diff --git a/articles/FreesearchR.html b/articles/FreesearchR.html index 95aa02f..03521e5 100644 --- a/articles/FreesearchR.html +++ b/articles/FreesearchR.html @@ -52,8 +52,8 @@ - -
+ +

FreesearchR

@@ -150,10 +150,112 @@ filtering options.

There are a number of plotting options to visualise different aspects of the data.

Below are the available plot types listed.

-
-
-
- + +++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Data typePlot typeDescription
continuousViolin plotA modern alternative to the classic boxplot to +visualise data distribution
continuousScatter plotA classic way of showing the association between to +variables
continuousBox plotA classic way to plot data distribution by groups
dichotomousStacked horizontal barsA classical way of visualising the distribution of an +ordinal scale like the modified Ranking Scale and known as Grotta +bars
dichotomousViolin plotA modern alternative to the classic boxplot to +visualise data distribution
dichotomousSankey plotA way of visualising change between groups
dichotomousBox plotA classic way to plot data distribution by groups
dichotomousEuler diagramGenerate area-proportional Euler diagrams to display +set relationships
ordinalStacked horizontal barsA classical way of visualising the distribution of an +ordinal scale like the modified Ranking Scale and known as Grotta +bars
ordinalViolin plotA modern alternative to the classic boxplot to +visualise data distribution
ordinalSankey plotA way of visualising change between groups
ordinalBox plotA classic way to plot data distribution by groups
categoricalStacked horizontal barsA classical way of visualising the distribution of an +ordinal scale like the modified Ranking Scale and known as Grotta +bars
categoricalViolin plotA modern alternative to the classic boxplot to +visualise data distribution
categoricalSankey plotA way of visualising change between groups
categoricalBox plotA classic way to plot data distribution by groups

Regression diff --git a/news/index.html b/news/index.html index 71c9c89..cadebe3 100644 --- a/news/index.html +++ b/news/index.html @@ -38,8 +38,8 @@

FreesearchR 25.4.2

Polished and simplified data import module including a much improved REDCap import module.

-
  • -CHANGE default_parsing() now ensure unique variable names.
    • +

    • CHANGE default_parsing() now ensure unique variable names.

      • +

    • NEW Working code output for all major modules including import, modifications, filter, evaluation, plotting and regression.

FreesearchR 25.4.1

diff --git a/pkgdown.yml b/pkgdown.yml index 5a357df..133b824 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.1.1 pkgdown_sha: ~ articles: FreesearchR: FreesearchR.html -last_built: 2025-04-08T12:20Z +last_built: 2025-04-09T10:49Z urls: reference: https://agdamsbo.github.io/FreesearchR/reference article: https://agdamsbo.github.io/FreesearchR/articles diff --git a/reference/create_overview_datagrid.html b/reference/create_overview_datagrid.html index 6e4b4a0..356e0a5 100644 --- a/reference/create_overview_datagrid.html +++ b/reference/create_overview_datagrid.html @@ -42,7 +42,7 @@

Usage

- 
create_overview_datagrid(data)
+ 
create_overview_datagrid(data, ...)
diff --git a/reference/data-summary.html b/reference/data-summary.html index 8542983..2aaf96b 100644 --- a/reference/data-summary.html +++ b/reference/data-summary.html @@ -68,7 +68,7 @@
...
-

arguments passed to toastui::datagrid

+

arguments passed to create_overview_datagrid

diff --git a/reference/expression_string.html b/reference/expression_string.html new file mode 100644 index 0000000..0c63a41 --- /dev/null +++ b/reference/expression_string.html @@ -0,0 +1,89 @@ + +Deparses expression as string, substitutes native pipe and adds assign — expression_string • FreesearchR + Skip to contents + + +
+
+
+ +

Deparses expression as string, substitutes native pipe and adds assign

+ Source: R/helpers.R +
expression_string.Rd
+
+ +
+

Deparses expression as string, substitutes native pipe and adds assign

+
+ +
+

Usage

+ 
expression_string(data, assign.str = "data <- ")
+
+ +
+

Arguments

+ + +
data
+

expression

+ +
+
+

Value

+

string

+
+ +
+

Examples

+ 
list(
+rlang::call2(.fn = "select",!!!list(c("cyl","disp")),.ns = "dplyr"),
+rlang::call2(.fn = "default_parsing",.ns = "FreesearchR")
+) |> merge_expression() |> expression_string()
+#> [1] "data<-dplyr::select(c('cyl','disp'))|>\nFreesearchR::default_parsing()"
+
+
+
+ + +
+

Site built with pkgdown 2.1.1.

+
+ +
+

Developed by Andreas Gammelgaard Damsbo. Provided without any warranty.

+
+ +
+ + + + + + + diff --git a/reference/getfun.html b/reference/getfun.html index 40b2c53..1fe47d0 100644 --- a/reference/getfun.html +++ b/reference/getfun.html @@ -133,7 +133,7 @@ #> z$qr <- NULL #> z #> } -#> <bytecode: 0x55a0c02c5460> +#> <bytecode: 0x559101e5a0d0> #> <environment: namespace:stats>
diff --git a/reference/index.html b/reference/index.html index 52f6d95..165ae14 100644 --- a/reference/index.html +++ b/reference/index.html @@ -209,6 +209,12 @@
Drop empty events from REDCap export
+ expression_string() + +
+
Deparses expression as string, substitutes native pipe and adds assign
+
+ factorize()
@@ -359,6 +365,12 @@
Shiny UI module to load a data file
+ merge_expression() + +
+
Merge list of expressions
+
+ merge_long()
diff --git a/reference/merge_expression.html b/reference/merge_expression.html new file mode 100644 index 0000000..31effa5 --- /dev/null +++ b/reference/merge_expression.html @@ -0,0 +1,89 @@ + +Merge list of expressions — merge_expression • FreesearchR + Skip to contents + + +
+
+
+ +

Merge list of expressions

+ Source: R/helpers.R +
merge_expression.Rd
+
+ +
+

Merge list of expressions

+
+ +
+

Usage

+ 
merge_expression(data)
+
+ +
+

Arguments

+ + +
data
+

list

+ +
+
+

Value

+

expression

+
+ +
+

Examples

+ 
list(
+rlang::call2(.fn = "select",!!!list(c("cyl","disp")),.ns = "dplyr"),
+rlang::call2(.fn = "default_parsing",.ns = "FreesearchR")
+) |> merge_expression()
+#> dplyr::select(c("cyl", "disp")) %>% FreesearchR::default_parsing()
+
+
+
+ + +
+

Site built with pkgdown 2.1.1.

+
+ +
+

Developed by Andreas Gammelgaard Damsbo. Provided without any warranty.

+
+ +
+ + + + + + + diff --git a/reference/regression_model.html b/reference/regression_model.html index 1dd5f2d..a26835c 100644 --- a/reference/regression_model.html +++ b/reference/regression_model.html @@ -931,6 +931,7 @@ argsstring2list() or list of arguments. Default is NULL.

) ls <- regression_model_list(data = default_parsing(mtcars), outcome.str = "cyl", fun.descr = "Ordinal logistic regression model") summary(ls$model) +ls <- regression_model_list(data = default_parsing(mtcars), outcome.str = "mpg", fun.descr = "Linear regression model") ls <- regression_model_list(data = default_parsing(gtsummary::trial), outcome.str = "trt", fun.descr = "Logistic regression model") tbl <- gtsummary::tbl_regression(ls$model, exponentiate = TRUE) @@ -940,7 +941,7 @@ argsstring2list() or list of arguments. Default is NULL.

outcome.str = "trt", fun = "stats::glm", formula.str = "{outcome.str}~.", - args.list = list(family = stats::binomial(link = "logit")) + args.list = list(family = "binomial") ) tbl2 <- gtsummary::tbl_regression(m, exponentiate = TRUE) broom::tidy(ls$model) @@ -956,6 +957,7 @@ argsstring2list() or list of arguments. Default is NULL.

lapply(broom::tidy) |> dplyr::bind_rows() ms <- regression_model_uv_list(data = default_parsing(mtcars), outcome.str = "mpg", fun.descr = "Linear regression model") +ms$code lapply(ms$model, broom::tidy) |> dplyr::bind_rows() } # }

diff --git a/reference/supported_functions.html b/reference/supported_functions.html index 3c9755e..7c2c38e 100644 --- a/reference/supported_functions.html +++ b/reference/supported_functions.html @@ -99,10 +99,7 @@ unique for each element on list.

#> #> $glm$args.list #> $glm$args.list$family -#> -#> Family: binomial -#> Link function: logit -#> +#> [1] "binomial" #> #> #> $glm$formula.str diff --git a/search.json b/search.json index 33cfb49..caf2bc9 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":[]},{"path":"https://agdamsbo.github.io/FreesearchR/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://agdamsbo.github.io/FreesearchR/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://agdamsbo.github.io/FreesearchR/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. 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/FreesearchR/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/FreesearchR/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/FreesearchR/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/FreesearchR/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/FreesearchR/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. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://agdamsbo.github.io/FreesearchR/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://agdamsbo.github.io/FreesearchR/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. 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Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://agdamsbo.github.io/FreesearchR/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.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://agdamsbo.github.io/FreesearchR/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/FreesearchR/LICENSE.html","id":"id_0-definitions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"0. 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However, include work’s System Libraries, general-purpose tools generally available free programs used unmodified performing activities part work. example, Corresponding Source includes interface definition files associated source files work, source code shared libraries dynamically linked subprograms work specifically designed require, intimate data communication control flow subprograms parts work. Corresponding Source need include anything users can regenerate automatically parts Corresponding Source. Corresponding Source work source code form work.","code":""},{"path":"https://agdamsbo.github.io/FreesearchR/LICENSE.html","id":"id_2-basic-permissions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"2. Basic Permissions.","title":"GNU Affero General Public License","text":"rights granted License granted term copyright Program, irrevocable provided stated conditions met. 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/FreesearchR/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/FreesearchR/LICENSE.html","id":"id_4-conveying-verbatim-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"4. 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Convey individual copies object code copy written offer provide Corresponding Source. alternative allowed occasionally noncommercially, received object code offer, accord subsection 6b. Convey object code offering access designated place (gratis charge), offer equivalent access Corresponding Source way place charge. need require recipients copy Corresponding Source along object code. place copy object code network server, Corresponding Source may different server (operated third party) supports equivalent copying facilities, provided maintain clear directions next object code saying find Corresponding Source. Regardless server hosts Corresponding Source, remain obligated ensure available long needed satisfy requirements. Convey object code using peer--peer transmission, provided inform peers object code Corresponding Source work offered general public charge subsection 6d. separable portion object code, whose source code excluded Corresponding Source System Library, need included conveying object code work. “User Product” either (1) “consumer product”, means tangible personal property normally used personal, family, household purposes, (2) anything designed sold incorporation dwelling. determining whether product consumer product, doubtful cases shall resolved favor coverage. particular product received particular user, “normally used” refers typical common use class product, regardless status particular user way particular user actually uses, expects expected use, product. product consumer product regardless whether product substantial commercial, industrial non-consumer uses, unless uses represent significant mode use product. “Installation Information” User Product means methods, procedures, authorization keys, information required install execute modified versions covered work User Product modified version Corresponding Source. information must suffice ensure continued functioning modified object code case prevented interfered solely modification made. convey object code work section , , specifically use , User Product, conveying occurs part transaction right possession use User Product transferred recipient perpetuity fixed term (regardless transaction characterized), Corresponding Source conveyed section must accompanied Installation Information. requirement apply neither third party retains ability install modified object code User Product (example, work installed ROM). requirement provide Installation Information include requirement continue provide support service, warranty, updates work modified installed recipient, User Product modified installed. 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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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Therefore, modifying propagating covered work, indicate acceptance License .","code":""},{"path":"https://agdamsbo.github.io/FreesearchR/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/FreesearchR/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/FreesearchR/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/FreesearchR/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/FreesearchR/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/FreesearchR/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/FreesearchR/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/FreesearchR/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/FreesearchR/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":" Copyright (C) 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 ."},{"path":"https://agdamsbo.github.io/FreesearchR/QA.html","id":null,"dir":"","previous_headings":"","what":"Questions and answers","title":"Questions and answers","text":"complete instructions set also available, collection questions answers project use FreesearchR app.","code":""},{"path":"https://agdamsbo.github.io/FreesearchR/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/FreesearchR/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/FreesearchR/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/FreesearchR/articles/FreesearchR.html","id":"getting-started-with-freesearchr","dir":"Articles","previous_headings":"","what":"Getting started with FreesearchR","title":"FreesearchR","text":"simple walk-trough basic instructions functions FreesearchR app.","code":""},{"path":"https://agdamsbo.github.io/FreesearchR/articles/FreesearchR.html","id":"launching","dir":"Articles","previous_headings":"Getting started with FreesearchR","what":"Launching","title":"FreesearchR","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 FreesearchR launch app: small note, standalone Windows app version drawing board well, time frame available.","code":"require(\"pak\") pak::pak(\"agdamsbo/FreesearchR\") library(FreesearchR) FreesearchR::launch_FreesearchR()"},{"path":"https://agdamsbo.github.io/FreesearchR/articles/FreesearchR.html","id":"importing-data","dir":"Articles","previous_headings":"Getting started with FreesearchR","what":"Importing data","title":"FreesearchR","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/FreesearchR/articles/FreesearchR.html","id":"file-upload","dir":"Articles","previous_headings":"Getting started with FreesearchR > Importing data","what":"File upload","title":"FreesearchR","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. notification posted error success. succesfull import data can previewed directly clicking “click see data” notification.","code":""},{"path":"https://agdamsbo.github.io/FreesearchR/articles/FreesearchR.html","id":"redcap-server-export","dir":"Articles","previous_headings":"Getting started with FreesearchR > Importing data","what":"REDCap server export","title":"FreesearchR","text":"Export data directly REDCap server. need first generate API-token (see instruction) REDCap. Make sure necessary rights . Please don’t store API-key device unless encrypted keyring, may compromise data safety. Log REDCap server retrieve token needed. Type correct webaddress REDCap server. module validate information can click “Connect”. unfold options preview data dictionary (main database metadata), choose fields/variables download well filtering options.","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://agdamsbo.github.io/FreesearchR/articles/FreesearchR.html","id":"visuals","dir":"Articles","previous_headings":"Getting started with FreesearchR","what":"Visuals","title":"FreesearchR","text":"number plotting options visualise different aspects data. available plot types listed.","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://agdamsbo.github.io/FreesearchR/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/FreesearchR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Damsbo (2025). FreesearchR: Browser Based Data Analysis. R package version 25.4.1, https://agdamsbo.github.io/FreesearchR/, https://github.com/agdamsbo/FreesearchR.","code":"@Manual{, title = {FreesearchR: Browser Based Data Analysis}, author = {Andreas Gammelgaard Damsbo}, year = {2025}, note = {R package version 25.4.1, https://agdamsbo.github.io/FreesearchR/}, url = {https://github.com/agdamsbo/FreesearchR}, }"},{"path":"https://agdamsbo.github.io/FreesearchR/index.html","id":"freesearchr","dir":"","previous_headings":"","what":"Browser Based Data Analysis","title":"Browser Based Data Analysis","text":"package backbone FreesearchR, free open-source browser based data exploration analysis tool clinicians researchers publication ready output. package FreesearchR-tool part larger initiative democratize health data analysis remove barriers clinicians engage health research. FreesearchR-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/FreesearchR/index.html","id":"install-locally","dir":"","previous_headings":"","what":"Install locally","title":"Browser Based Data Analysis","text":"FreesearchR-tool can also launched locally. data.frame available global environment accessible interface.","code":"require(\"devtools\") devtools::install_github(\"agdamsbo/FreesearchR\") library(FreesearchR) # By loading mtcars to the environment, it will be available # in the interface like any other data.frame data(mtcars) launch_FreesearchR()"},{"path":"https://agdamsbo.github.io/FreesearchR/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Browser Based Data Analysis","text":"Please note FreesearchR project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://agdamsbo.github.io/FreesearchR/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/FreesearchR/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/FreesearchR/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/FreesearchR/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/FreesearchR/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>\",\"<\\/i>\",\"<\\/i>\",\"<\\/i>\",\"<\\/i>\",\"<\\/i>\",\"<\\/i>\",\"<\\/i>\",\"<\\/i>\",\"<\\/i>\",\"<\\/i>\"]}},\"width\":60},{\"header\":\"type\",\"name\":\"type\",\"sortable\":true,\"align\":\"left\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}},{\"header\":\"name\",\"name\":\"name\",\"sortable\":true,\"align\":\"left\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}},{\"header\":\"n_missing\",\"name\":\"n_missing\",\"sortable\":true,\"align\":\"right\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}},{\"header\":\"p_complete\",\"name\":\"p_complete\",\"sortable\":true,\"align\":\"right\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}},{\"header\":\"n_unique\",\"name\":\"n_unique\",\"sortable\":true,\"align\":\"right\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}},{\"header\":\"vals\",\"name\":\"vals\",\"sortable\":true,\"align\":\"left\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}}],\"bodyHeight\":\"fitToParent\",\"draggable\":false,\"usageStatistics\":false,\"contextMenu\":null,\"rowHeight\":\"auto\"},\"theme\":\"clean\",\"themeOptions\":{\"cell\":{\"normal\":{\"showHorizontalBorder\":true}}},\"language\":\"en\",\"languageOptions\":[],\"filters\":false,\"rowAttributes\":[],\"validationInput\":false,\"dataAsInput\":false,\"dragInput\":false},\"evals\":[\"options.columns.0.renderer.type\"],\"jsHooks\":[]}"},{"path":"https://agdamsbo.github.io/FreesearchR/reference/add_sparkline.html","id":null,"dir":"Reference","previous_headings":"","what":"Add sparkline to datagrid — add_sparkline","title":"Add sparkline to datagrid — add_sparkline","text":"Add sparkline datagrid","code":""},{"path":"https://agdamsbo.github.io/FreesearchR/reference/add_sparkline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add sparkline to datagrid — add_sparkline","text":"","code":"add_sparkline( grid, column = \"vals\", color.main = \"#2a8484\", color.sec = \"#84EF84\" )"},{"path":"https://agdamsbo.github.io/FreesearchR/reference/add_sparkline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add sparkline to datagrid — add_sparkline","text":"grid grid column clumn transform","code":""},{"path":"https://agdamsbo.github.io/FreesearchR/reference/add_sparkline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add sparkline to datagrid — add_sparkline","text":"datagrid","code":""},{"path":"https://agdamsbo.github.io/FreesearchR/reference/add_sparkline.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add sparkline to datagrid — add_sparkline","text":"","code":"grid <- mtcars |> default_parsing() |> overview_vars() |> toastui::datagrid() |> add_sparkline() grid 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<\\/div>\\n