectInputIcon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a select input control with icon(s) — selectInputIcon","text":"numeric input control can added UI definition.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":null,"dir":"Reference","previous_headings":"","what":"Launch the freesearcheR tool locally — shiny_freesearcheR","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"data.frames global environment accessible app.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"","code":"shiny_freesearcheR(...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"... arguments passed shiny::runApp()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"shiny app","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"","code":"if (FALSE) { # \\dontrun{ data(mtcars) shiny_freesearcheR(launch.browser = TRUE) } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":null,"dir":"Reference","previous_headings":"","what":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"Specify format arguments include qmd header/frontmatter","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"","code":"specify_qmd_format(data, fileformat = c(\"docx\", \"odt\", \"pdf\", \"all\"))"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"data vector fileformat format include","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":null,"dir":"Reference","previous_headings":"","what":"Easily subset by data type function — subset_types","title":"Easily subset by data type function — subset_types","text":"Easily subset data type function","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Easily subset by data type function — subset_types","text":"","code":"subset_types(data, types, type.fun = outcome_type)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Easily subset by data type function — subset_types","text":"data data types desired types type.fun function get type. Default outcome_type","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Easily subset by data type function — subset_types","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Easily subset by data type function — subset_types","text":"","code":"default_parsing(mtcars) |> subset_types(\"ordinal\") #> # A tibble: 32 × 3 #>    cyl   gear  carb  #>    <fct> <fct> <fct> #>  1 6     4     4     #>  2 6     4     4     #>  3 4     4     1     #>  4 6     3     1     #>  5 8     3     2     #>  6 6     3     1     #>  7 8     3     4     #>  8 4     4     2     #>  9 4     4     2     #> 10 6     4     4     #> # ℹ 22 more rows default_parsing(mtcars) |> subset_types(c(\"dichotomous\", \"ordinal\")) #> # A tibble: 32 × 5 #>    cyl   vs    am    gear  carb  #>    <fct> <fct> <fct> <fct> <fct> #>  1 6     0     1     4     4     #>  2 6     0     1     4     4     #>  3 4     1     1     4     1     #>  4 6     1     0     3     1     #>  5 8     0     0     3     2     #>  6 6     1     0     3     1     #>  7 8     0     0     3     4     #>  8 4     1     0     4     2     #>  9 4     1     0     4     2     #> 10 6     1     0     4     4     #> # ℹ 22 more rows #' default_parsing(mtcars) |> subset_types(\"factor\",class)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Implemented functions — supported_functions","title":"Implemented functions — supported_functions","text":"Library supported functions. list name \"descr\" element unique element list.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Implemented functions — supported_functions","text":"","code":"supported_functions()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Implemented functions — supported_functions","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Implemented functions — supported_functions","text":"","code":"supported_functions() #> $lm #> $lm$descr #> [1] \"Linear regression model\" #>  #> $lm$design #> [1] \"cross-sectional\" #>  #> $lm$out.type #> [1] \"continuous\" #>  #> $lm$fun #> [1] \"stats::lm\" #>  #> $lm$args.list #> NULL #>  #> $lm$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $lm$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $lm$table.args.list #> $lm$table.args.list$exponentiate #> [1] FALSE #>  #>  #>  #> $glm #> $glm$descr #> [1] \"Logistic regression model\" #>  #> $glm$design #> [1] \"cross-sectional\" #>  #> $glm$out.type #> [1] \"dichotomous\" #>  #> $glm$fun #> [1] \"stats::glm\" #>  #> $glm$args.list #> $glm$args.list$family #>  #> Family: binomial  #> Link function: logit  #>  #>  #>  #> $glm$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $glm$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $glm$table.args.list #> list() #>  #>  #> $polr #> $polr$descr #> [1] \"Ordinal logistic regression model\" #>  #> $polr$design #> [1] \"cross-sectional\" #>  #> $polr$out.type #> [1] \"ordinal\" #>  #> $polr$fun #> [1] \"MASS::polr\" #>  #> $polr$args.list #> $polr$args.list$Hess #> [1] TRUE #>  #> $polr$args.list$method #> [1] \"logistic\" #>  #>  #> $polr$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $polr$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $polr$table.args.list #> list() #>  #>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Implemented functions — supported_plots","title":"Implemented functions — supported_plots","text":"Library supported functions. list name \"descr\" element unique element list. descr: Plot description primary.type: Primary variable data type (continuous, dichotomous ordinal) secondary.type: Secondary variable data type (continuous, dichotomous ordinal) secondary.extra: \"none\" NULL option choose none. tertiary.type: Tertiary variable data type (continuous, dichotomous ordinal)","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Implemented functions — supported_plots","text":"","code":"supported_plots()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Implemented functions — supported_plots","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Implemented functions — supported_plots","text":"","code":"supported_plots() |> str() #> List of 5 #>  $ plot_hbars  :List of 8 #>   ..$ fun            : chr \"plot_hbars\" #>   ..$ descr          : chr \"Stacked horizontal bars\" #>   ..$ note           : chr \"A classical way of visualising the distribution of an ordinal scale like the modified Ranking Scale and known as Grotta bars\" #>   ..$ primary.type   : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.type : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.multi: logi FALSE #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: chr \"none\" #>  $ plot_violin :List of 8 #>   ..$ fun            : chr \"plot_violin\" #>   ..$ descr          : chr \"Violin plot\" #>   ..$ note           : chr \"A modern alternative to the classic boxplot to visualise data distribution\" #>   ..$ primary.type   : chr [1:3] \"continuous\" \"dichotomous\" \"ordinal\" #>   ..$ secondary.type : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.multi: logi FALSE #>   ..$ secondary.extra: chr \"none\" #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>  $ plot_sankey :List of 8 #>   ..$ fun            : chr \"plot_sankey\" #>   ..$ descr          : chr \"Sankey plot\" #>   ..$ note           : chr \"A way of visualising change between groups\" #>   ..$ primary.type   : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.type : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.multi: logi FALSE #>   ..$ secondary.extra: NULL #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>  $ plot_scatter:List of 8 #>   ..$ fun            : chr \"plot_scatter\" #>   ..$ descr          : chr \"Scatter plot\" #>   ..$ note           : chr \"A classic way of showing the association between to variables\" #>   ..$ primary.type   : chr \"continuous\" #>   ..$ secondary.type : chr [1:2] \"continuous\" \"ordinal\" #>   ..$ secondary.multi: logi FALSE #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: NULL #>  $ plot_euler  :List of 9 #>   ..$ fun            : chr \"plot_euler\" #>   ..$ descr          : chr \"Euler diagram\" #>   ..$ note           : chr \"Generate area-proportional Euler diagrams to display set relationships\" #>   ..$ primary.type   : chr \"dichotomous\" #>   ..$ secondary.type : chr \"dichotomous\" #>   ..$ secondary.multi: logi TRUE #>   ..$ secondary.max  : num 4 #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: NULL"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/tbl_merge.html","id":null,"dir":"Reference","previous_headings":"","what":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","title":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","text":"substitue gtsummary::tbl_merge, use list names tab spanner names.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/tbl_merge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","text":"","code":"tbl_merge(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/tbl_merge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","text":"data gtsummary list object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/tbl_merge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","text":"gt summary list object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-factor.html","id":null,"dir":"Reference","previous_headings":"","what":"Module to Reorder the Levels of a Factor Variable — update-factor","title":"Module to Reorder the Levels of a Factor Variable — update-factor","text":"module contain interface reorder levels factor variable.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-factor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module to Reorder the Levels of a Factor Variable — update-factor","text":"","code":"update_factor_ui(id)  update_factor_server(id, data_r = reactive(NULL))  modal_update_factor(   id,   title = i18n(\"Update levels of a factor\"),   easyClose = TRUE,   size = \"l\",   footer = NULL )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-factor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module to Reorder the Levels of a Factor Variable — update-factor","text":"id Module ID. data_r shiny::reactive() function returning data.frame. title optional title dialog. easyClose TRUE, modal dialog can dismissed clicking outside dialog box, pressing Escape key. FALSE (default), modal dialog dismissed ways; instead must dismissed clicking modalButton(), call removeModal() server. size One \"s\" small, \"m\" (default) medium, \"l\" large, \"xl\" extra large. Note \"xl\" works Bootstrap 4 (opt-Bootstrap 4+, pass bslib::bs_theme() theme argument page container like fluidPage()). footer UI footer. Use NULL footer.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-factor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module to Reorder the Levels of a Factor Variable — update-factor","text":"shiny::reactive() function returning data.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-variables.html","id":null,"dir":"Reference","previous_headings":"","what":"Select, rename and convert variables — update-variables","title":"Select, rename and convert variables — update-variables","text":"Select, rename convert variables","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-variables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Select, rename and convert variables — update-variables","text":"","code":"update_variables_ui(id, title = \"\")  update_variables_server(   id,   data,   height = NULL,   return_data_on_init = FALSE,   try_silent = FALSE )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-variables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Select, rename and convert variables — update-variables","text":"id Module's ID title Module's title, TRUE use default title, use NULL title shiny.tag custom one. data data.frame reactive function returning data.frame. height Height table. return_data_on_init Return initial data module called. try_silent logical: report error messages suppressed?","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-variables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Select, rename and convert variables — update-variables","text":"shiny::reactive() function returning updated data.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update_variables_datagrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Modified from the datamods pacakge — update_variables_datagrid","title":"Modified from the datamods pacakge — update_variables_datagrid","text":"Modified datamods pacakge","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update_variables_datagrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modified from the datamods pacakge — update_variables_datagrid","text":"","code":"update_variables_datagrid(   data,   height = NULL,   selectionId = NULL,   buttonId = NULL )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update_variables_datagrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modified from the datamods pacakge — update_variables_datagrid","text":"data data height height selectionId selectionId buttonId buttonId","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update_variables_datagrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Modified from the datamods pacakge — update_variables_datagrid","text":"","code":"mtcars |>   summary_vars() |>   update_variables_datagrid() #> Error in update_variables_datagrid(summary_vars(mtcars)): could not find function \"update_variables_datagrid\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vectorSelectInput.html","id":null,"dir":"Reference","previous_headings":"","what":"A selectizeInput customized for named vectors — vectorSelectInput","title":"A selectizeInput customized for named vectors — vectorSelectInput","text":"selectizeInput customized named vectors","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vectorSelectInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A selectizeInput customized for named vectors — vectorSelectInput","text":"","code":"vectorSelectInput(   inputId,   label,   choices,   selected = \"\",   ...,   placeholder = \"\",   onInitialize )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vectorSelectInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A selectizeInput customized for named vectors — vectorSelectInput","text":"inputId passed selectizeInput label passed selectizeInput choices named vector fields populated selected default selection ... passed selectizeInput placeholder passed selectizeInput options onInitialize passed selectizeInput options","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vectorSelectInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A selectizeInput customized for named vectors — vectorSelectInput","text":"selectizeInput dropdown element","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vectorSelectInput.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A selectizeInput customized for named vectors — vectorSelectInput","text":"","code":"if (shiny::interactive()) { shinyApp(   ui = fluidPage(     shiny::uiOutput(\"select\"),     tableOutput(\"data\")   ),   server = function(input, output) {     output$select <- shiny::renderUI({       vectorSelectInput(         inputId = \"variable\", label = \"Variable:\",         data = c(           \"Cylinders\" = \"cyl\",           \"Transmission\" = \"am\",           \"Gears\" = \"gear\"         )       )     })      output$data <- renderTable(       {         mtcars[, c(\"mpg\", input$variable), drop = FALSE]       },       rownames = TRUE     )   } ) } #> Error: 'interactive' is not an exported object from 'namespace:shiny'"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vertical_stacked_bars.html","id":null,"dir":"Reference","previous_headings":"","what":"Vertical stacked bar plot wrapper — vertical_stacked_bars","title":"Vertical stacked bar plot wrapper — vertical_stacked_bars","text":"Vertical stacked bar plot wrapper","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vertical_stacked_bars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vertical stacked bar plot wrapper — vertical_stacked_bars","text":"","code":"vertical_stacked_bars(   data,   score = \"full_score\",   group = \"pase_0_q\",   strata = NULL,   t.size = 10,   l.color = \"black\",   l.size = 0.5,   draw.lines = TRUE )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vertical_stacked_bars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vertical stacked bar plot wrapper — vertical_stacked_bars","text":"data data.frame score outcome variable group grouping variable strata stratifying variable t.size text size","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vertical_stacked_bars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Vertical stacked bar plot wrapper — vertical_stacked_bars","text":"ggplot2 object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/wide2long.html","id":null,"dir":"Reference","previous_headings":"","what":"Alternative pivoting method for easily pivoting based on name pattern — wide2long","title":"Alternative pivoting method for easily pivoting based on name pattern — wide2long","text":"function requires assumes systematic naming variables. now supports one level pivoting. Adding levels require added \"ignore\" string pattern similarly. Example 2.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/wide2long.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Alternative pivoting method for easily pivoting based on name pattern — wide2long","text":"","code":"wide2long(   data,   pattern,   type = c(\"prefix\", \"infix\", \"suffix\"),   id.col = 1,   instance.name = \"instance\" )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/wide2long.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Alternative pivoting method for easily pivoting based on name pattern — wide2long","text":"data data pattern pattern(s) match. Character vector length 1 . type type match. can one \"prefix\",\"infix\" \"suffix\". id.col ID column. fill ID . Column name numeric index. Default \"1\", first column. instance.name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/wide2long.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Alternative pivoting method for easily pivoting based on name pattern — wide2long","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/wide2long.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Alternative pivoting method for easily pivoting based on name pattern — wide2long","text":"","code":"data.frame(   1:20, sample(70:80, 20, TRUE),   sample(70:100, 20, TRUE),   sample(70:100, 20, TRUE),   sample(170:200, 20, TRUE) ) |>   setNames(c(\"id\", \"age\", \"weight_0\", \"weight_1\", \"height_1\")) |>   wide2long(pattern = c(\"_0\", \"_1\"), type = \"suffix\") #>    id age instance weight height #> 1   1  71        0     95     NA #> 2   1  NA        1     98    179 #> 3   2  72        0     77     NA #> 4   2  NA        1     98    182 #> 5   3  70        0     85     NA #> 6   3  NA        1     74    197 #> 7   4  71        0     83     NA #> 8   4  NA        1     82    199 #> 9   5  72        0     90     NA #> 10  5  NA        1     88    179 #> 11  6  75        0     94     NA #> 12  6  NA        1     94    175 #> 13  7  74        0     75     NA #> 14  7  NA        1    100    179 #> 15  8  71        0     91     NA #> 16  8  NA        1     83    195 #> 17  9  78        0     77     NA #> 18  9  NA        1     96    176 #> 19 10  79        0     90     NA #> 20 10  NA        1     92    187 #> 21 11  78        0     93     NA #> 22 11  NA        1     96    188 #> 23 12  71        0     72     NA #> 24 12  NA        1     73    193 #> 25 13  71        0     77     NA #> 26 13  NA        1     89    187 #> 27 14  76        0     74     NA #> 28 14  NA        1    100    192 #> 29 15  73        0     83     NA #> 30 15  NA        1     96    190 #> 31 16  75        0     96     NA #> 32 16  NA        1     82    183 #> 33 17  71        0     82     NA #> 34 17  NA        1     72    192 #> 35 18  76        0     88     NA #> 36 18  NA        1     77    195 #> 37 19  78        0     72     NA #> 38 19  NA        1     93    184 #> 39 20  75        0     97     NA #> 40 20  NA        1     98    198 data.frame(   1:20, sample(70:80, 20, TRUE),   sample(70:100, 20, TRUE),   sample(70:100, 20, TRUE),   sample(170:200, 20, TRUE) ) |>   setNames(c(\"id\", \"age\", \"weight_0\", \"weight_a_1\", \"height_b_1\")) |>   wide2long(pattern = c(\"_0\", \"_1\"), type = \"suffix\") #>    id age instance weight weight_a height_b #> 1   1  79        0     75       NA       NA #> 2   1  NA        1     NA       71      171 #> 3   2  74        0     93       NA       NA #> 4   2  NA        1     NA       97      199 #> 5   3  75        0     95       NA       NA #> 6   3  NA        1     NA       81      192 #> 7   4  70        0     97       NA       NA #> 8   4  NA        1     NA       75      195 #> 9   5  70        0     77       NA       NA #> 10  5  NA        1     NA       83      191 #> 11  6  75        0     90       NA       NA #> 12  6  NA        1     NA       95      178 #> 13  7  75        0     76       NA       NA #> 14  7  NA        1     NA       78      200 #> 15  8  79        0     72       NA       NA #> 16  8  NA        1     NA       76      185 #> 17  9  75        0     79       NA       NA #> 18  9  NA        1     NA       88      195 #> 19 10  78        0     70       NA       NA #> 20 10  NA        1     NA       74      199 #> 21 11  70        0     99       NA       NA #> 22 11  NA        1     NA       86      176 #> 23 12  77        0     74       NA       NA #> 24 12  NA        1     NA       78      174 #> 25 13  75        0     74       NA       NA #> 26 13  NA        1     NA       91      192 #> 27 14  70        0     73       NA       NA #> 28 14  NA        1     NA       81      176 #> 29 15  79        0     80       NA       NA #> 30 15  NA        1     NA       91      176 #> 31 16  72        0     78       NA       NA #> 32 16  NA        1     NA       94      181 #> 33 17  77        0     71       NA       NA #> 34 17  NA        1     NA       82      181 #> 35 18  80        0     97       NA       NA #> 36 18  NA        1     NA       81      200 #> 37 19  80        0     79       NA       NA #> 38 19  NA        1     NA       72      195 #> 39 20  74        0     71       NA       NA #> 40 20  NA        1     NA       77      171 # Optional filling of missing values by last observation carried forward # Needed for mmrm analyses long_missings |>   # Fills record ID assuming none are missing   tidyr::fill(record_id) |>   # Grouping by ID for the last step   dplyr::group_by(record_id) |>   # Filling missing data by ID   tidyr::fill(names(long_missings)[!names(long_missings) %in% new_names]) |>   # Remove grouping   dplyr::ungroup() #> Error: object 'long_missings' not found"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/write_quarto.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to save data in RDS, load into specified qmd and render — write_quarto","title":"Wrapper to save data in RDS, load into specified qmd and render — write_quarto","text":"Wrapper save data RDS, load specified qmd render","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/write_quarto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to save data in RDS, load into specified qmd and render — write_quarto","text":"","code":"write_quarto(data, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/write_quarto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to save data in RDS, load into specified qmd and render — write_quarto","text":"data list pass qmd ... Passed quarto::quarto_render()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/write_quarto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper to save data in RDS, load into specified qmd and render — write_quarto","text":"output file name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/news/index.html","id":"freesearcher-2532","dir":"Changelog","previous_headings":"","what":"freesearcheR 25.3.2","title":"freesearcheR 25.3.2","text":"Focus polish improved ui/ux. First steps towards updated name (FreesearchR), renamed repository. Also, repo move organisation (named FreesearchR). Testing file upload conducted improved. Working omproving code export.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/news/index.html","id":"freesearcher-2531","dir":"Changelog","previous_headings":"","what":"freesearcheR 25.3.1","title":"freesearcheR 25.3.1","text":"First steps towards focused simplified interface. Focus ease use, handling basic functionality data inspection descriptive analyses. Inspired Stroke Center implementation guidelines WSO, apply similar approach project order keep interface simple robust. Basic functions descriptive analyses data browsing basics. advanced features like regression analyses added learning purposes, really done one self software like R ensure learning reproducibility. Teal dependencies removed. teal framework really seems powerful promising, also mean less control clutter. May come later. main components implemented: Data import different sources Data management (variable creation, re-classing, naming, labelling ) Basic data comparisons descriptive analyses Basic data visualisations select set plot types great publication purposes Regression analysis basic clinical cross-sectional data (mixed models repeated measures survival analyses table) Export outputs (descriptive analyses regression) well modified dataset (code also showed, working ) Next steps : Polished code export Improved workflow descriptive text well thorough step-wise guide/documentation (possibly small videos) Implement clinical projects Implement data analysis courses Extensive testing bug squashing","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/news/index.html","id":"freesearcher-2511","dir":"Changelog","previous_headings":"","what":"freesearcheR 25.1.1","title":"freesearcheR 25.1.1","text":"UI tweaks. NEW: Option set class hms using hms package. NEW: summary grid sparklines. Speed improvements better regression analysis handling. Preparations extending analysis options study designs.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/news/index.html","id":"freesearcher-24121","dir":"Changelog","previous_headings":"","what":"freesearcheR 24.12.1","title":"freesearcheR 24.12.1","text":"Initial release Zenodo.","code":""}]