From aa962f2d9f5e24e07f6ee14b04ec53f9a58ef4c5 Mon Sep 17 00:00:00 2001
From: agdamsbo <43278243+agdamsbo@users.noreply.github.com>
Date: Tue, 27 Feb 2024 12:10:13 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20agdamsbo?=
 =?UTF-8?q?/REDCapCAST@a0730cb41c68f1d41d1fe0ff82b5e6de14fcd66a=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 articles/Introduction.html | 212 ++++++++++++++++++-------------------
 index.html                 |  10 +-
 news/index.html            |   3 +-
 pkgdown.yml                |   2 +-
 search.json                |   2 +-
 5 files changed, 115 insertions(+), 114 deletions(-)

diff --git a/articles/Introduction.html b/articles/Introduction.html
index b04b6e4..b3b0a96 100644
--- a/articles/Introduction.html
+++ b/articles/Introduction.html
@@ -100,23 +100,23 @@ demonstration of the functions.</p>
 </h2>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">redcapcast_data</span> <span class="op">|&gt;</span> <span class="fu">gt</span><span class="fu">::</span><span class="fu"><a href="https://gt.rstudio.com/reference/gt.html" class="external-link">gt</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
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-<style>#tapeacohhi table {
+<div id="byxlgnpfbb" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
+<style>#byxlgnpfbb table {
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-#tapeacohhi thead, #tapeacohhi tbody, #tapeacohhi tfoot, #tapeacohhi tr, #tapeacohhi td, #tapeacohhi th {
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+#byxlgnpfbb p {
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+#byxlgnpfbb .gt_table {
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@@ -142,12 +142,12 @@ demonstration of the functions.</p>
   border-left-color: #D3D3D3;
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+#byxlgnpfbb .gt_caption {
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@@ -159,7 +159,7 @@ demonstration of the functions.</p>
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@@ -171,7 +171,7 @@ demonstration of the functions.</p>
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+#byxlgnpfbb .gt_heading {
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@@ -183,13 +183,13 @@ demonstration of the functions.</p>
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@@ -204,7 +204,7 @@ demonstration of the functions.</p>
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+#byxlgnpfbb .gt_col_heading {
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@@ -224,7 +224,7 @@ demonstration of the functions.</p>
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@@ -236,15 +236,15 @@ demonstration of the functions.</p>
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+#byxlgnpfbb .gt_column_spanner_outer:first-child {
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@@ -256,11 +256,11 @@ demonstration of the functions.</p>
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+#byxlgnpfbb .gt_group_heading {
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@@ -286,7 +286,7 @@ demonstration of the functions.</p>
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+#byxlgnpfbb .gt_empty_group_heading {
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@@ -301,15 +301,15 @@ demonstration of the functions.</p>
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@@ -328,7 +328,7 @@ demonstration of the functions.</p>
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@@ -341,7 +341,7 @@ demonstration of the functions.</p>
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@@ -355,15 +355,15 @@ demonstration of the functions.</p>
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@@ -373,16 +373,16 @@ demonstration of the functions.</p>
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@@ -458,7 +458,7 @@ demonstration of the functions.</p>
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@@ -480,63 +480,63 @@ demonstration of the functions.</p>
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@@ -1067,23 +1067,23 @@ demonstration of the functions.</p>
 </div>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">redcapcast_meta</span> <span class="op">|&gt;</span> <span class="fu">gt</span><span class="fu">::</span><span class="fu"><a href="https://gt.rstudio.com/reference/gt.html" class="external-link">gt</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
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-<style>#xreuzzriun table {
+<div id="pwssudkjrt" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
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@@ -1253,7 +1253,7 @@ demonstration of the functions.</p>
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+#pwssudkjrt .gt_footnote {
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@@ -1425,7 +1425,7 @@ demonstration of the functions.</p>
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diff --git a/index.html b/index.html
index e280a24..284bfe5 100644
--- a/index.html
+++ b/index.html
@@ -15,8 +15,8 @@
     1) an intuitive interface for validated data capture; 2) audit trails for
     tracking data manipulation and export procedures; 3) automated export
     procedures for seamless data downloads to common statistical packages; and
-    4) procedures for data integration and interoperability with external sources
-    (Harris et al (2009) &lt;doi:10.1016/j.jbi.2008.08.010&gt;; 
+    4) procedures for data integration and interoperability with external 
+    sources (Harris et al (2009) &lt;doi:10.1016/j.jbi.2008.08.010&gt;; 
     Harris et al (2019) &lt;doi:10.1016/j.jbi.2019.103208&gt;).">
 <title>REDCap Castellated Data Handling • REDCapCAST</title>
 <!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
@@ -40,8 +40,8 @@
     1) an intuitive interface for validated data capture; 2) audit trails for
     tracking data manipulation and export procedures; 3) automated export
     procedures for seamless data downloads to common statistical packages; and
-    4) procedures for data integration and interoperability with external sources
-    (Harris et al (2009) &lt;doi:10.1016/j.jbi.2008.08.010&gt;; 
+    4) procedures for data integration and interoperability with external 
+    sources (Harris et al (2009) &lt;doi:10.1016/j.jbi.2008.08.010&gt;; 
     Harris et al (2019) &lt;doi:10.1016/j.jbi.2019.103208&gt;).">
 <meta property="og:image" content="https://agdamsbo.github.io/REDCapCAST/logo.png">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -118,7 +118,7 @@
 <li><p><code><a href="reference/redcap_wider.html">redcap_wider()</a></code>: joins and pivots a list of data frames with repeated instruments to a wide format utilizing the <a href="https://tidyr.tidyverse.org/reference/pivot_wider.html" class="external-link"><code>tidyr::pivot_wider()</code></a> from the <a href="https://www.tidyverse.org/" class="external-link">tidyverse</a>.</p></li>
 <li><p><code><a href="reference/easy_redcap.html">easy_redcap()</a></code>: combines secure API key storage with the <code>keyring</code>-package, focused data retrieval and optional widening. This is the recommended approach for easy data access and analysis.</p></li>
 <li><p><code><a href="reference/ds2dd_detailed.html">ds2dd_detailed()</a></code>: Converts a data set to a data dictionary for upload to a new REDCap database. Variables (fields) and instruments in a REDCap data base are defined by this data dictionary.</p></li>
-<li><p><code><a href="reference/shiny_cast.html">shiny_cast()</a></code>: <a href="">Shiny</a> application to ease the process of converting a spreadsheet/data set to a REDCap database. The app runs locally and data is transferred securely. You can just create and upload the data dictionary, but you can also transfer the given data in the same process.</p></li>
+<li><p><code><a href="reference/shiny_cast.html">shiny_cast()</a></code>: <a href="https://www.rstudio.com/products/shiny/" class="external-link">Shiny</a> application to ease the process of converting a spreadsheet/data set to a REDCap database. The app runs locally and data is transferred securely. You can just create and upload the data dictionary, but you can also transfer the given data in the same process.</p></li>
 </ul>
 </div>
 <div class="section level2">
diff --git a/news/index.html b/news/index.html
index da16b08..2775570 100644
--- a/news/index.html
+++ b/news/index.html
@@ -61,7 +61,8 @@
 <li><p>Fix: <code><a href="../reference/redcap_wider.html">redcap_wider()</a></code>: updated to accept more formats and allow handling of simple projects without repeating instruments and not longitudinal.</p></li>
 <li><p>Fix: <code><a href="../reference/read_redcap_tables.html">read_redcap_tables()</a></code>: now handles non-longitudinal project without repeatable instruments.</p></li>
 <li><p>NEW: <code><a href="../reference/ds2dd_detailed.html">ds2dd_detailed()</a></code>: extension of the <code><a href="../reference/ds2dd.html">ds2dd()</a></code>, which serves to preserve as much metadata as possible automatically. Depends on a group of helper functions also introduced. Of special note is the <code><a href="../reference/guess_time_only_filter.html">guess_time_only_filter()</a></code>, which will try to guess which columns/variables should be formatted as time only formats. Supports hms time format. DETAILED INSTRUCTION AND VIGNETTE IS PENDING.</p></li>
-<li><p>NEW: <code><a href="../reference/read_redcap_instrument.html">read_redcap_instrument()</a></code> convenience function to retrieve complete instrument. Goes a little against the focused approach. DETAILED INSTRUCTION IS PENDING.</p></li>
+<li><p>NEW: <code><a href="../reference/read_redcap_instrument.html">read_redcap_instrument()</a></code>: convenience function to retrieve complete instrument. Goes a little against the focused approach. With <code><a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_read.html" class="external-link">REDCapR::redcap_read()</a></code> you can specify a form to download. You have to also specify the record id variable though. This is done for you with <code><a href="../reference/read_redcap_instrument.html">read_redcap_instrument()</a></code>. Nothing fancy.</p></li>
+<li><p>NEW: <code><a href="../reference/shiny_cast.html">shiny_cast()</a></code>: <a href="https://www.rstudio.com/products/shiny/" class="external-link">Shiny</a> application to ease the process of converting a spreadsheet/data set to a REDCap database. The app runs locally and data is transferred securely. You can just create and upload the data dictionary, but you can also transfer the given data in the same process. I plan to host the app with shinyapps.io, but for now you can run it locally.</p></li>
 </ul></div>
 <div class="section level4">
 <h4 id="other-24-2-1">Other<a class="anchor" aria-label="anchor" href="#other-24-2-1"></a></h4>
diff --git a/pkgdown.yml b/pkgdown.yml
index e02baa0..6fe041b 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,7 +5,7 @@ articles:
   Database-creation: Database-creation.html
   Introduction: Introduction.html
   Shiny-app: Shiny-app.html
-last_built: 2024-02-27T11:56Z
+last_built: 2024-02-27T12:09Z
 urls:
   reference: https://agdamsbo.github.io/REDCapCAST/reference
   article: https://agdamsbo.github.io/REDCapCAST/articles
diff --git a/search.json b/search.json
index 3f8f0e2..ccfb6ed 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
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Interpretation of Sections 15 and 16","title":"GNU 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/REDCapCAST/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 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. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see <http://www.gnu.org/licenses/>. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","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 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 General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"easy-data-set-to-data-base-workflow","dir":"Articles","previous_headings":"","what":"Easy data set to data base workflow","title":"Database-creation","text":"first iteration dataset data dictionary function ds2dd(), creates basic data dictionary variables stored text. sufficient just storing old datasets/spreadsheets securely REDCap. advanced ds2dd_detailed() natural development. try apply common data classes data validation assume first column id number. outputs list dataset modified variable names comply REDCap naming conventions data dictionary. dataset correctly formatted data dictionary preserve much information possible. Additional specifications DataDictionary can made manually, can uploaded modified manually graphical user interface web page.","code":"mtcars |>   dplyr::mutate(record_id = seq_len(dplyr::n())) |>   ds2dd() |> str() dd_ls <- mtcars |>   dplyr::mutate(record_id = seq_len(dplyr::n())) |>   dplyr::select(record_id, dplyr::everything()) |>   ds2dd_detailed() dd_ls |> str()"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"step-3---meta-data-upload","dir":"Articles","previous_headings":"Easy data set to data base workflow","what":"Step 3 - Meta data upload","title":"Database-creation","text":"Now DataDictionary can exported spreadsheet uploaded can uploaded using REDCapR package (projects “Development” status). Use one two approaches :","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"manual-upload","dir":"Articles","previous_headings":"Easy data set to data base workflow > Step 3 - Meta data upload","what":"Manual upload","title":"Database-creation","text":"","code":"write.csv(dd_ls$meta, \"datadictionary.csv\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"upload-with-redcapr","dir":"Articles","previous_headings":"Easy data set to data base workflow > Step 3 - Meta data upload","what":"Upload with REDCapR","title":"Database-creation","text":"“REDCap R Handbook” written interfacing REDCap R using library(keyring)store credentials chapter 1.1.","code":"REDCapR::redcap_metadata_write(   dd_ls$meta,   redcap_uri = keyring::key_get(\"DB_URI\"),   token = keyring::key_get(\"DB_TOKEN\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"step-4---data-upload","dir":"Articles","previous_headings":"Easy data set to data base workflow","what":"Step 4 - Data upload","title":"Database-creation","text":"two options available data upload meta data upload: manual REDCapR. latter shown .","code":"REDCapR::redcap_write(   dd_ls$data,   redcap_uri = keyring::key_get(\"DB_URI\"),   token = keyring::key_get(\"DB_TOKEN\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Introduction.html","id":"splitting-the-dataset","dir":"Articles","previous_headings":"","what":"Splitting the dataset","title":"Introduction","text":"","code":"redcapcast_data |> gt::gt() redcapcast_meta |> gt::gt() list <-   REDCap_split(records = redcapcast_data,                            metadata = redcapcast_meta,                            forms = \"repeating\")|> sanitize_split() str(list) #> List of 2 #>  $          : tibble [10 × 17] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id                   : num [1:10] 1 2 2 3 3 3 4 4 5 6 #>   ..$ redcap_event_name           : chr [1:10] \"inclusion\" \"inclusion\" \"follow1\" \"inclusion\" ... #>   ..$ cpr                         : chr [1:10] \"1203401OB4\" \"0102342303\" NA \"2301569823\" ... #>   ..$ inclusion                   : Date[1:10], format: \"2023-03-13\" \"2023-03-01\" ... #>   ..$ dob                         : Date[1:10], format: \"1940-03-12\" \"1934-02-01\" ... #>   ..$ age                         : num [1:10] 83 89.1 NA 66.1 NA ... #>   ..$ age_integer                 : num [1:10] 83 89 NA 66 NA NA 117 NA 126 91 #>   ..$ sex                         : chr [1:10] \"female\" \"male\" NA \"male\" ... #>   ..$ cohabitation                : chr [1:10] \"Yes\" \"Yes\" NA \"No\" ... #>   ..$ hypertension                : chr [1:10] \"No\" \"No\" NA \"Yes\" ... #>   ..$ diabetes                    : chr [1:10] \"Yes\" \"No\" NA \"Yes\" ... #>   ..$ region                      : chr [1:10] \"East\" \"South\" NA \"North\" ... #>   ..$ baseline_data_start_complete: chr [1:10] \"Incomplete\" \"Incomplete\" NA \"Incomplete\" ... #>   ..$ mrs_assessed                : chr [1:10] \"Yes\" \"Yes\" \"Yes\" NA ... #>   ..$ mrs_date                    : Date[1:10], format: \"2023-03-13\" \"2023-03-07\" ... #>   ..$ mrs_score                   : num [1:10] 1 1 3 NA 2 1 NA NA NA NA #>   ..$ mrs_complete                : chr [1:10] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>  $ new_event: tibble [9 × 6] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id               : num [1:9] 2 3 3 3 3 3 4 4 4 #>   ..$ redcap_event_name       : chr [1:9] \"follow1\" \"follow1\" \"follow1\" \"follow2\" ... #>   ..$ redcap_repeat_instrument: chr [1:9] \"new_event\" \"new_event\" \"new_event\" \"new_event\" ... #>   ..$ redcap_repeat_instance  : num [1:9] 1 1 2 1 2 3 1 2 3 #>   ..$ event_type              : chr [1:9] \"TIA\" \"AIS\" \"ICH\" \"ICH\" ... #>   ..$ new_event_complete      : chr [1:9] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... list <-   REDCap_split(records = redcapcast_data,                            metadata = redcapcast_meta,                            forms = \"all\") |> sanitize_split() str(list) #> List of 3 #>  $ baseline_data_start: tibble [6 × 13] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id                   : num [1:6] 1 2 3 4 5 6 #>   ..$ redcap_event_name           : chr [1:6] \"inclusion\" \"inclusion\" \"inclusion\" \"inclusion\" ... #>   ..$ cpr                         : chr [1:6] \"1203401OB4\" \"0102342303\" \"2301569823\" \"0204051342\" ... #>   ..$ inclusion                   : Date[1:6], format: \"2023-03-13\" \"2023-03-01\" ... #>   ..$ dob                         : Date[1:6], format: \"1940-03-12\" \"1934-02-01\" ... #>   ..$ age                         : num [1:6] 83 89.1 66.1 117.9 126.2 ... #>   ..$ age_integer                 : num [1:6] 83 89 66 117 126 91 #>   ..$ sex                         : chr [1:6] \"female\" \"male\" \"male\" \"female\" ... #>   ..$ cohabitation                : chr [1:6] \"Yes\" \"Yes\" \"No\" NA ... #>   ..$ hypertension                : chr [1:6] \"No\" \"No\" \"Yes\" NA ... #>   ..$ diabetes                    : chr [1:6] \"Yes\" \"No\" \"Yes\" NA ... #>   ..$ region                      : chr [1:6] \"East\" \"South\" \"North\" NA ... #>   ..$ baseline_data_start_complete: chr [1:6] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>  $ mrs                : tibble [5 × 6] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id        : num [1:5] 1 2 2 3 3 #>   ..$ redcap_event_name: chr [1:5] \"inclusion\" \"inclusion\" \"follow1\" \"follow1\" ... #>   ..$ mrs_assessed     : chr [1:5] \"Yes\" \"Yes\" \"Yes\" \"Yes\" ... #>   ..$ mrs_date         : Date[1:5], format: \"2023-03-13\" \"2023-03-07\" ... #>   ..$ mrs_score        : num [1:5] 1 1 3 2 1 #>   ..$ mrs_complete     : chr [1:5] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>  $ new_event          : tibble [9 × 6] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id               : num [1:9] 2 3 3 3 3 3 4 4 4 #>   ..$ redcap_event_name       : chr [1:9] \"follow1\" \"follow1\" \"follow1\" \"follow2\" ... #>   ..$ redcap_repeat_instrument: chr [1:9] \"new_event\" \"new_event\" \"new_event\" \"new_event\" ... #>   ..$ redcap_repeat_instance  : num [1:9] 1 1 2 1 2 3 1 2 3 #>   ..$ event_type              : chr [1:9] \"TIA\" \"AIS\" \"ICH\" \"ICH\" ... #>   ..$ new_event_complete      : chr [1:9] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ..."},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Introduction.html","id":"reading-data-from-redcap","dir":"Articles","previous_headings":"","what":"Reading data from REDCap","title":"Introduction","text":"function wraps demonstrated function get dataset, metadata, apply REDCap_splitfunction bit cleaning. just cuts outs steps easier approach. function works similar REDCapR::redcap_read() allowing specify fields, events forms export instead exporting whole database filtering afterwards. believe better safer, focused approach.","code":"# read_redcap_tables(uri = \"YOUR URI\", token = \"YOUR TOKEN\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Introduction.html","id":"pivotting-to-wider-format","dir":"Articles","previous_headings":"","what":"Pivotting to wider format","title":"Introduction","text":"","code":"redcap_wider(list) |> str() #> Joining with `by = join_by(record_id)` #> Joining with `by = join_by(record_id)` #> 'data.frame':    6 obs. of  36 variables: #>  $ record_id                   : num  1 2 3 4 5 6 #>  $ cpr                         : chr  \"1203401OB4\" \"0102342303\" \"2301569823\" \"0204051342\" ... #>  $ inclusion                   : Date, format: \"2023-03-13\" \"2023-03-01\" ... #>  $ dob                         : Date, format: \"1940-03-12\" \"1934-02-01\" ... #>  $ age                         : num  83 89.1 66.1 117.9 126.2 ... #>  $ age_integer                 : num  83 89 66 117 126 91 #>  $ sex                         : chr  \"female\" \"male\" \"male\" \"female\" ... #>  $ cohabitation                : chr  \"Yes\" \"Yes\" \"No\" NA ... #>  $ hypertension                : chr  \"No\" \"No\" \"Yes\" NA ... #>  $ diabetes                    : chr  \"Yes\" \"No\" \"Yes\" NA ... #>  $ region                      : chr  \"East\" \"South\" \"North\" NA ... #>  $ baseline_data_start_complete: chr  \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>  $ mrs_assessed_inclusion      : chr  \"Yes\" \"Yes\" NA NA ... #>  $ mrs_assessed_follow1        : chr  NA \"Yes\" \"Yes\" NA ... #>  $ mrs_assessed_follow2        : chr  NA NA \"Yes\" NA ... #>  $ mrs_date_inclusion          : Date, format: \"2023-03-13\" \"2023-03-07\" ... #>  $ mrs_date_follow1            : Date, format: NA \"2023-03-09\" ... #>  $ mrs_date_follow2            : Date, format: NA NA ... #>  $ mrs_score_inclusion         : num  1 1 NA NA NA NA #>  $ mrs_score_follow1           : num  NA 3 2 NA NA NA #>  $ mrs_score_follow2           : num  NA NA 1 NA NA NA #>  $ mrs_complete_inclusion      : chr  \"Incomplete\" \"Incomplete\" NA NA ... #>  $ mrs_complete_follow1        : chr  NA \"Incomplete\" \"Incomplete\" NA ... #>  $ mrs_complete_follow2        : chr  NA NA \"Incomplete\" NA ... #>  $ event_type_1_follow1        : chr  NA \"TIA\" \"AIS\" NA ... #>  $ event_type_1_follow2        : chr  NA NA \"ICH\" \"AIS\" ... #>  $ new_event_complete_1_follow1: chr  NA \"Incomplete\" \"Incomplete\" NA ... #>  $ new_event_complete_1_follow2: chr  NA NA \"Incomplete\" \"Complete\" ... #>  $ event_type_2_follow1        : chr  NA NA \"ICH\" NA ... #>  $ event_type_2_follow2        : chr  NA NA \"TIA\" \"ICH\" ... #>  $ event_type_3_follow1        : chr  NA NA NA NA ... #>  $ event_type_3_follow2        : chr  NA NA \"AIS\" \"Unknown\" ... #>  $ new_event_complete_2_follow1: chr  NA NA \"Incomplete\" NA ... #>  $ new_event_complete_2_follow2: chr  NA NA \"Incomplete\" \"Incomplete\" ... #>  $ new_event_complete_3_follow1: chr  NA NA NA NA ... #>  $ new_event_complete_3_follow2: chr  NA NA \"Incomplete\" \"Complete\" ..."},{"path":"https://agdamsbo.github.io/REDCapCAST/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Andreas Gammelgaard Damsbo. Author, maintainer. Paul Egeler. Author.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Damsbo , Egeler P (2024). REDCapCAST: REDCap Castellated Data Handling. R package version 24.2.1, https://agdamsbo.github.io/REDCapCAST/, https://github.com/agdamsbo/REDCapCAST.","code":"@Manual{,   title = {REDCapCAST: REDCap Castellated Data Handling},   author = {Andreas Gammelgaard Damsbo and Paul Egeler},   year = {2024},   note = {R package version 24.2.1, https://agdamsbo.github.io/REDCapCAST/},   url = {https://github.com/agdamsbo/REDCapCAST}, }"},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"redcapcast-package-","dir":"","previous_headings":"","what":"REDCap Castellated Data Handling","title":"REDCap Castellated Data Handling","text":"REDCap database casting handling castellated data using repeated instruments longitudinal projects. package fork pegeler/REDCapRITS. REDCapRITS represents great extensive work handle castellated REDCap data different programming languages. fork purely minded R usage includes implementations main REDCap_split function. package much seen attempt R--REDCap--R foundry handling transition dataset/variable list database way, REDCap database tidy dataset. goal also allow “minimal data” approach allowing filter records, instruments variables export download data needed. think approach desirable handling sensitive, clinical data. Please refer REDCap-Tools great tools working REDCap R.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"use-and-immprovements","dir":"","previous_headings":"","what":"Use and immprovements","title":"REDCap Castellated Data Handling","text":"just short description main functions: REDcap_split(): Works largely original REDCapRITS::REDCap_split(). takes REDCap dataset metadata (data dictionary) split data set list dataframes instruments. read_redcap_tables(): wraps use REDCapR::redcap_read() REDCap_split() ease export REDCap data. Default output list data frames one data frame REDCap instrument. redcap_wider(): joins pivots list data frames repeated instruments wide format utilizing tidyr::pivot_wider() tidyverse. easy_redcap(): combines secure API key storage keyring-package, focused data retrieval optional widening. recommended approach easy data access analysis. ds2dd_detailed(): Converts data set data dictionary upload new REDCap database. Variables (fields) instruments REDCap data base defined data dictionary. shiny_cast(): Shiny application ease process converting spreadsheet/data set REDCap database. app runs locally data transferred securely. can just create upload data dictionary, can also transfer given data process.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"future","dir":"","previous_headings":"","what":"Future","title":"REDCap Castellated Data Handling","text":"plan package bundled Handbook working REDCap R. work progress limited time available. Please feel free contact create issue ideas future additions.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"REDCap Castellated Data Handling","text":"package available CRAN. Install latest version: Install latest version directly GitHub:","code":"install.packages(\"REDCapCAST\") remotes::install_github(\"agdamsbo/REDCapCAST\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":null,"dir":"Reference","previous_headings":"","what":"Split REDCap repeating instruments table into multiple tables — REDCap_split","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"take output REDCap export split base table child tables repeating instrument. Metadata used determine fields included resultant table.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"","code":"REDCap_split(   records,   metadata,   primary_table_name = \"\",   forms = c(\"repeating\", \"all\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"records Exported project records. May data.frame, response, character vector containing JSON API call. metadata Project metadata (data dictionary). May data.frame, response, character vector containing JSON API call. primary_table_name Name given list element primary output table (described README.md). Ignored forms = ''. forms Indicate whether create separate tables repeating instruments forms.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"list \"data.frame\"s. number tables differ   depending forms option selected.  'repeating': one base table one     tables repeating instrument. '': data.frame instrument, regardless     whether repeating instrument .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"Paul W. Egeler, M.S., GStat","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"","code":"if (FALSE) { # Using an API call -------------------------------------------------------  library(RCurl)  # Get the records records <- postForm(   uri = api_url,     # Supply your site-specific URI   token = api_token, # Supply your own API token   content = 'record',   format = 'json',   returnFormat = 'json' )  # Get the metadata metadata <- postForm(   uri = api_url,     # Supply your site-specific URI   token = api_token, # Supply your own API token   content = 'metadata',   format = 'json' )  # Convert exported JSON strings into a list of data.frames REDCapRITS::REDCap_split(records, metadata)  # Using a raw data export -------------------------------------------------  # Get the records records <- read.csv(\"/path/to/data/ExampleProject_DATA_2018-06-03_1700.csv\")  # Get the metadata metadata <- read.csv( \"/path/to/data/ExampleProject_DataDictionary_2018-06-03.csv\")  # Split the tables REDCapRITS::REDCap_split(records, metadata)  # In conjunction with the R export script ---------------------------------  # You must set the working directory first since the REDCap data export # script contains relative file references. old <- getwd() setwd(\"/path/to/data/\")  # Run the data export script supplied by REDCap. # This will create a data.frame of your records called 'data' source(\"ExampleProject_R_2018-06-03_1700.r\")  # Get the metadatan metadata <- read.csv(\"ExampleProject_DataDictionary_2018-06-03.csv\")  # Split the tables REDCapRITS::REDCap_split(data, metadata) setwd(old) }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":null,"dir":"Reference","previous_headings":"","what":"clean_redcap_name — clean_redcap_name","title":"clean_redcap_name — clean_redcap_name","text":"Stepwise removal non-alphanumeric characters, trailing white space, substitutes spaces underscores converts lower case. Trying make different naming conventions.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"clean_redcap_name — clean_redcap_name","text":"","code":"clean_redcap_name(x)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"clean_redcap_name — clean_redcap_name","text":"x vector data frame cleaning","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"clean_redcap_name — clean_redcap_name","text":"vector data frame, format input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert single digits to words — d2w","title":"Convert single digits to words — d2w","text":"Convert single digits words","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert single digits to words — d2w","text":"","code":"d2w(x, lang = \"en\", neutrum = FALSE, everything = FALSE)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert single digits to words — d2w","text":"x data. Handle vectors, data.frames lists lang language. Danish (da) English (en), Default \"en\" neutrum numbers depending counted word everything flag also split numbers >9 single digits","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert single digits to words — d2w","text":"returns characters format input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert single digits to words — d2w","text":"","code":"d2w(c(2:8, 21)) #> [1] \"two\"   \"three\" \"four\"  \"five\"  \"six\"   \"seven\" \"eight\" \"21\"    d2w(data.frame(2:7, 3:8, 1), lang = \"da\", neutrum = TRUE) #>   X2.7 X3.8 X1 #> 1   to  tre et #> 2  tre fire et #> 3 fire  fem et #> 4  fem seks et #> 5 seks  syv et #> 6  syv otte et  ## If everything=T, also larger numbers are reduced. ## Elements in the list are same length as input d2w(list(2:8, c(2, 6, 4, 23), 2), everything = TRUE) #> [[1]] #> [1] \"two\"   \"three\" \"four\"  \"five\"  \"six\"   \"seven\" \"eight\" #>  #> [[2]] #> [1] \"two\"       \"six\"       \"four\"      \"two three\" #>  #> [[3]] #> [1] \"two\" #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/deploy_shiny.html","id":null,"dir":"Reference","previous_headings":"","what":"Deploy the Shiny app with rsconnect — deploy_shiny","title":"Deploy the Shiny app with rsconnect — deploy_shiny","text":"Deploy Shiny app rsconnect","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/deploy_shiny.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deploy the Shiny app with rsconnect — deploy_shiny","text":"","code":"deploy_shiny(path = here::here(\"app/\"), name.app = \"shiny_cast\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/deploy_shiny.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Deploy the Shiny app with rsconnect — deploy_shiny","text":"path app folder path name.app name deployed app","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/deploy_shiny.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Deploy the Shiny app with rsconnect — deploy_shiny","text":"deploy","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/deploy_shiny.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Deploy the Shiny app with rsconnect — deploy_shiny","text":"","code":"# deploy_shiny"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":null,"dir":"Reference","previous_headings":"","what":"(DEPRECATED) Data set to data dictionary function — ds2dd","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"Creates basic data dictionary skeleton. Please see `ds2dd_detailed()` advanced function.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"","code":"ds2dd(   ds,   record.id = \"record_id\",   form.name = \"basis\",   field.type = \"text\",   field.label = NULL,   include.column.names = FALSE,   metadata = metadata_names )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"ds data set record.id name column number id variable, moved first row data dictionary, character integer. Default \"record_id\". form.name vector form names, character string, length 1 length equal number variables. Default \"basis\". field.type vector field types, character string, length 1 length equal number variables. Default \"text. field.label vector form names, character string, length 1 length equal number variables. Default NULL identical field names. include.column.names Flag give detailed output including new column names original data set upload. metadata Metadata column names. Default included REDCapCAST::metadata_names.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"data.frame list data.frame vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"Migrated stRoke ds2dd(). Fits better functionality 'REDCapCAST'.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"","code":"redcapcast_data$record_id <- seq_len(nrow(redcapcast_data)) ds2dd(redcapcast_data, include.column.names=TRUE) #> $DataDictionary #>                      field_name form_name section_header field_type #> 1                     record_id     basis             NA       text #> 2             redcap_event_name     basis             NA       text #> 3      redcap_repeat_instrument     basis             NA       text #> 4        redcap_repeat_instance     basis             NA       text #> 5                           cpr     basis             NA       text #> 6                     inclusion     basis             NA       text #> 7                inclusion_time     basis             NA       text #> 8                           dob     basis             NA       text #> 9                           age     basis             NA       text #> 10                  age_integer     basis             NA       text #> 11                          sex     basis             NA       text #> 12                 cohabitation     basis             NA       text #> 13                 hypertension     basis             NA       text #> 14                     diabetes     basis             NA       text #> 15                       region     basis             NA       text #> 16 baseline_data_start_complete     basis             NA       text #> 17                 mrs_assessed     basis             NA       text #> 18                     mrs_date     basis             NA       text #> 19                    mrs_score     basis             NA       text #> 20                 mrs_complete     basis             NA       text #> 21               event_datetime     basis             NA       text #> 22                    event_age     basis             NA       text #> 23                   event_type     basis             NA       text #> 24           new_event_complete     basis             NA       text #>                     field_label select_choices_or_calculations field_note #> 1                     record_id                             NA         NA #> 2             redcap_event_name                             NA         NA #> 3      redcap_repeat_instrument                             NA         NA #> 4        redcap_repeat_instance                             NA         NA #> 5                           cpr                             NA         NA #> 6                     inclusion                             NA         NA #> 7                inclusion_time                             NA         NA #> 8                           dob                             NA         NA #> 9                           age                             NA         NA #> 10                  age_integer                             NA         NA #> 11                          sex                             NA         NA #> 12                 cohabitation                             NA         NA #> 13                 hypertension                             NA         NA #> 14                     diabetes                             NA         NA #> 15                       region                             NA         NA #> 16 baseline_data_start_complete                             NA         NA #> 17                 mrs_assessed                             NA         NA #> 18                     mrs_date                             NA         NA #> 19                    mrs_score                             NA         NA #> 20                 mrs_complete                             NA         NA #> 21               event_datetime                             NA         NA #> 22                    event_age                             NA         NA #> 23                   event_type                             NA         NA #> 24           new_event_complete                             NA         NA #>    text_validation_type_or_show_slider_number text_validation_min #> 1                                          NA                  NA #> 2                                          NA                  NA #> 3                                          NA                  NA #> 4                                          NA                  NA #> 5                                          NA                  NA #> 6                                          NA                  NA #> 7                                          NA                  NA #> 8                                          NA                  NA #> 9                                          NA                  NA #> 10                                         NA                  NA #> 11                                         NA                  NA #> 12                                         NA                  NA #> 13                                         NA                  NA #> 14                                         NA                  NA #> 15                                         NA                  NA #> 16                                         NA                  NA #> 17                                         NA                  NA #> 18                                         NA                  NA #> 19                                         NA                  NA #> 20                                         NA                  NA #> 21                                         NA                  NA #> 22                                         NA                  NA #> 23                                         NA                  NA #> 24                                         NA                  NA #>    text_validation_max identifier branching_logic required_field #> 1                   NA         NA              NA             NA #> 2                   NA         NA              NA             NA #> 3                   NA         NA              NA             NA #> 4                   NA         NA              NA             NA #> 5                   NA         NA              NA             NA #> 6                   NA         NA              NA             NA #> 7                   NA         NA              NA             NA #> 8                   NA         NA              NA             NA #> 9                   NA         NA              NA             NA #> 10                  NA         NA              NA             NA #> 11                  NA         NA              NA             NA #> 12                  NA         NA              NA             NA #> 13                  NA         NA              NA             NA #> 14                  NA         NA              NA             NA #> 15                  NA         NA              NA             NA #> 16                  NA         NA              NA             NA #> 17                  NA         NA              NA             NA #> 18                  NA         NA              NA             NA #> 19                  NA         NA              NA             NA #> 20                  NA         NA              NA             NA #> 21                  NA         NA              NA             NA #> 22                  NA         NA              NA             NA #> 23                  NA         NA              NA             NA #> 24                  NA         NA              NA             NA #>    custom_alignment question_number matrix_group_name matrix_ranking #> 1                NA              NA                NA             NA #> 2                NA              NA                NA             NA #> 3                NA              NA                NA             NA #> 4                NA              NA                NA             NA #> 5                NA              NA                NA             NA #> 6                NA              NA                NA             NA #> 7                NA              NA                NA             NA #> 8                NA              NA                NA             NA #> 9                NA              NA                NA             NA #> 10               NA              NA                NA             NA #> 11               NA              NA                NA             NA #> 12               NA              NA                NA             NA #> 13               NA              NA                NA             NA #> 14               NA              NA                NA             NA #> 15               NA              NA                NA             NA #> 16               NA              NA                NA             NA #> 17               NA              NA                NA             NA #> 18               NA              NA                NA             NA #> 19               NA              NA                NA             NA #> 20               NA              NA                NA             NA #> 21               NA              NA                NA             NA #> 22               NA              NA                NA             NA #> 23               NA              NA                NA             NA #> 24               NA              NA                NA             NA #>    field_annotation #> 1                NA #> 2                NA #> 3                NA #> 4                NA #> 5                NA #> 6                NA #> 7                NA #> 8                NA #> 9                NA #> 10               NA #> 11               NA #> 12               NA #> 13               NA #> 14               NA #> 15               NA #> 16               NA #> 17               NA #> 18               NA #> 19               NA #> 20               NA #> 21               NA #> 22               NA #> 23               NA #> 24               NA #>  #> $`Column names` #>  [1] \"record_id\"                    \"redcap_event_name\"            #>  [3] \"redcap_repeat_instrument\"     \"redcap_repeat_instance\"       #>  [5] \"cpr\"                          \"inclusion\"                    #>  [7] \"inclusion_time\"               \"dob\"                          #>  [9] \"age\"                          \"age_integer\"                  #> [11] \"sex\"                          \"cohabitation\"                 #> [13] \"hypertension\"                 \"diabetes\"                     #> [15] \"region\"                       \"baseline_data_start_complete\" #> [17] \"mrs_assessed\"                 \"mrs_date\"                     #> [19] \"mrs_score\"                    \"mrs_complete\"                 #> [21] \"event_datetime\"               \"event_age\"                    #> [23] \"event_type\"                   \"new_event_complete\"           #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract data from stata file for data dictionary — ds2dd_detailed","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"Extract data stata file data dictionary","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"","code":"ds2dd_detailed(   data,   add.auto.id = FALSE,   date.format = \"dmy\",   form.name = NULL,   field.type = NULL,   field.label = NULL,   field.label.attr = \"label\",   field.validation = NULL,   metadata = metadata_names,   validate.time = FALSE,   time.var.sel.pos = \"[Tt]i[d(me)]\",   time.var.sel.neg = \"[Dd]at[eo]\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"data data frame add.auto.id flag add id column date.format date format, character string. ymd/dmy/mdy. dafault dmy. form.name manually specify form name(s). Vector length 1 ncol(data). Default NULL \"data\" used. field.type manually specify field type(s). Vector length 1 ncol(data). Default NULL \"text\" used everything factors, wil get \"radio\". field.label manually specify field label(s). Vector length 1 ncol(data). Default NULL colnames(data) used attribute `field.label.attr` haven_labelled data set (imported .dta file `haven::read_dta()`). field.label.attr attribute name named labels haven_labelled data set (imported .dta file `haven::read_dta()`. Default \"label\" field.validation manually specify field validation(s). Vector length 1 ncol(data). Default NULL `levels()` used factors attribute `factor.labels.attr` haven_labelled data set (imported .dta file `haven::read_dta()`). metadata redcap metadata headings. Default REDCapCAST:::metadata_names. validate.time Flag validate guessed time columns time.var.sel.pos Positive selection regex string passed `gues_time_only_filter()` sel.pos. time.var.sel.neg Negative selection regex string passed `gues_time_only_filter()` sel.neg.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"list length 2","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"function natural development ds2dd() function. assumes first column ID-column. checks. Please, always inspect data dictionary upload. Ensure, data set formatted much information possible. `field.type` can supplied","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"","code":"data <- redcapcast_data data |> ds2dd_detailed(validate.time = TRUE) #> $is.POSIX #> # A tibble: 19 × 2 #>    inclusion_time event_datetime      #>    <time>         <dttm>              #>  1 12:38:49       NA                  #>  2 10:38:57       NA                  #>  3       NA       NA                  #>  4       NA       2024-01-18 12:49:42 #>  5 12:01:07       NA                  #>  6       NA       NA                  #>  7       NA       NA                  #>  8       NA       2024-01-18 12:49:58 #>  9       NA       2024-01-18 12:50:01 #> 10       NA       2024-01-18 12:50:05 #> 11       NA       2024-01-18 12:50:07 #> 12       NA       2024-01-18 12:50:09 #> 13 20:39:19       NA                  #> 14       NA       NA                  #> 15       NA       2024-01-18 12:50:19 #> 16       NA       2024-01-18 12:50:22 #> 17       NA       2024-01-18 12:50:24 #> 18 08:50:31       NA                  #> 19 08:49:28       NA                  #>  #> $is.datetime #> # A tibble: 19 × 1 #>    event_datetime      #>    <dttm>              #>  1 NA                  #>  2 NA                  #>  3 NA                  #>  4 2024-01-18 12:49:42 #>  5 NA                  #>  6 NA                  #>  7 NA                  #>  8 2024-01-18 12:49:58 #>  9 2024-01-18 12:50:01 #> 10 2024-01-18 12:50:05 #> 11 2024-01-18 12:50:07 #> 12 2024-01-18 12:50:09 #> 13 NA                  #> 14 NA                  #> 15 2024-01-18 12:50:19 #> 16 2024-01-18 12:50:22 #> 17 2024-01-18 12:50:24 #> 18 NA                  #> 19 NA                  #>  #> $is.time_only #> # A tibble: 19 × 1 #>    inclusion_time #>    <time>         #>  1 12:38:49       #>  2 10:38:57       #>  3       NA       #>  4       NA       #>  5 12:01:07       #>  6       NA       #>  7       NA       #>  8       NA       #>  9       NA       #> 10       NA       #> 11       NA       #> 12       NA       #> 13 20:39:19       #> 14       NA       #> 15       NA       #> 16       NA       #> 17       NA       #> 18 08:50:31       #> 19 08:49:28       #>  data |> ds2dd_detailed() #> $data #> # A tibble: 19 × 24 #>    record_id redcap_event_name redcap_repeat_instrument redcap_repeat_instance #>        <dbl> <chr>             <chr>                                     <dbl> #>  1         1 inclusion         NA                                           NA #>  2         2 inclusion         NA                                           NA #>  3         2 follow1           NA                                           NA #>  4         2 follow1           New Event (?)                                 1 #>  5         3 inclusion         NA                                           NA #>  6         3 follow1           NA                                           NA #>  7         3 follow2           NA                                           NA #>  8         3 follow1           New Event (?)                                 1 #>  9         3 follow1           New Event (?)                                 2 #> 10         3 follow2           New Event (?)                                 1 #> 11         3 follow2           New Event (?)                                 2 #> 12         3 follow2           New Event (?)                                 3 #> 13         4 inclusion         NA                                           NA #> 14         4 follow2           NA                                           NA #> 15         4 follow2           New Event (?)                                 1 #> 16         4 follow2           New Event (?)                                 2 #> 17         4 follow2           New Event (?)                                 3 #> 18         5 inclusion         NA                                           NA #> 19         6 inclusion         NA                                           NA #> # ℹ 20 more variables: cpr <chr>, inclusion <date>, inclusion_time <chr>, #> #   dob <date>, age <dbl>, age_integer <dbl>, sex <chr>, cohabitation <chr>, #> #   hypertension <chr>, diabetes <chr>, region <chr>, #> #   baseline_data_start_complete <chr>, mrs_assessed <chr>, mrs_date <date>, #> #   mrs_score <dbl>, mrs_complete <chr>, event_datetime <dttm>, #> #   event_age <lgl>, event_type <chr>, new_event_complete <chr> #>  #> $meta #> # A tibble: 24 × 18 #>    field_name               form_name section_header field_type field_label      #>    <chr>                    <chr>     <lgl>          <chr>      <chr>            #>  1 record_id                data      NA             text       record_id        #>  2 redcap_event_name        data      NA             text       redcap_event_na… #>  3 redcap_repeat_instrument data      NA             text       redcap_repeat_i… #>  4 redcap_repeat_instance   data      NA             text       redcap_repeat_i… #>  5 cpr                      data      NA             text       cpr              #>  6 inclusion                data      NA             text       inclusion        #>  7 inclusion_time           data      NA             text       inclusion_time   #>  8 dob                      data      NA             text       dob              #>  9 age                      data      NA             text       age              #> 10 age_integer              data      NA             text       age_integer      #> # ℹ 14 more rows #> # ℹ 13 more variables: select_choices_or_calculations <lgl>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> #>  iris |> ds2dd_detailed(add.auto.id = TRUE) #> A default id column has been added #> $data #> # A tibble: 150 × 6 #>    default_trial_id sepal.length sepal.width petal.length petal.width species #>               <int>        <dbl>       <dbl>        <dbl>       <dbl> <fct>   #>  1                1          5.1         3.5          1.4         0.2 setosa  #>  2                2          4.9         3            1.4         0.2 setosa  #>  3                3          4.7         3.2          1.3         0.2 setosa  #>  4                4          4.6         3.1          1.5         0.2 setosa  #>  5                5          5           3.6          1.4         0.2 setosa  #>  6                6          5.4         3.9          1.7         0.4 setosa  #>  7                7          4.6         3.4          1.4         0.3 setosa  #>  8                8          5           3.4          1.5         0.2 setosa  #>  9                9          4.4         2.9          1.4         0.2 setosa  #> 10               10          4.9         3.1          1.5         0.1 setosa  #> # ℹ 140 more rows #>  #> $meta #> # A tibble: 6 × 18 #>   field_name       form_name section_header field_type field_label      #>   <chr>            <chr>     <lgl>          <chr>      <chr>            #> 1 default_trial_id data      NA             text       default_trial_id #> 2 sepal.length     data      NA             text       Sepal.Length     #> 3 sepal.width      data      NA             text       Sepal.Width      #> 4 petal.length     data      NA             text       Petal.Length     #> 5 petal.width      data      NA             text       Petal.Width      #> 6 species          data      NA             radio      Species          #> # ℹ 13 more variables: select_choices_or_calculations <chr>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> #>  mtcars |> ds2dd_detailed(add.auto.id = TRUE) #> A default id column has been added #> $data #> # A tibble: 32 × 12 #>    default_trial_id   mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear #>               <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1                1  21       6  160    110  3.9   2.62  16.5     0     1     4 #>  2                2  21       6  160    110  3.9   2.88  17.0     0     1     4 #>  3                3  22.8     4  108     93  3.85  2.32  18.6     1     1     4 #>  4                4  21.4     6  258    110  3.08  3.22  19.4     1     0     3 #>  5                5  18.7     8  360    175  3.15  3.44  17.0     0     0     3 #>  6                6  18.1     6  225    105  2.76  3.46  20.2     1     0     3 #>  7                7  14.3     8  360    245  3.21  3.57  15.8     0     0     3 #>  8                8  24.4     4  147.    62  3.69  3.19  20       1     0     4 #>  9                9  22.8     4  141.    95  3.92  3.15  22.9     1     0     4 #> 10               10  19.2     6  168.   123  3.92  3.44  18.3     1     0     4 #> # ℹ 22 more rows #> # ℹ 1 more variable: carb <dbl> #>  #> $meta #> # A tibble: 12 × 18 #>    field_name       form_name section_header field_type field_label      #>    <chr>            <chr>     <lgl>          <chr>      <chr>            #>  1 default_trial_id data      NA             text       default_trial_id #>  2 mpg              data      NA             text       mpg              #>  3 cyl              data      NA             text       cyl              #>  4 disp             data      NA             text       disp             #>  5 hp               data      NA             text       hp               #>  6 drat             data      NA             text       drat             #>  7 wt               data      NA             text       wt               #>  8 qsec             data      NA             text       qsec             #>  9 vs               data      NA             text       vs               #> 10 am               data      NA             text       am               #> 11 gear             data      NA             text       gear             #> 12 carb             data      NA             text       carb             #> # ℹ 13 more variables: select_choices_or_calculations <lgl>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":null,"dir":"Reference","previous_headings":"","what":"Secure API key storage and data acquisition in one — easy_redcap","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"Secure API key storage data acquisition one","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"","code":"easy_redcap(project.name, widen.data = TRUE, uri, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"project.name name current project (key storage `keyring::key_set()`, using default keyring) widen.data argument widen exported data uri REDCap database API uri ... arguments passed `REDCapCAST::read_redcap_tables()`","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"data.frame list depending widen.data","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper to import files correctly — file_extension","title":"Helper to import files correctly — file_extension","text":"Helper import files correctly","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper to import files correctly — file_extension","text":"","code":"file_extension(filenames)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper to import files correctly — file_extension","text":"filenames file names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper to import files correctly — file_extension","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper to import files correctly — file_extension","text":"","code":"file_extension(list.files(here::here(\"\"))[[2]])[[1]] #> [1] \"md\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"focused_metadata — focused_metadata","title":"focused_metadata — focused_metadata","text":"Extracts limited metadata variables dataset","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"focused_metadata — focused_metadata","text":"","code":"focused_metadata(metadata, vars_in_data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"focused_metadata — focused_metadata","text":"metadata dataframe containing metadata vars_in_data Vector variable names dataset","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"focused_metadata — focused_metadata","text":"dataframe containing metadata variables dataset","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"Retrieve project API key stored, , set retrieve","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"","code":"get_api_key(key.name)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"key.name character vector key name","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the id name — get_id_name","title":"Get the id name — get_id_name","text":"Get id name","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the id name — get_id_name","text":"","code":"get_id_name(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the id name — get_id_name","text":"data data frame list","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the id name — get_id_name","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":null,"dir":"Reference","previous_headings":"","what":"Try at determining which are true time only variables — guess_time_only_filter","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"just try guessing data type based data class column names hoping tiny bit naming consistency. R include time-data format natively, \"hms\" class `readr` used. converted character class REDCap upload.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"","code":"guess_time_only_filter(   data,   validate = FALSE,   sel.pos = \"[Tt]i[d(me)]\",   sel.neg = \"[Dd]at[eo]\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"data data set validate flag output validation data. output list. sel.pos Positive selection regex string sel.neg Negative selection regex string","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"character vector list depending `validate` flag.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"","code":"data <- redcapcast_data data |> guess_time_only_filter() #> [1] \"inclusion_time\" data |> guess_time_only_filter(validate = TRUE) |> lapply(head) #> $is.POSIX #> # A tibble: 6 × 2 #>   inclusion_time event_datetime      #>   <time>         <dttm>              #> 1 12:38:49       NA                  #> 2 10:38:57       NA                  #> 3       NA       NA                  #> 4       NA       2024-01-18 12:49:42 #> 5 12:01:07       NA                  #> 6       NA       NA                  #>  #> $is.datetime #> # A tibble: 6 × 1 #>   event_datetime      #>   <dttm>              #> 1 NA                  #> 2 NA                  #> 3 NA                  #> 4 2024-01-18 12:49:42 #> 5 NA                  #> 6 NA                  #>  #> $is.time_only #> # A tibble: 6 × 1 #>   inclusion_time #>   <time>         #> 1 12:38:49       #> 2 10:38:57       #> 3       NA       #> 4       NA       #> 5 12:01:07       #> 6       NA       #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":null,"dir":"Reference","previous_headings":"","what":"Change ","title":"Change ","text":"Change \"hms\" \"character\" REDCap upload.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change ","text":"","code":"hms2character(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change ","text":"data data set","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change ","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Change ","text":"","code":"data <- redcapcast_data ## data |> time_only_correction() |> hms2character()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if repeatable or longitudinal — is_repeated_longitudinal","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"Test repeatable longitudinal","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"","code":"is_repeated_longitudinal(   data,   generics = c(\"redcap_event_name\", \"redcap_repeat_instrument\", \"redcap_repeat_instance\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"data data set generics default \"redcap_event_name\", \"redcap_repeat_instrument\" \"redcap_repeat_instance\"","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"logical","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"","code":"is_repeated_longitudinal(c(\"record_id\", \"age\", \"record_id\", \"gender\")) #> [1] FALSE is_repeated_longitudinal(redcapcast_data) #> [1] TRUE is_repeated_longitudinal(list(redcapcast_data)) #> [1] TRUE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":null,"dir":"Reference","previous_headings":"","what":"Completion marking based on completed upload — mark_complete","title":"Completion marking based on completed upload — mark_complete","text":"Completion marking based completed upload","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Completion marking based on completed upload — mark_complete","text":"","code":"mark_complete(upload, ls)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Completion marking based on completed upload — mark_complete","text":"upload output list `REDCapR::redcap_write()` ls output list `ds2dd_detailed()`","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Completion marking based on completed upload — mark_complete","text":"list `REDCapR::redcap_write()` results","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":null,"dir":"Reference","previous_headings":"","what":"Match fields to forms — match_fields_to_form","title":"Match fields to forms — match_fields_to_form","text":"Match fields forms","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Match fields to forms — match_fields_to_form","text":"","code":"match_fields_to_form(metadata, vars_in_data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Match fields to forms — match_fields_to_form","text":"metadata data frame containing field names form names vars_in_data character vector variable names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Match fields to forms — match_fields_to_form","text":"data frame containing field names form names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html","id":null,"dir":"Reference","previous_headings":"","what":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","title":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","text":"mtcars dataset slightly modified use Shiny app upload demonstration","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","text":"","code":"data(mtcars_redcap)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","text":"data frame 13 variables: record_id ID, numeric mpg ID, numeric cyl ID, numeric disp ID, numeric hp ID, numeric drat ID, numeric wt ID, numeric qsec ID, numeric vs ID, numeric ID, numeric gear ID, numeric carb ID, numeric name original rownames, charater","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/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/REDCapCAST/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/REDCapCAST/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/REDCapCAST/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/REDCapCAST/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/REDCapCAST/reference/read_redcap_instrument.html","id":null,"dir":"Reference","previous_headings":"","what":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"Convenience function download complete instrument, using token storage keyring.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"","code":"read_redcap_instrument(   key,   uri,   instrument,   raw_or_label = \"raw\",   id_name = \"record_id\",   records = NULL )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"key key name standard keyring token retrieval. uri REDCap database API uri instrument instrument name raw_or_label raw label passed `REDCapR::redcap_read()` id_name id variable name. Default \"record_id\". records specify records download. Index numbers. Numeric vector.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":null,"dir":"Reference","previous_headings":"","what":"Download REDCap data — read_redcap_tables","title":"Download REDCap data — read_redcap_tables","text":"Implementation REDCap_split focused data acquisition approach using REDCapR::redcap_read downloading specified fields, forms /events using built-focused_metadata including clean-. Works classical longitudinal projects without repeating instruments.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download REDCap data — read_redcap_tables","text":"","code":"read_redcap_tables(   uri,   token,   records = NULL,   fields = NULL,   events = NULL,   forms = NULL,   raw_or_label = \"label\",   split_forms = \"all\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download REDCap data — read_redcap_tables","text":"uri REDCap database API uri token API token records records download fields fields download events events download forms forms download raw_or_label raw label tags split_forms Whether split \"repeating\" \"\" forms, default .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download REDCap data — read_redcap_tables","text":"list instruments","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download REDCap data — read_redcap_tables","text":"","code":"# Examples will be provided later"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":null,"dir":"Reference","previous_headings":"","what":"Redcap Wider — redcap_wider","title":"Redcap Wider — redcap_wider","text":"Converts list REDCap data frames long wide format. Handles longitudinal projects, yet repeated instruments.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Redcap Wider — redcap_wider","text":"","code":"redcap_wider(   data,   event.glue = \"{.value}_{redcap_event_name}\",   inst.glue = \"{.value}_{redcap_repeat_instance}\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Redcap Wider — redcap_wider","text":"data list data frames. event.glue dplyr::glue string repeated events naming inst.glue dplyr::glue string repeated instruments naming","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Redcap Wider — redcap_wider","text":"list data frames wide format.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Redcap Wider — redcap_wider","text":"","code":"# Longitudinal list1 <- list(data.frame(record_id = c(1,2,1,2), redcap_event_name = c(\"baseline\", \"baseline\", \"followup\", \"followup\"), age = c(25,26,27,28)), data.frame(record_id = c(1,2), redcap_event_name = c(\"baseline\", \"baseline\"), gender = c(\"male\", \"female\"))) redcap_wider(list1) #> Joining with `by = join_by(record_id)` #>   record_id age_baseline age_followup gender #> 1         1           25           27   male #> 2         2           26           28 female # Simpel with two instruments list2 <- list(data.frame(record_id = c(1,2), age = c(25,26)), data.frame(record_id = c(1,2), gender = c(\"male\", \"female\"))) redcap_wider(list2) #> Joining with `by = join_by(record_id)` #>   record_id age gender #> 1         1  25   male #> 2         2  26 female # Simple with single instrument list3 <- list(data.frame(record_id = c(1,2), age = c(25,26))) redcap_wider(list3) #>   record_id age #> 1         1  25 #> 2         2  26 # Longitudinal with repeatable instruments list4 <- list(data.frame(record_id = c(1,2,1,2), redcap_event_name = c(\"baseline\", \"baseline\", \"followup\", \"followup\"), age = c(25,26,27,28)), data.frame(record_id = c(1,1,1,1,2,2,2,2), redcap_event_name = c(\"baseline\", \"baseline\", \"followup\", \"followup\", \"baseline\", \"baseline\", \"followup\", \"followup\"), redcap_repeat_instrument = \"walk\", redcap_repeat_instance=c(1,2,1,2,1,2,1,2), dist = c(40, 32, 25, 33, 28, 24, 23, 36)), data.frame(record_id = c(1,2), redcap_event_name = c(\"baseline\", \"baseline\"), gender = c(\"male\", \"female\"))) redcap_wider(list4) #> Joining with `by = join_by(record_id)` #> Joining with `by = join_by(record_id)` #>   record_id age_baseline age_followup dist_1_baseline dist_1_followup #> 1         1           25           27              40              25 #> 2         2           26           28              28              23 #>   dist_2_baseline dist_2_followup gender #> 1              32              33   male #> 2              24              36 female"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Data set for demonstration — redcapcast_data","title":"Data set for demonstration — redcapcast_data","text":"small dataset REDCap database demonstrational purposes. Contains synthetic data.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data set for demonstration — redcapcast_data","text":"","code":"data(redcapcast_data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data set for demonstration — redcapcast_data","text":"data frame 22 variables: record_id ID, numeric redcap_event_name Event name, character redcap_repeat_instrument Repeat instrument, character redcap_repeat_instance Repeat instance, numeric cpr CPR number, character inclusion Inclusion date, Date inclusion_time Inclusion time, hms dob Date birth, Date age Age decimal, numeric age_integer Age integer, numeric sex Legal sex, character cohabitation Cohabitation status, character hypertension Hypertension, character diabetes diabetes, character region region, character baseline_data_start_complete Completed, character mrs_assessed mRS Assessed, character mrs_date Assesment date, Date mrs_score Categorical score, numeric mrs_complete Complete, numeric event_datetime Event datetime, POSIXct event_age Age time event, numeric event_type Event type, character new_event_complete Completed, character","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_meta.html","id":null,"dir":"Reference","previous_headings":"","what":"REDCap metadata from data base — redcapcast_meta","title":"REDCap metadata from data base — redcapcast_meta","text":"metadata dataset REDCap database demonstrational purposes.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_meta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"REDCap metadata from data base — redcapcast_meta","text":"","code":"data(redcapcast_meta)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_meta.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"REDCap metadata from data base — redcapcast_meta","text":"data frame 22 variables: field_name field_name, character form_name form_name, character section_header section_header, character field_type field_type, character field_label field_label, character select_choices_or_calculations select_choices_or_calculations, character field_note field_note, character text_validation_type_or_show_slider_number text_validation_type_or_show_slider_number, character text_validation_min text_validation_min, character text_validation_max text_validation_max, character identifier identifier, character branching_logic branching_logic, character required_field required_field, character custom_alignment custom_alignment, character question_number question_number, character matrix_group_name matrix_group_name, character matrix_ranking matrix_ranking, character field_annotation field_annotation, character","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":null,"dir":"Reference","previous_headings":"","what":"Sanitize list of data frames — sanitize_split","title":"Sanitize list of data frames — sanitize_split","text":"Removing empty rows","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sanitize list of data frames — sanitize_split","text":"","code":"sanitize_split(   l,   generic.names = c(\"redcap_event_name\", \"redcap_repeat_instrument\",     \"redcap_repeat_instance\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sanitize list of data frames — sanitize_split","text":"l list data frames. generic.names vector generic names excluded.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sanitize list of data frames — sanitize_split","text":"list data frames generic names excluded.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/server_factory.html","id":null,"dir":"Reference","previous_headings":"","what":"Shiny server factory — server_factory","title":"Shiny server factory — server_factory","text":"Shiny server factory","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/server_factory.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shiny server factory — server_factory","text":"","code":"server_factory()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/server_factory.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shiny server factory — server_factory","text":"shiny server","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":null,"dir":"Reference","previous_headings":"","what":"Launch the included Shiny-app for database casting and upload — shiny_cast","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"Launch included Shiny-app database casting upload","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"","code":"shiny_cast()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"shiny app","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"","code":"# shiny_cast()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":null,"dir":"Reference","previous_headings":"","what":"Split a data frame into separate tables for each form — split_non_repeating_forms","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"Split data frame separate tables form","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"","code":"split_non_repeating_forms(table, universal_fields, fields)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"table data frame universal_fields character vector fields included every table fields two-column matrix containing names fields included form","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"list data frames, one non-repeating form","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"","code":"# Create a table table <- data.frame(   id = c(1, 2, 3, 4, 5),   form_a_name = c(\"John\", \"Alice\", \"Bob\", \"Eve\", \"Mallory\"),   form_a_age = c(25, 30, 25, 15, 20),   form_b_name = c(\"John\", \"Alice\", \"Bob\", \"Eve\", \"Mallory\"),   form_b_gender = c(\"M\", \"F\", \"M\", \"F\", \"F\") )  # Create the universal fields universal_fields <- c(\"id\")  # Create the fields fields <- matrix(   c(     \"form_a_name\", \"form_a\",     \"form_a_age\", \"form_a\",     \"form_b_name\", \"form_b\",     \"form_b_gender\", \"form_b\"   ),   ncol = 2, byrow = TRUE )  # Split the table split_non_repeating_forms(table, universal_fields, fields) #> $form_a_age #>   id #> 1  1 #> 2  2 #> 3  3 #> 4  4 #> 5  5 #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":null,"dir":"Reference","previous_headings":"","what":"Extended string splitting — strsplitx","title":"Extended string splitting — strsplitx","text":"Can used substitute base function. Main claim fame easing split around defined delimiter, see example.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extended string splitting — strsplitx","text":"","code":"strsplitx(x, split, type = \"classic\", perl = FALSE, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extended string splitting — strsplitx","text":"x data split delimiter type Split type. Can c(\"classic\", \"\", \"\", \"around\") perl perl param strsplit() ... additional parameters passed base strsplit handling splits","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extended string splitting — strsplitx","text":"list","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extended string splitting — strsplitx","text":"","code":"test <- c(\"12 months follow-up\", \"3 steps\", \"mRS 6 weeks\", \"Counting to 231 now\") strsplitx(test, \"[0-9]\", type = \"around\") #> [[1]] #> [1] \"1\"                 \"2\"                 \" months follow-up\" #>  #> [[2]] #> [1] \"3\"      \" steps\" #>  #> [[3]] #> [1] \"mRS \"   \"6\"      \" weeks\" #>  #> [[4]] #> [1] \"Counting to \" \"2\"            \"3\"            \"1\"            \" now\"         #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":null,"dir":"Reference","previous_headings":"","what":"Correction based on time_only_filter function. Introduces new class for easier\nvalidation labelling. — time_only_correction","title":"Correction based on time_only_filter function. Introduces new class for easier\nvalidation labelling. — time_only_correction","text":"Dependens data class \"hms\" introduced `guess_time_only_filter()` converts ","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correction based on time_only_filter function. Introduces new class for easier\nvalidation labelling. — time_only_correction","text":"","code":"time_only_correction(data, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correction based on time_only_filter function. Introduces new class for easier\nvalidation labelling. — time_only_correction","text":"data data set ... arguments passed `guess_time_only_filter()`","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correction based on time_only_filter function. Introduces new class for easier\nvalidation labelling. — time_only_correction","text":"tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correction based on time_only_filter function. Introduces new class for easier\nvalidation labelling. — time_only_correction","text":"","code":"data <- redcapcast_data ## data |> time_only_correction()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ui_factory.html","id":null,"dir":"Reference","previous_headings":"","what":"UI factory for shiny app — ui_factory","title":"UI factory for shiny app — ui_factory","text":"UI factory shiny app","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ui_factory.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI factory for shiny app — ui_factory","text":"","code":"ui_factory()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ui_factory.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"UI factory for shiny app — ui_factory","text":"shiny ui","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-2-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 24.2.1","text":"Fix: ds2dd(): uses correct default dd column names. deprecated. Fix: easy_redcap(): fixed actually allow project naming. also specifically asks uri. widening updated work. Fix: redcap_wider(): updated accept formats allow handling simple projects without repeating instruments longitudinal. Fix: read_redcap_tables(): now handles non-longitudinal project without repeatable instruments. NEW: ds2dd_detailed(): extension ds2dd(), serves preserve much metadata possible automatically. Depends group helper functions also introduced. special note guess_time_only_filter(), try guess columns/variables formatted time formats. Supports hms time format. DETAILED INSTRUCTION VIGNETTE PENDING. NEW: read_redcap_instrument() convenience function retrieve complete instrument. Goes little focused approach. DETAILED INSTRUCTION PENDING.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"other-24-2-1","dir":"Changelog","previous_headings":"","what":"Other","title":"REDCapCAST 24.2.1","text":"believe renv now added runs correctly. clone, renv::restore() install necessary package modify package.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"whishes-before-cran-release-24-2-1","dir":"Changelog","previous_headings":"","what":"Whishes before CRAN release","title":"REDCapCAST 24.2.1","text":"Vignette ds2dd_detailed() Tests ds2dd_detailed() Tests new functions.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2411","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.1.1","title":"REDCapCAST 24.1.1","text":"CRAN release: 2024-01-09","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-1-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 24.1.1","text":"Fix: read_redcap_tables(): checking form names based data dictionary allow handling non-longitudinal projects. Prints invalid form names invalid event names. invalid form names supplied REDCapR::redcap_read() (backbone), forms exported, want focused approach. Invalid event names give output rather peculiar formatting. Checking field names validity also added.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-23121","dir":"Changelog","previous_headings":"","what":"REDCapCAST 23.12.1","title":"REDCapCAST 23.12.1","text":"CRAN release: 2023-12-20 One new function ease secure dataset retrieval bug fixes.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-23-12-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 23.12.1","text":"New: easy_redcap() function ease retrieval dataset read_redcap_tables() keyring-package based key storage, handles secure API set, storage retrieval. Relies small helper function, get_api_key(), wraps relevant keyring-functions. Includes option cast data wide format flag widen.data. Fix: REDCap_split(): using function , supplying data set check boxes fail metadata supplied tibble. Metadata now converted data.frame. Fixed. Fix: read_redcap_tables(): fixed bug supplying events.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2362","dir":"Changelog","previous_headings":"","what":"REDCapCAST 23.6.2","title":"REDCapCAST 23.6.2","text":"CRAN release: 2023-07-04 version marks introduction helper functions handle database creation.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-23-6-2","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 23.6.2","text":"New: ds2dd() function migrating stRoke-package. Assists building data dictionary REDCap dataset. New: strsplitx() function ease string splitting extension base::strsplit(). Inspiration https://stackoverflow.com//11014253/21019325 https://www.r-bloggers.com/2018/04/strsplit--keeping--delimiter/. New: d2n() function converts single digits written numbers. Used sanitize variable form names REDCap database creation. universal number word suggest english::word() xfun::numbers_to_words(), though testing .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2361","dir":"Changelog","previous_headings":"","what":"REDCapCAST 23.6.1","title":"REDCapCAST 23.6.1","text":"CRAN release: 2023-06-06","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-23-6-1","dir":"Changelog","previous_headings":"","what":"Documentation:","title":"REDCapCAST 23.6.1","text":"Updated description. Look! hex icon! Heading CRAN.","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-23-4-1","dir":"Changelog","previous_headings":"","what":"Documentation:","title":"REDCapCAST 23.4.1","text":"Aiming CRAN","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-23-3-2","dir":"Changelog","previous_headings":"","what":"Documentation:","title":"REDCapCAST 23.3.2","text":"Page added. Vignettes follow. GithubActions tests added code coverage assessed. Badge galore..","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"new-name-redcapcast-23-3-1","dir":"Changelog","previous_headings":"","what":"New name: REDCapCAST","title":"REDCapCAST 23.3.1","text":"reflect new functions limitation working R, changed naming fork, still, course, maintaining status fork. versioning moved monthly naming convention. main goal package keep option export defined subset whole dataset REDCap server made possible REDCapR::redcap_read() function, combine work put REDCapRITS package handling longitudinal projects /projects repeated instruments.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-23-3-1","dir":"Changelog","previous_headings":"","what":"Functions:","title":"REDCapCAST 23.3.1","text":"read_redcap_tables() NEW: function mainly implementation combined use REDCapR::readcap_read() REDCap_split() maintain focused nature REDCapR::readcap_read(), download specified data. Also implements tests valid form names event names. usual fall-back solution get data. redcap_wider() NEW: function pivots long data frames read_redcap_tables() using tidyr::pivot_wider(). focused_metadata() NEW: hidden helper function enable focused data acquisition approach handle subset metadata corresponding focused dataset.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"notes-23-3-1","dir":"Changelog","previous_headings":"","what":"Notes:","title":"REDCapCAST 23.3.1","text":"metadata handling IMPROVED: improved handling different column names matadata (DataDictionary) REDCap dependent whether acquired thorugh api og downloaded server.","code":""}]
+[{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . 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. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. Developers use GNU GPL protect rights two steps: (1) assert copyright software, (2) offer License giving legal permission copy, distribute /modify . developers’ authors’ protection, GPL clearly explains warranty free software. users’ authors’ sake, GPL requires modified versions marked changed, problems attributed erroneously authors previous versions. devices designed deny users access install run modified versions software inside , although manufacturer can . fundamentally incompatible aim protecting users’ freedom change software. systematic pattern abuse occurs area products individuals use, precisely unacceptable. Therefore, designed version GPL prohibit practice products. problems arise substantially domains, stand ready extend provision domains future versions GPL, needed protect freedom users. Finally, every program threatened constantly software patents. States allow patents restrict development use software general-purpose computers, , wish avoid special danger patents applied free program make effectively proprietary. prevent , GPL assures patents used render program non-free. precise terms conditions copying, distribution modification follow.","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":"id_0-definitions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"0. Definitions","title":"GNU General Public License","text":"“License” refers version 3 GNU 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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Source Code","title":"GNU General Public License","text":"“source code” work means preferred form work making modifications . “Object code” means non-source form work. “Standard Interface” means interface either official standard defined recognized standards body, , case interfaces specified particular programming language, one widely used among developers working language. “System Libraries” executable work include anything, work whole, () included normal form packaging Major Component, part Major Component, (b) serves enable use work Major Component, implement Standard Interface implementation available public source code form. “Major Component”, context, means major essential component (kernel, window system, ) specific operating system () executable work runs, compiler used produce work, object code interpreter used run . “Corresponding Source” work object code form means source code needed generate, install, (executable work) run object code modify work, including scripts control activities. 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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/REDCapCAST/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 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/REDCapCAST/LICENSE.html","id":"id_4-conveying-verbatim-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"4. Conveying Verbatim Copies","title":"GNU 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/REDCapCAST/LICENSE.html","id":"id_5-conveying-modified-source-versions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"5. Conveying Modified Source Versions","title":"GNU 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. b) work must carry prominent notices stating released License conditions added section 7. requirement modifies requirement section 4 “keep intact notices”. c) 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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Termination","title":"GNU 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. 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Interpretation of Sections 15 and 16","title":"GNU 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/REDCapCAST/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 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. 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If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"easy-data-set-to-data-base-workflow","dir":"Articles","previous_headings":"","what":"Easy data set to data base workflow","title":"Database-creation","text":"first iteration dataset data dictionary function ds2dd(), creates basic data dictionary variables stored text. sufficient just storing old datasets/spreadsheets securely REDCap. advanced ds2dd_detailed() natural development. try apply common data classes data validation assume first column id number. outputs list dataset modified variable names comply REDCap naming conventions data dictionary. dataset correctly formatted data dictionary preserve much information possible. Additional specifications DataDictionary can made manually, can uploaded modified manually graphical user interface web page.","code":"mtcars |>   dplyr::mutate(record_id = seq_len(dplyr::n())) |>   ds2dd() |> str() dd_ls <- mtcars |>   dplyr::mutate(record_id = seq_len(dplyr::n())) |>   dplyr::select(record_id, dplyr::everything()) |>   ds2dd_detailed() dd_ls |> str()"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"step-3---meta-data-upload","dir":"Articles","previous_headings":"Easy data set to data base workflow","what":"Step 3 - Meta data upload","title":"Database-creation","text":"Now DataDictionary can exported spreadsheet uploaded can uploaded using REDCapR package (projects “Development” status). Use one two approaches :","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"manual-upload","dir":"Articles","previous_headings":"Easy data set to data base workflow > Step 3 - Meta data upload","what":"Manual upload","title":"Database-creation","text":"","code":"write.csv(dd_ls$meta, \"datadictionary.csv\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"upload-with-redcapr","dir":"Articles","previous_headings":"Easy data set to data base workflow > Step 3 - Meta data upload","what":"Upload with REDCapR","title":"Database-creation","text":"“REDCap R Handbook” written interfacing REDCap R using library(keyring)store credentials chapter 1.1.","code":"REDCapR::redcap_metadata_write(   dd_ls$meta,   redcap_uri = keyring::key_get(\"DB_URI\"),   token = keyring::key_get(\"DB_TOKEN\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"step-4---data-upload","dir":"Articles","previous_headings":"Easy data set to data base workflow","what":"Step 4 - Data upload","title":"Database-creation","text":"two options available data upload meta data upload: manual REDCapR. latter shown .","code":"REDCapR::redcap_write(   dd_ls$data,   redcap_uri = keyring::key_get(\"DB_URI\"),   token = keyring::key_get(\"DB_TOKEN\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Introduction.html","id":"splitting-the-dataset","dir":"Articles","previous_headings":"","what":"Splitting the dataset","title":"Introduction","text":"","code":"redcapcast_data |> gt::gt() redcapcast_meta |> gt::gt() list <-   REDCap_split(records = redcapcast_data,                            metadata = redcapcast_meta,                            forms = \"repeating\")|> sanitize_split() str(list) #> List of 2 #>  $          : tibble [10 × 17] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id                   : num [1:10] 1 2 2 3 3 3 4 4 5 6 #>   ..$ redcap_event_name           : chr [1:10] \"inclusion\" \"inclusion\" \"follow1\" \"inclusion\" ... #>   ..$ cpr                         : chr [1:10] \"1203401OB4\" \"0102342303\" NA \"2301569823\" ... #>   ..$ inclusion                   : Date[1:10], format: \"2023-03-13\" \"2023-03-01\" ... #>   ..$ dob                         : Date[1:10], format: \"1940-03-12\" \"1934-02-01\" ... #>   ..$ age                         : num [1:10] 83 89.1 NA 66.1 NA ... #>   ..$ age_integer                 : num [1:10] 83 89 NA 66 NA NA 117 NA 126 91 #>   ..$ sex                         : chr [1:10] \"female\" \"male\" NA \"male\" ... #>   ..$ cohabitation                : chr [1:10] \"Yes\" \"Yes\" NA \"No\" ... #>   ..$ hypertension                : chr [1:10] \"No\" \"No\" NA \"Yes\" ... #>   ..$ diabetes                    : chr [1:10] \"Yes\" \"No\" NA \"Yes\" ... #>   ..$ region                      : chr [1:10] \"East\" \"South\" NA \"North\" ... #>   ..$ baseline_data_start_complete: chr [1:10] \"Incomplete\" \"Incomplete\" NA \"Incomplete\" ... #>   ..$ mrs_assessed                : chr [1:10] \"Yes\" \"Yes\" \"Yes\" NA ... #>   ..$ mrs_date                    : Date[1:10], format: \"2023-03-13\" \"2023-03-07\" ... #>   ..$ mrs_score                   : num [1:10] 1 1 3 NA 2 1 NA NA NA NA #>   ..$ mrs_complete                : chr [1:10] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>  $ new_event: tibble [9 × 6] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id               : num [1:9] 2 3 3 3 3 3 4 4 4 #>   ..$ redcap_event_name       : chr [1:9] \"follow1\" \"follow1\" \"follow1\" \"follow2\" ... #>   ..$ redcap_repeat_instrument: chr [1:9] \"new_event\" \"new_event\" \"new_event\" \"new_event\" ... #>   ..$ redcap_repeat_instance  : num [1:9] 1 1 2 1 2 3 1 2 3 #>   ..$ event_type              : chr [1:9] \"TIA\" \"AIS\" \"ICH\" \"ICH\" ... #>   ..$ new_event_complete      : chr [1:9] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... list <-   REDCap_split(records = redcapcast_data,                            metadata = redcapcast_meta,                            forms = \"all\") |> sanitize_split() str(list) #> List of 3 #>  $ baseline_data_start: tibble [6 × 13] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id                   : num [1:6] 1 2 3 4 5 6 #>   ..$ redcap_event_name           : chr [1:6] \"inclusion\" \"inclusion\" \"inclusion\" \"inclusion\" ... #>   ..$ cpr                         : chr [1:6] \"1203401OB4\" \"0102342303\" \"2301569823\" \"0204051342\" ... #>   ..$ inclusion                   : Date[1:6], format: \"2023-03-13\" \"2023-03-01\" ... #>   ..$ dob                         : Date[1:6], format: \"1940-03-12\" \"1934-02-01\" ... #>   ..$ age                         : num [1:6] 83 89.1 66.1 117.9 126.2 ... #>   ..$ age_integer                 : num [1:6] 83 89 66 117 126 91 #>   ..$ sex                         : chr [1:6] \"female\" \"male\" \"male\" \"female\" ... #>   ..$ cohabitation                : chr [1:6] \"Yes\" \"Yes\" \"No\" NA ... #>   ..$ hypertension                : chr [1:6] \"No\" \"No\" \"Yes\" NA ... #>   ..$ diabetes                    : chr [1:6] \"Yes\" \"No\" \"Yes\" NA ... #>   ..$ region                      : chr [1:6] \"East\" \"South\" \"North\" NA ... #>   ..$ baseline_data_start_complete: chr [1:6] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>  $ mrs                : tibble [5 × 6] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id        : num [1:5] 1 2 2 3 3 #>   ..$ redcap_event_name: chr [1:5] \"inclusion\" \"inclusion\" \"follow1\" \"follow1\" ... #>   ..$ mrs_assessed     : chr [1:5] \"Yes\" \"Yes\" \"Yes\" \"Yes\" ... #>   ..$ mrs_date         : Date[1:5], format: \"2023-03-13\" \"2023-03-07\" ... #>   ..$ mrs_score        : num [1:5] 1 1 3 2 1 #>   ..$ mrs_complete     : chr [1:5] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>  $ new_event          : tibble [9 × 6] (S3: tbl_df/tbl/data.frame) #>   ..$ record_id               : num [1:9] 2 3 3 3 3 3 4 4 4 #>   ..$ redcap_event_name       : chr [1:9] \"follow1\" \"follow1\" \"follow1\" \"follow2\" ... #>   ..$ redcap_repeat_instrument: chr [1:9] \"new_event\" \"new_event\" \"new_event\" \"new_event\" ... #>   ..$ redcap_repeat_instance  : num [1:9] 1 1 2 1 2 3 1 2 3 #>   ..$ event_type              : chr [1:9] \"TIA\" \"AIS\" \"ICH\" \"ICH\" ... #>   ..$ new_event_complete      : chr [1:9] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ..."},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Introduction.html","id":"reading-data-from-redcap","dir":"Articles","previous_headings":"","what":"Reading data from REDCap","title":"Introduction","text":"function wraps demonstrated function get dataset, metadata, apply REDCap_splitfunction bit cleaning. just cuts outs steps easier approach. function works similar REDCapR::redcap_read() allowing specify fields, events forms export instead exporting whole database filtering afterwards. believe better safer, focused approach.","code":"# read_redcap_tables(uri = \"YOUR URI\", token = \"YOUR TOKEN\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Introduction.html","id":"pivotting-to-wider-format","dir":"Articles","previous_headings":"","what":"Pivotting to wider format","title":"Introduction","text":"","code":"redcap_wider(list) |> str() #> Joining with `by = join_by(record_id)` #> Joining with `by = join_by(record_id)` #> 'data.frame':    6 obs. of  36 variables: #>  $ record_id                   : num  1 2 3 4 5 6 #>  $ cpr                         : chr  \"1203401OB4\" \"0102342303\" \"2301569823\" \"0204051342\" ... #>  $ inclusion                   : Date, format: \"2023-03-13\" \"2023-03-01\" ... #>  $ dob                         : Date, format: \"1940-03-12\" \"1934-02-01\" ... #>  $ age                         : num  83 89.1 66.1 117.9 126.2 ... #>  $ age_integer                 : num  83 89 66 117 126 91 #>  $ sex                         : chr  \"female\" \"male\" \"male\" \"female\" ... #>  $ cohabitation                : chr  \"Yes\" \"Yes\" \"No\" NA ... #>  $ hypertension                : chr  \"No\" \"No\" \"Yes\" NA ... #>  $ diabetes                    : chr  \"Yes\" \"No\" \"Yes\" NA ... #>  $ region                      : chr  \"East\" \"South\" \"North\" NA ... #>  $ baseline_data_start_complete: chr  \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #>  $ mrs_assessed_inclusion      : chr  \"Yes\" \"Yes\" NA NA ... #>  $ mrs_assessed_follow1        : chr  NA \"Yes\" \"Yes\" NA ... #>  $ mrs_assessed_follow2        : chr  NA NA \"Yes\" NA ... #>  $ mrs_date_inclusion          : Date, format: \"2023-03-13\" \"2023-03-07\" ... #>  $ mrs_date_follow1            : Date, format: NA \"2023-03-09\" ... #>  $ mrs_date_follow2            : Date, format: NA NA ... #>  $ mrs_score_inclusion         : num  1 1 NA NA NA NA #>  $ mrs_score_follow1           : num  NA 3 2 NA NA NA #>  $ mrs_score_follow2           : num  NA NA 1 NA NA NA #>  $ mrs_complete_inclusion      : chr  \"Incomplete\" \"Incomplete\" NA NA ... #>  $ mrs_complete_follow1        : chr  NA \"Incomplete\" \"Incomplete\" NA ... #>  $ mrs_complete_follow2        : chr  NA NA \"Incomplete\" NA ... #>  $ event_type_1_follow1        : chr  NA \"TIA\" \"AIS\" NA ... #>  $ event_type_1_follow2        : chr  NA NA \"ICH\" \"AIS\" ... #>  $ new_event_complete_1_follow1: chr  NA \"Incomplete\" \"Incomplete\" NA ... #>  $ new_event_complete_1_follow2: chr  NA NA \"Incomplete\" \"Complete\" ... #>  $ event_type_2_follow1        : chr  NA NA \"ICH\" NA ... #>  $ event_type_2_follow2        : chr  NA NA \"TIA\" \"ICH\" ... #>  $ event_type_3_follow1        : chr  NA NA NA NA ... #>  $ event_type_3_follow2        : chr  NA NA \"AIS\" \"Unknown\" ... #>  $ new_event_complete_2_follow1: chr  NA NA \"Incomplete\" NA ... #>  $ new_event_complete_2_follow2: chr  NA NA \"Incomplete\" \"Incomplete\" ... #>  $ new_event_complete_3_follow1: chr  NA NA NA NA ... #>  $ new_event_complete_3_follow2: chr  NA NA \"Incomplete\" \"Complete\" ..."},{"path":"https://agdamsbo.github.io/REDCapCAST/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Andreas Gammelgaard Damsbo. Author, maintainer. Paul Egeler. Author.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Damsbo , Egeler P (2024). REDCapCAST: REDCap Castellated Data Handling. R package version 24.2.1, https://agdamsbo.github.io/REDCapCAST/, https://github.com/agdamsbo/REDCapCAST.","code":"@Manual{,   title = {REDCapCAST: REDCap Castellated Data Handling},   author = {Andreas Gammelgaard Damsbo and Paul Egeler},   year = {2024},   note = {R package version 24.2.1, https://agdamsbo.github.io/REDCapCAST/},   url = {https://github.com/agdamsbo/REDCapCAST}, }"},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"redcapcast-package-","dir":"","previous_headings":"","what":"REDCap Castellated Data Handling","title":"REDCap Castellated Data Handling","text":"REDCap database casting handling castellated data using repeated instruments longitudinal projects. package fork pegeler/REDCapRITS. REDCapRITS represents great extensive work handle castellated REDCap data different programming languages. fork purely minded R usage includes implementations main REDCap_split function. package much seen attempt R--REDCap--R foundry handling transition dataset/variable list database way, REDCap database tidy dataset. goal also allow “minimal data” approach allowing filter records, instruments variables export download data needed. think approach desirable handling sensitive, clinical data. Please refer REDCap-Tools great tools working REDCap R.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"use-and-immprovements","dir":"","previous_headings":"","what":"Use and immprovements","title":"REDCap Castellated Data Handling","text":"just short description main functions: REDcap_split(): Works largely original REDCapRITS::REDCap_split(). takes REDCap dataset metadata (data dictionary) split data set list dataframes instruments. read_redcap_tables(): wraps use REDCapR::redcap_read() REDCap_split() ease export REDCap data. Default output list data frames one data frame REDCap instrument. redcap_wider(): joins pivots list data frames repeated instruments wide format utilizing tidyr::pivot_wider() tidyverse. easy_redcap(): combines secure API key storage keyring-package, focused data retrieval optional widening. recommended approach easy data access analysis. ds2dd_detailed(): Converts data set data dictionary upload new REDCap database. Variables (fields) instruments REDCap data base defined data dictionary. shiny_cast(): Shiny application ease process converting spreadsheet/data set REDCap database. app runs locally data transferred securely. can just create upload data dictionary, can also transfer given data process.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"future","dir":"","previous_headings":"","what":"Future","title":"REDCap Castellated Data Handling","text":"plan package bundled Handbook working REDCap R. work progress limited time available. Please feel free contact create issue ideas future additions.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"REDCap Castellated Data Handling","text":"package available CRAN. Install latest version: Install latest version directly GitHub:","code":"install.packages(\"REDCapCAST\") remotes::install_github(\"agdamsbo/REDCapCAST\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":null,"dir":"Reference","previous_headings":"","what":"Split REDCap repeating instruments table into multiple tables — REDCap_split","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"take output REDCap export split base table child tables repeating instrument. Metadata used determine fields included resultant table.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"","code":"REDCap_split(   records,   metadata,   primary_table_name = \"\",   forms = c(\"repeating\", \"all\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"records Exported project records. May data.frame, response, character vector containing JSON API call. metadata Project metadata (data dictionary). May data.frame, response, character vector containing JSON API call. primary_table_name Name given list element primary output table (described README.md). Ignored forms = ''. forms Indicate whether create separate tables repeating instruments forms.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"list \"data.frame\"s. number tables differ   depending forms option selected.  'repeating': one base table one     tables repeating instrument. '': data.frame instrument, regardless     whether repeating instrument .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"Paul W. Egeler, M.S., GStat","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"","code":"if (FALSE) { # Using an API call -------------------------------------------------------  library(RCurl)  # Get the records records <- postForm(   uri = api_url,     # Supply your site-specific URI   token = api_token, # Supply your own API token   content = 'record',   format = 'json',   returnFormat = 'json' )  # Get the metadata metadata <- postForm(   uri = api_url,     # Supply your site-specific URI   token = api_token, # Supply your own API token   content = 'metadata',   format = 'json' )  # Convert exported JSON strings into a list of data.frames REDCapRITS::REDCap_split(records, metadata)  # Using a raw data export -------------------------------------------------  # Get the records records <- read.csv(\"/path/to/data/ExampleProject_DATA_2018-06-03_1700.csv\")  # Get the metadata metadata <- read.csv( \"/path/to/data/ExampleProject_DataDictionary_2018-06-03.csv\")  # Split the tables REDCapRITS::REDCap_split(records, metadata)  # In conjunction with the R export script ---------------------------------  # You must set the working directory first since the REDCap data export # script contains relative file references. old <- getwd() setwd(\"/path/to/data/\")  # Run the data export script supplied by REDCap. # This will create a data.frame of your records called 'data' source(\"ExampleProject_R_2018-06-03_1700.r\")  # Get the metadatan metadata <- read.csv(\"ExampleProject_DataDictionary_2018-06-03.csv\")  # Split the tables REDCapRITS::REDCap_split(data, metadata) setwd(old) }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":null,"dir":"Reference","previous_headings":"","what":"clean_redcap_name — clean_redcap_name","title":"clean_redcap_name — clean_redcap_name","text":"Stepwise removal non-alphanumeric characters, trailing white space, substitutes spaces underscores converts lower case. Trying make different naming conventions.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"clean_redcap_name — clean_redcap_name","text":"","code":"clean_redcap_name(x)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"clean_redcap_name — clean_redcap_name","text":"x vector data frame cleaning","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_redcap_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"clean_redcap_name — clean_redcap_name","text":"vector data frame, format input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert single digits to words — d2w","title":"Convert single digits to words — d2w","text":"Convert single digits words","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert single digits to words — d2w","text":"","code":"d2w(x, lang = \"en\", neutrum = FALSE, everything = FALSE)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert single digits to words — d2w","text":"x data. Handle vectors, data.frames lists lang language. Danish (da) English (en), Default \"en\" neutrum numbers depending counted word everything flag also split numbers >9 single digits","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert single digits to words — d2w","text":"returns characters format input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert single digits to words — d2w","text":"","code":"d2w(c(2:8, 21)) #> [1] \"two\"   \"three\" \"four\"  \"five\"  \"six\"   \"seven\" \"eight\" \"21\"    d2w(data.frame(2:7, 3:8, 1), lang = \"da\", neutrum = TRUE) #>   X2.7 X3.8 X1 #> 1   to  tre et #> 2  tre fire et #> 3 fire  fem et #> 4  fem seks et #> 5 seks  syv et #> 6  syv otte et  ## If everything=T, also larger numbers are reduced. ## Elements in the list are same length as input d2w(list(2:8, c(2, 6, 4, 23), 2), everything = TRUE) #> [[1]] #> [1] \"two\"   \"three\" \"four\"  \"five\"  \"six\"   \"seven\" \"eight\" #>  #> [[2]] #> [1] \"two\"       \"six\"       \"four\"      \"two three\" #>  #> [[3]] #> [1] \"two\" #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/deploy_shiny.html","id":null,"dir":"Reference","previous_headings":"","what":"Deploy the Shiny app with rsconnect — deploy_shiny","title":"Deploy the Shiny app with rsconnect — deploy_shiny","text":"Deploy Shiny app rsconnect","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/deploy_shiny.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deploy the Shiny app with rsconnect — deploy_shiny","text":"","code":"deploy_shiny(path = here::here(\"app/\"), name.app = \"shiny_cast\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/deploy_shiny.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Deploy the Shiny app with rsconnect — deploy_shiny","text":"path app folder path name.app name deployed app","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/deploy_shiny.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Deploy the Shiny app with rsconnect — deploy_shiny","text":"deploy","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/deploy_shiny.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Deploy the Shiny app with rsconnect — deploy_shiny","text":"","code":"# deploy_shiny"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":null,"dir":"Reference","previous_headings":"","what":"(DEPRECATED) Data set to data dictionary function — ds2dd","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"Creates basic data dictionary skeleton. Please see `ds2dd_detailed()` advanced function.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"","code":"ds2dd(   ds,   record.id = \"record_id\",   form.name = \"basis\",   field.type = \"text\",   field.label = NULL,   include.column.names = FALSE,   metadata = metadata_names )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"ds data set record.id name column number id variable, moved first row data dictionary, character integer. Default \"record_id\". form.name vector form names, character string, length 1 length equal number variables. Default \"basis\". field.type vector field types, character string, length 1 length equal number variables. Default \"text. field.label vector form names, character string, length 1 length equal number variables. Default NULL identical field names. include.column.names Flag give detailed output including new column names original data set upload. metadata Metadata column names. Default included REDCapCAST::metadata_names.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"data.frame list data.frame vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"Migrated stRoke ds2dd(). Fits better functionality 'REDCapCAST'.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"","code":"redcapcast_data$record_id <- seq_len(nrow(redcapcast_data)) ds2dd(redcapcast_data, include.column.names=TRUE) #> $DataDictionary #>                      field_name form_name section_header field_type #> 1                     record_id     basis             NA       text #> 2             redcap_event_name     basis             NA       text #> 3      redcap_repeat_instrument     basis             NA       text #> 4        redcap_repeat_instance     basis             NA       text #> 5                           cpr     basis             NA       text #> 6                     inclusion     basis             NA       text #> 7                inclusion_time     basis             NA       text #> 8                           dob     basis             NA       text #> 9                           age     basis             NA       text #> 10                  age_integer     basis             NA       text #> 11                          sex     basis             NA       text #> 12                 cohabitation     basis             NA       text #> 13                 hypertension     basis             NA       text #> 14                     diabetes     basis             NA       text #> 15                       region     basis             NA       text #> 16 baseline_data_start_complete     basis             NA       text #> 17                 mrs_assessed     basis             NA       text #> 18                     mrs_date     basis             NA       text #> 19                    mrs_score     basis             NA       text #> 20                 mrs_complete     basis             NA       text #> 21               event_datetime     basis             NA       text #> 22                    event_age     basis             NA       text #> 23                   event_type     basis             NA       text #> 24           new_event_complete     basis             NA       text #>                     field_label select_choices_or_calculations field_note #> 1                     record_id                             NA         NA #> 2             redcap_event_name                             NA         NA #> 3      redcap_repeat_instrument                             NA         NA #> 4        redcap_repeat_instance                             NA         NA #> 5                           cpr                             NA         NA #> 6                     inclusion                             NA         NA #> 7                inclusion_time                             NA         NA #> 8                           dob                             NA         NA #> 9                           age                             NA         NA #> 10                  age_integer                             NA         NA #> 11                          sex                             NA         NA #> 12                 cohabitation                             NA         NA #> 13                 hypertension                             NA         NA #> 14                     diabetes                             NA         NA #> 15                       region                             NA         NA #> 16 baseline_data_start_complete                             NA         NA #> 17                 mrs_assessed                             NA         NA #> 18                     mrs_date                             NA         NA #> 19                    mrs_score                             NA         NA #> 20                 mrs_complete                             NA         NA #> 21               event_datetime                             NA         NA #> 22                    event_age                             NA         NA #> 23                   event_type                             NA         NA #> 24           new_event_complete                             NA         NA #>    text_validation_type_or_show_slider_number text_validation_min #> 1                                          NA                  NA #> 2                                          NA                  NA #> 3                                          NA                  NA #> 4                                          NA                  NA #> 5                                          NA                  NA #> 6                                          NA                  NA #> 7                                          NA                  NA #> 8                                          NA                  NA #> 9                                          NA                  NA #> 10                                         NA                  NA #> 11                                         NA                  NA #> 12                                         NA                  NA #> 13                                         NA                  NA #> 14                                         NA                  NA #> 15                                         NA                  NA #> 16                                         NA                  NA #> 17                                         NA                  NA #> 18                                         NA                  NA #> 19                                         NA                  NA #> 20                                         NA                  NA #> 21                                         NA                  NA #> 22                                         NA                  NA #> 23                                         NA                  NA #> 24                                         NA                  NA #>    text_validation_max identifier branching_logic required_field #> 1                   NA         NA              NA             NA #> 2                   NA         NA              NA             NA #> 3                   NA         NA              NA             NA #> 4                   NA         NA              NA             NA #> 5                   NA         NA              NA             NA #> 6                   NA         NA              NA             NA #> 7                   NA         NA              NA             NA #> 8                   NA         NA              NA             NA #> 9                   NA         NA              NA             NA #> 10                  NA         NA              NA             NA #> 11                  NA         NA              NA             NA #> 12                  NA         NA              NA             NA #> 13                  NA         NA              NA             NA #> 14                  NA         NA              NA             NA #> 15                  NA         NA              NA             NA #> 16                  NA         NA              NA             NA #> 17                  NA         NA              NA             NA #> 18                  NA         NA              NA             NA #> 19                  NA         NA              NA             NA #> 20                  NA         NA              NA             NA #> 21                  NA         NA              NA             NA #> 22                  NA         NA              NA             NA #> 23                  NA         NA              NA             NA #> 24                  NA         NA              NA             NA #>    custom_alignment question_number matrix_group_name matrix_ranking #> 1                NA              NA                NA             NA #> 2                NA              NA                NA             NA #> 3                NA              NA                NA             NA #> 4                NA              NA                NA             NA #> 5                NA              NA                NA             NA #> 6                NA              NA                NA             NA #> 7                NA              NA                NA             NA #> 8                NA              NA                NA             NA #> 9                NA              NA                NA             NA #> 10               NA              NA                NA             NA #> 11               NA              NA                NA             NA #> 12               NA              NA                NA             NA #> 13               NA              NA                NA             NA #> 14               NA              NA                NA             NA #> 15               NA              NA                NA             NA #> 16               NA              NA                NA             NA #> 17               NA              NA                NA             NA #> 18               NA              NA                NA             NA #> 19               NA              NA                NA             NA #> 20               NA              NA                NA             NA #> 21               NA              NA                NA             NA #> 22               NA              NA                NA             NA #> 23               NA              NA                NA             NA #> 24               NA              NA                NA             NA #>    field_annotation #> 1                NA #> 2                NA #> 3                NA #> 4                NA #> 5                NA #> 6                NA #> 7                NA #> 8                NA #> 9                NA #> 10               NA #> 11               NA #> 12               NA #> 13               NA #> 14               NA #> 15               NA #> 16               NA #> 17               NA #> 18               NA #> 19               NA #> 20               NA #> 21               NA #> 22               NA #> 23               NA #> 24               NA #>  #> $`Column names` #>  [1] \"record_id\"                    \"redcap_event_name\"            #>  [3] \"redcap_repeat_instrument\"     \"redcap_repeat_instance\"       #>  [5] \"cpr\"                          \"inclusion\"                    #>  [7] \"inclusion_time\"               \"dob\"                          #>  [9] \"age\"                          \"age_integer\"                  #> [11] \"sex\"                          \"cohabitation\"                 #> [13] \"hypertension\"                 \"diabetes\"                     #> [15] \"region\"                       \"baseline_data_start_complete\" #> [17] \"mrs_assessed\"                 \"mrs_date\"                     #> [19] \"mrs_score\"                    \"mrs_complete\"                 #> [21] \"event_datetime\"               \"event_age\"                    #> [23] \"event_type\"                   \"new_event_complete\"           #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract data from stata file for data dictionary — ds2dd_detailed","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"Extract data stata file data dictionary","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"","code":"ds2dd_detailed(   data,   add.auto.id = FALSE,   date.format = \"dmy\",   form.name = NULL,   field.type = NULL,   field.label = NULL,   field.label.attr = \"label\",   field.validation = NULL,   metadata = metadata_names,   validate.time = FALSE,   time.var.sel.pos = \"[Tt]i[d(me)]\",   time.var.sel.neg = \"[Dd]at[eo]\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"data data frame add.auto.id flag add id column date.format date format, character string. ymd/dmy/mdy. dafault dmy. form.name manually specify form name(s). Vector length 1 ncol(data). Default NULL \"data\" used. field.type manually specify field type(s). Vector length 1 ncol(data). Default NULL \"text\" used everything factors, wil get \"radio\". field.label manually specify field label(s). Vector length 1 ncol(data). Default NULL colnames(data) used attribute `field.label.attr` haven_labelled data set (imported .dta file `haven::read_dta()`). field.label.attr attribute name named labels haven_labelled data set (imported .dta file `haven::read_dta()`. Default \"label\" field.validation manually specify field validation(s). Vector length 1 ncol(data). Default NULL `levels()` used factors attribute `factor.labels.attr` haven_labelled data set (imported .dta file `haven::read_dta()`). metadata redcap metadata headings. Default REDCapCAST:::metadata_names. validate.time Flag validate guessed time columns time.var.sel.pos Positive selection regex string passed `gues_time_only_filter()` sel.pos. time.var.sel.neg Negative selection regex string passed `gues_time_only_filter()` sel.neg.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"list length 2","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"function natural development ds2dd() function. assumes first column ID-column. checks. Please, always inspect data dictionary upload. Ensure, data set formatted much information possible. `field.type` can supplied","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"","code":"data <- redcapcast_data data |> ds2dd_detailed(validate.time = TRUE) #> $is.POSIX #> # A tibble: 19 × 2 #>    inclusion_time event_datetime      #>    <time>         <dttm>              #>  1 12:38:49       NA                  #>  2 10:38:57       NA                  #>  3       NA       NA                  #>  4       NA       2024-01-18 12:49:42 #>  5 12:01:07       NA                  #>  6       NA       NA                  #>  7       NA       NA                  #>  8       NA       2024-01-18 12:49:58 #>  9       NA       2024-01-18 12:50:01 #> 10       NA       2024-01-18 12:50:05 #> 11       NA       2024-01-18 12:50:07 #> 12       NA       2024-01-18 12:50:09 #> 13 20:39:19       NA                  #> 14       NA       NA                  #> 15       NA       2024-01-18 12:50:19 #> 16       NA       2024-01-18 12:50:22 #> 17       NA       2024-01-18 12:50:24 #> 18 08:50:31       NA                  #> 19 08:49:28       NA                  #>  #> $is.datetime #> # A tibble: 19 × 1 #>    event_datetime      #>    <dttm>              #>  1 NA                  #>  2 NA                  #>  3 NA                  #>  4 2024-01-18 12:49:42 #>  5 NA                  #>  6 NA                  #>  7 NA                  #>  8 2024-01-18 12:49:58 #>  9 2024-01-18 12:50:01 #> 10 2024-01-18 12:50:05 #> 11 2024-01-18 12:50:07 #> 12 2024-01-18 12:50:09 #> 13 NA                  #> 14 NA                  #> 15 2024-01-18 12:50:19 #> 16 2024-01-18 12:50:22 #> 17 2024-01-18 12:50:24 #> 18 NA                  #> 19 NA                  #>  #> $is.time_only #> # A tibble: 19 × 1 #>    inclusion_time #>    <time>         #>  1 12:38:49       #>  2 10:38:57       #>  3       NA       #>  4       NA       #>  5 12:01:07       #>  6       NA       #>  7       NA       #>  8       NA       #>  9       NA       #> 10       NA       #> 11       NA       #> 12       NA       #> 13 20:39:19       #> 14       NA       #> 15       NA       #> 16       NA       #> 17       NA       #> 18 08:50:31       #> 19 08:49:28       #>  data |> ds2dd_detailed() #> $data #> # A tibble: 19 × 24 #>    record_id redcap_event_name redcap_repeat_instrument redcap_repeat_instance #>        <dbl> <chr>             <chr>                                     <dbl> #>  1         1 inclusion         NA                                           NA #>  2         2 inclusion         NA                                           NA #>  3         2 follow1           NA                                           NA #>  4         2 follow1           New Event (?)                                 1 #>  5         3 inclusion         NA                                           NA #>  6         3 follow1           NA                                           NA #>  7         3 follow2           NA                                           NA #>  8         3 follow1           New Event (?)                                 1 #>  9         3 follow1           New Event (?)                                 2 #> 10         3 follow2           New Event (?)                                 1 #> 11         3 follow2           New Event (?)                                 2 #> 12         3 follow2           New Event (?)                                 3 #> 13         4 inclusion         NA                                           NA #> 14         4 follow2           NA                                           NA #> 15         4 follow2           New Event (?)                                 1 #> 16         4 follow2           New Event (?)                                 2 #> 17         4 follow2           New Event (?)                                 3 #> 18         5 inclusion         NA                                           NA #> 19         6 inclusion         NA                                           NA #> # ℹ 20 more variables: cpr <chr>, inclusion <date>, inclusion_time <chr>, #> #   dob <date>, age <dbl>, age_integer <dbl>, sex <chr>, cohabitation <chr>, #> #   hypertension <chr>, diabetes <chr>, region <chr>, #> #   baseline_data_start_complete <chr>, mrs_assessed <chr>, mrs_date <date>, #> #   mrs_score <dbl>, mrs_complete <chr>, event_datetime <dttm>, #> #   event_age <lgl>, event_type <chr>, new_event_complete <chr> #>  #> $meta #> # A tibble: 24 × 18 #>    field_name               form_name section_header field_type field_label      #>    <chr>                    <chr>     <lgl>          <chr>      <chr>            #>  1 record_id                data      NA             text       record_id        #>  2 redcap_event_name        data      NA             text       redcap_event_na… #>  3 redcap_repeat_instrument data      NA             text       redcap_repeat_i… #>  4 redcap_repeat_instance   data      NA             text       redcap_repeat_i… #>  5 cpr                      data      NA             text       cpr              #>  6 inclusion                data      NA             text       inclusion        #>  7 inclusion_time           data      NA             text       inclusion_time   #>  8 dob                      data      NA             text       dob              #>  9 age                      data      NA             text       age              #> 10 age_integer              data      NA             text       age_integer      #> # ℹ 14 more rows #> # ℹ 13 more variables: select_choices_or_calculations <lgl>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> #>  iris |> ds2dd_detailed(add.auto.id = TRUE) #> A default id column has been added #> $data #> # A tibble: 150 × 6 #>    default_trial_id sepal.length sepal.width petal.length petal.width species #>               <int>        <dbl>       <dbl>        <dbl>       <dbl> <fct>   #>  1                1          5.1         3.5          1.4         0.2 setosa  #>  2                2          4.9         3            1.4         0.2 setosa  #>  3                3          4.7         3.2          1.3         0.2 setosa  #>  4                4          4.6         3.1          1.5         0.2 setosa  #>  5                5          5           3.6          1.4         0.2 setosa  #>  6                6          5.4         3.9          1.7         0.4 setosa  #>  7                7          4.6         3.4          1.4         0.3 setosa  #>  8                8          5           3.4          1.5         0.2 setosa  #>  9                9          4.4         2.9          1.4         0.2 setosa  #> 10               10          4.9         3.1          1.5         0.1 setosa  #> # ℹ 140 more rows #>  #> $meta #> # A tibble: 6 × 18 #>   field_name       form_name section_header field_type field_label      #>   <chr>            <chr>     <lgl>          <chr>      <chr>            #> 1 default_trial_id data      NA             text       default_trial_id #> 2 sepal.length     data      NA             text       Sepal.Length     #> 3 sepal.width      data      NA             text       Sepal.Width      #> 4 petal.length     data      NA             text       Petal.Length     #> 5 petal.width      data      NA             text       Petal.Width      #> 6 species          data      NA             radio      Species          #> # ℹ 13 more variables: select_choices_or_calculations <chr>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> #>  mtcars |> ds2dd_detailed(add.auto.id = TRUE) #> A default id column has been added #> $data #> # A tibble: 32 × 12 #>    default_trial_id   mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear #>               <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1                1  21       6  160    110  3.9   2.62  16.5     0     1     4 #>  2                2  21       6  160    110  3.9   2.88  17.0     0     1     4 #>  3                3  22.8     4  108     93  3.85  2.32  18.6     1     1     4 #>  4                4  21.4     6  258    110  3.08  3.22  19.4     1     0     3 #>  5                5  18.7     8  360    175  3.15  3.44  17.0     0     0     3 #>  6                6  18.1     6  225    105  2.76  3.46  20.2     1     0     3 #>  7                7  14.3     8  360    245  3.21  3.57  15.8     0     0     3 #>  8                8  24.4     4  147.    62  3.69  3.19  20       1     0     4 #>  9                9  22.8     4  141.    95  3.92  3.15  22.9     1     0     4 #> 10               10  19.2     6  168.   123  3.92  3.44  18.3     1     0     4 #> # ℹ 22 more rows #> # ℹ 1 more variable: carb <dbl> #>  #> $meta #> # A tibble: 12 × 18 #>    field_name       form_name section_header field_type field_label      #>    <chr>            <chr>     <lgl>          <chr>      <chr>            #>  1 default_trial_id data      NA             text       default_trial_id #>  2 mpg              data      NA             text       mpg              #>  3 cyl              data      NA             text       cyl              #>  4 disp             data      NA             text       disp             #>  5 hp               data      NA             text       hp               #>  6 drat             data      NA             text       drat             #>  7 wt               data      NA             text       wt               #>  8 qsec             data      NA             text       qsec             #>  9 vs               data      NA             text       vs               #> 10 am               data      NA             text       am               #> 11 gear             data      NA             text       gear             #> 12 carb             data      NA             text       carb             #> # ℹ 13 more variables: select_choices_or_calculations <lgl>, field_note <lgl>, #> #   text_validation_type_or_show_slider_number <chr>, #> #   text_validation_min <lgl>, text_validation_max <lgl>, identifier <lgl>, #> #   branching_logic <lgl>, required_field <lgl>, custom_alignment <lgl>, #> #   question_number <lgl>, matrix_group_name <lgl>, matrix_ranking <lgl>, #> #   field_annotation <lgl> #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":null,"dir":"Reference","previous_headings":"","what":"Secure API key storage and data acquisition in one — easy_redcap","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"Secure API key storage data acquisition one","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"","code":"easy_redcap(project.name, widen.data = TRUE, uri, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"project.name name current project (key storage `keyring::key_set()`, using default keyring) widen.data argument widen exported data uri REDCap database API uri ... arguments passed `REDCapCAST::read_redcap_tables()`","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"data.frame list depending widen.data","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper to import files correctly — file_extension","title":"Helper to import files correctly — file_extension","text":"Helper import files correctly","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper to import files correctly — file_extension","text":"","code":"file_extension(filenames)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper to import files correctly — file_extension","text":"filenames file names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper to import files correctly — file_extension","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper to import files correctly — file_extension","text":"","code":"file_extension(list.files(here::here(\"\"))[[2]])[[1]] #> [1] \"md\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"focused_metadata — focused_metadata","title":"focused_metadata — focused_metadata","text":"Extracts limited metadata variables dataset","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"focused_metadata — focused_metadata","text":"","code":"focused_metadata(metadata, vars_in_data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"focused_metadata — focused_metadata","text":"metadata dataframe containing metadata vars_in_data Vector variable names dataset","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"focused_metadata — focused_metadata","text":"dataframe containing metadata variables dataset","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"Retrieve project API key stored, , set retrieve","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"","code":"get_api_key(key.name)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"key.name character vector key name","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the id name — get_id_name","title":"Get the id name — get_id_name","text":"Get id name","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the id name — get_id_name","text":"","code":"get_id_name(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the id name — get_id_name","text":"data data frame list","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the id name — get_id_name","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":null,"dir":"Reference","previous_headings":"","what":"Try at determining which are true time only variables — guess_time_only_filter","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"just try guessing data type based data class column names hoping tiny bit naming consistency. R include time-data format natively, \"hms\" class `readr` used. converted character class REDCap upload.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"","code":"guess_time_only_filter(   data,   validate = FALSE,   sel.pos = \"[Tt]i[d(me)]\",   sel.neg = \"[Dd]at[eo]\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"data data set validate flag output validation data. output list. sel.pos Positive selection regex string sel.neg Negative selection regex string","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"character vector list depending `validate` flag.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"","code":"data <- redcapcast_data data |> guess_time_only_filter() #> [1] \"inclusion_time\" data |> guess_time_only_filter(validate = TRUE) |> lapply(head) #> $is.POSIX #> # A tibble: 6 × 2 #>   inclusion_time event_datetime      #>   <time>         <dttm>              #> 1 12:38:49       NA                  #> 2 10:38:57       NA                  #> 3       NA       NA                  #> 4       NA       2024-01-18 12:49:42 #> 5 12:01:07       NA                  #> 6       NA       NA                  #>  #> $is.datetime #> # A tibble: 6 × 1 #>   event_datetime      #>   <dttm>              #> 1 NA                  #> 2 NA                  #> 3 NA                  #> 4 2024-01-18 12:49:42 #> 5 NA                  #> 6 NA                  #>  #> $is.time_only #> # A tibble: 6 × 1 #>   inclusion_time #>   <time>         #> 1 12:38:49       #> 2 10:38:57       #> 3       NA       #> 4       NA       #> 5 12:01:07       #> 6       NA       #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":null,"dir":"Reference","previous_headings":"","what":"Change ","title":"Change ","text":"Change \"hms\" \"character\" REDCap upload.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change ","text":"","code":"hms2character(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change ","text":"data data set","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change ","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Change ","text":"","code":"data <- redcapcast_data ## data |> time_only_correction() |> hms2character()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if repeatable or longitudinal — is_repeated_longitudinal","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"Test repeatable longitudinal","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"","code":"is_repeated_longitudinal(   data,   generics = c(\"redcap_event_name\", \"redcap_repeat_instrument\", \"redcap_repeat_instance\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"data data set generics default \"redcap_event_name\", \"redcap_repeat_instrument\" \"redcap_repeat_instance\"","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"logical","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"","code":"is_repeated_longitudinal(c(\"record_id\", \"age\", \"record_id\", \"gender\")) #> [1] FALSE is_repeated_longitudinal(redcapcast_data) #> [1] TRUE is_repeated_longitudinal(list(redcapcast_data)) #> [1] TRUE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":null,"dir":"Reference","previous_headings":"","what":"Completion marking based on completed upload — mark_complete","title":"Completion marking based on completed upload — mark_complete","text":"Completion marking based completed upload","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Completion marking based on completed upload — mark_complete","text":"","code":"mark_complete(upload, ls)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Completion marking based on completed upload — mark_complete","text":"upload output list `REDCapR::redcap_write()` ls output list `ds2dd_detailed()`","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Completion marking based on completed upload — mark_complete","text":"list `REDCapR::redcap_write()` results","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":null,"dir":"Reference","previous_headings":"","what":"Match fields to forms — match_fields_to_form","title":"Match fields to forms — match_fields_to_form","text":"Match fields forms","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Match fields to forms — match_fields_to_form","text":"","code":"match_fields_to_form(metadata, vars_in_data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Match fields to forms — match_fields_to_form","text":"metadata data frame containing field names form names vars_in_data character vector variable names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Match fields to forms — match_fields_to_form","text":"data frame containing field names form names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html","id":null,"dir":"Reference","previous_headings":"","what":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","title":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","text":"mtcars dataset slightly modified use Shiny app upload demonstration","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","text":"","code":"data(mtcars_redcap)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","text":"data frame 13 variables: record_id ID, numeric mpg ID, numeric cyl ID, numeric disp ID, numeric hp ID, numeric drat ID, numeric wt ID, numeric qsec ID, numeric vs ID, numeric ID, numeric gear ID, numeric carb ID, numeric name original rownames, charater","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/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/REDCapCAST/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/REDCapCAST/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/REDCapCAST/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/REDCapCAST/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/REDCapCAST/reference/read_redcap_instrument.html","id":null,"dir":"Reference","previous_headings":"","what":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"Convenience function download complete instrument, using token storage keyring.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"","code":"read_redcap_instrument(   key,   uri,   instrument,   raw_or_label = \"raw\",   id_name = \"record_id\",   records = NULL )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"key key name standard keyring token retrieval. uri REDCap database API uri instrument instrument name raw_or_label raw label passed `REDCapR::redcap_read()` id_name id variable name. Default \"record_id\". records specify records download. Index numbers. Numeric vector.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":null,"dir":"Reference","previous_headings":"","what":"Download REDCap data — read_redcap_tables","title":"Download REDCap data — read_redcap_tables","text":"Implementation REDCap_split focused data acquisition approach using REDCapR::redcap_read downloading specified fields, forms /events using built-focused_metadata including clean-. Works classical longitudinal projects without repeating instruments.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download REDCap data — read_redcap_tables","text":"","code":"read_redcap_tables(   uri,   token,   records = NULL,   fields = NULL,   events = NULL,   forms = NULL,   raw_or_label = \"label\",   split_forms = \"all\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download REDCap data — read_redcap_tables","text":"uri REDCap database API uri token API token records records download fields fields download events events download forms forms download raw_or_label raw label tags split_forms Whether split \"repeating\" \"\" forms, default .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download REDCap data — read_redcap_tables","text":"list instruments","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download REDCap data — read_redcap_tables","text":"","code":"# Examples will be provided later"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":null,"dir":"Reference","previous_headings":"","what":"Redcap Wider — redcap_wider","title":"Redcap Wider — redcap_wider","text":"Converts list REDCap data frames long wide format. Handles longitudinal projects, yet repeated instruments.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Redcap Wider — redcap_wider","text":"","code":"redcap_wider(   data,   event.glue = \"{.value}_{redcap_event_name}\",   inst.glue = \"{.value}_{redcap_repeat_instance}\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Redcap Wider — redcap_wider","text":"data list data frames. event.glue dplyr::glue string repeated events naming inst.glue dplyr::glue string repeated instruments naming","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Redcap Wider — redcap_wider","text":"list data frames wide format.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Redcap Wider — redcap_wider","text":"","code":"# Longitudinal list1 <- list(data.frame(record_id = c(1,2,1,2), redcap_event_name = c(\"baseline\", \"baseline\", \"followup\", \"followup\"), age = c(25,26,27,28)), data.frame(record_id = c(1,2), redcap_event_name = c(\"baseline\", \"baseline\"), gender = c(\"male\", \"female\"))) redcap_wider(list1) #> Joining with `by = join_by(record_id)` #>   record_id age_baseline age_followup gender #> 1         1           25           27   male #> 2         2           26           28 female # Simpel with two instruments list2 <- list(data.frame(record_id = c(1,2), age = c(25,26)), data.frame(record_id = c(1,2), gender = c(\"male\", \"female\"))) redcap_wider(list2) #> Joining with `by = join_by(record_id)` #>   record_id age gender #> 1         1  25   male #> 2         2  26 female # Simple with single instrument list3 <- list(data.frame(record_id = c(1,2), age = c(25,26))) redcap_wider(list3) #>   record_id age #> 1         1  25 #> 2         2  26 # Longitudinal with repeatable instruments list4 <- list(data.frame(record_id = c(1,2,1,2), redcap_event_name = c(\"baseline\", \"baseline\", \"followup\", \"followup\"), age = c(25,26,27,28)), data.frame(record_id = c(1,1,1,1,2,2,2,2), redcap_event_name = c(\"baseline\", \"baseline\", \"followup\", \"followup\", \"baseline\", \"baseline\", \"followup\", \"followup\"), redcap_repeat_instrument = \"walk\", redcap_repeat_instance=c(1,2,1,2,1,2,1,2), dist = c(40, 32, 25, 33, 28, 24, 23, 36)), data.frame(record_id = c(1,2), redcap_event_name = c(\"baseline\", \"baseline\"), gender = c(\"male\", \"female\"))) redcap_wider(list4) #> Joining with `by = join_by(record_id)` #> Joining with `by = join_by(record_id)` #>   record_id age_baseline age_followup dist_1_baseline dist_1_followup #> 1         1           25           27              40              25 #> 2         2           26           28              28              23 #>   dist_2_baseline dist_2_followup gender #> 1              32              33   male #> 2              24              36 female"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Data set for demonstration — redcapcast_data","title":"Data set for demonstration — redcapcast_data","text":"small dataset REDCap database demonstrational purposes. Contains synthetic data.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data set for demonstration — redcapcast_data","text":"","code":"data(redcapcast_data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data set for demonstration — redcapcast_data","text":"data frame 22 variables: record_id ID, numeric redcap_event_name Event name, character redcap_repeat_instrument Repeat instrument, character redcap_repeat_instance Repeat instance, numeric cpr CPR number, character inclusion Inclusion date, Date inclusion_time Inclusion time, hms dob Date birth, Date age Age decimal, numeric age_integer Age integer, numeric sex Legal sex, character cohabitation Cohabitation status, character hypertension Hypertension, character diabetes diabetes, character region region, character baseline_data_start_complete Completed, character mrs_assessed mRS Assessed, character mrs_date Assesment date, Date mrs_score Categorical score, numeric mrs_complete Complete, numeric event_datetime Event datetime, POSIXct event_age Age time event, numeric event_type Event type, character new_event_complete Completed, character","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_meta.html","id":null,"dir":"Reference","previous_headings":"","what":"REDCap metadata from data base — redcapcast_meta","title":"REDCap metadata from data base — redcapcast_meta","text":"metadata dataset REDCap database demonstrational purposes.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_meta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"REDCap metadata from data base — redcapcast_meta","text":"","code":"data(redcapcast_meta)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_meta.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"REDCap metadata from data base — redcapcast_meta","text":"data frame 22 variables: field_name field_name, character form_name form_name, character section_header section_header, character field_type field_type, character field_label field_label, character select_choices_or_calculations select_choices_or_calculations, character field_note field_note, character text_validation_type_or_show_slider_number text_validation_type_or_show_slider_number, character text_validation_min text_validation_min, character text_validation_max text_validation_max, character identifier identifier, character branching_logic branching_logic, character required_field required_field, character custom_alignment custom_alignment, character question_number question_number, character matrix_group_name matrix_group_name, character matrix_ranking matrix_ranking, character field_annotation field_annotation, character","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":null,"dir":"Reference","previous_headings":"","what":"Sanitize list of data frames — sanitize_split","title":"Sanitize list of data frames — sanitize_split","text":"Removing empty rows","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sanitize list of data frames — sanitize_split","text":"","code":"sanitize_split(   l,   generic.names = c(\"redcap_event_name\", \"redcap_repeat_instrument\",     \"redcap_repeat_instance\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sanitize list of data frames — sanitize_split","text":"l list data frames. generic.names vector generic names excluded.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sanitize list of data frames — sanitize_split","text":"list data frames generic names excluded.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/server_factory.html","id":null,"dir":"Reference","previous_headings":"","what":"Shiny server factory — server_factory","title":"Shiny server factory — server_factory","text":"Shiny server factory","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/server_factory.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shiny server factory — server_factory","text":"","code":"server_factory()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/server_factory.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shiny server factory — server_factory","text":"shiny server","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":null,"dir":"Reference","previous_headings":"","what":"Launch the included Shiny-app for database casting and upload — shiny_cast","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"Launch included Shiny-app database casting upload","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"","code":"shiny_cast()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"shiny app","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"","code":"# shiny_cast()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":null,"dir":"Reference","previous_headings":"","what":"Split a data frame into separate tables for each form — split_non_repeating_forms","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"Split data frame separate tables form","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"","code":"split_non_repeating_forms(table, universal_fields, fields)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"table data frame universal_fields character vector fields included every table fields two-column matrix containing names fields included form","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"list data frames, one non-repeating form","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"","code":"# Create a table table <- data.frame(   id = c(1, 2, 3, 4, 5),   form_a_name = c(\"John\", \"Alice\", \"Bob\", \"Eve\", \"Mallory\"),   form_a_age = c(25, 30, 25, 15, 20),   form_b_name = c(\"John\", \"Alice\", \"Bob\", \"Eve\", \"Mallory\"),   form_b_gender = c(\"M\", \"F\", \"M\", \"F\", \"F\") )  # Create the universal fields universal_fields <- c(\"id\")  # Create the fields fields <- matrix(   c(     \"form_a_name\", \"form_a\",     \"form_a_age\", \"form_a\",     \"form_b_name\", \"form_b\",     \"form_b_gender\", \"form_b\"   ),   ncol = 2, byrow = TRUE )  # Split the table split_non_repeating_forms(table, universal_fields, fields) #> $form_a_age #>   id #> 1  1 #> 2  2 #> 3  3 #> 4  4 #> 5  5 #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":null,"dir":"Reference","previous_headings":"","what":"Extended string splitting — strsplitx","title":"Extended string splitting — strsplitx","text":"Can used substitute base function. Main claim fame easing split around defined delimiter, see example.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extended string splitting — strsplitx","text":"","code":"strsplitx(x, split, type = \"classic\", perl = FALSE, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extended string splitting — strsplitx","text":"x data split delimiter type Split type. Can c(\"classic\", \"\", \"\", \"around\") perl perl param strsplit() ... additional parameters passed base strsplit handling splits","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extended string splitting — strsplitx","text":"list","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extended string splitting — strsplitx","text":"","code":"test <- c(\"12 months follow-up\", \"3 steps\", \"mRS 6 weeks\", \"Counting to 231 now\") strsplitx(test, \"[0-9]\", type = \"around\") #> [[1]] #> [1] \"1\"                 \"2\"                 \" months follow-up\" #>  #> [[2]] #> [1] \"3\"      \" steps\" #>  #> [[3]] #> [1] \"mRS \"   \"6\"      \" weeks\" #>  #> [[4]] #> [1] \"Counting to \" \"2\"            \"3\"            \"1\"            \" now\"         #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":null,"dir":"Reference","previous_headings":"","what":"Correction based on time_only_filter function. Introduces new class for easier\nvalidation labelling. — time_only_correction","title":"Correction based on time_only_filter function. Introduces new class for easier\nvalidation labelling. — time_only_correction","text":"Dependens data class \"hms\" introduced `guess_time_only_filter()` converts ","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correction based on time_only_filter function. Introduces new class for easier\nvalidation labelling. — time_only_correction","text":"","code":"time_only_correction(data, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correction based on time_only_filter function. Introduces new class for easier\nvalidation labelling. — time_only_correction","text":"data data set ... arguments passed `guess_time_only_filter()`","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correction based on time_only_filter function. Introduces new class for easier\nvalidation labelling. — time_only_correction","text":"tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correction based on time_only_filter function. Introduces new class for easier\nvalidation labelling. — time_only_correction","text":"","code":"data <- redcapcast_data ## data |> time_only_correction()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ui_factory.html","id":null,"dir":"Reference","previous_headings":"","what":"UI factory for shiny app — ui_factory","title":"UI factory for shiny app — ui_factory","text":"UI factory shiny app","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ui_factory.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"UI factory for shiny app — ui_factory","text":"","code":"ui_factory()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ui_factory.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"UI factory for shiny app — ui_factory","text":"shiny ui","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-2-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 24.2.1","text":"Fix: ds2dd(): uses correct default dd column names. deprecated. Fix: easy_redcap(): fixed actually allow project naming. also specifically asks uri. widening updated work. Fix: redcap_wider(): updated accept formats allow handling simple projects without repeating instruments longitudinal. Fix: read_redcap_tables(): now handles non-longitudinal project without repeatable instruments. NEW: ds2dd_detailed(): extension ds2dd(), serves preserve much metadata possible automatically. Depends group helper functions also introduced. special note guess_time_only_filter(), try guess columns/variables formatted time formats. Supports hms time format. DETAILED INSTRUCTION VIGNETTE PENDING. NEW: read_redcap_instrument(): convenience function retrieve complete instrument. Goes little focused approach. REDCapR::redcap_read() can specify form download. also specify record id variable though. done read_redcap_instrument(). Nothing fancy. NEW: shiny_cast(): Shiny application ease process converting spreadsheet/data set REDCap database. app runs locally data transferred securely. can just create upload data dictionary, can also transfer given data process. plan host app shinyapps.io, now can run locally.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"other-24-2-1","dir":"Changelog","previous_headings":"","what":"Other","title":"REDCapCAST 24.2.1","text":"believe renv now added runs correctly. clone, renv::restore() install necessary package modify package.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"whishes-before-cran-release-24-2-1","dir":"Changelog","previous_headings":"","what":"Whishes before CRAN release","title":"REDCapCAST 24.2.1","text":"Vignette ds2dd_detailed() Tests ds2dd_detailed() Tests new functions.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2411","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.1.1","title":"REDCapCAST 24.1.1","text":"CRAN release: 2024-01-09","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-1-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 24.1.1","text":"Fix: read_redcap_tables(): checking form names based data dictionary allow handling non-longitudinal projects. Prints invalid form names invalid event names. invalid form names supplied REDCapR::redcap_read() (backbone), forms exported, want focused approach. Invalid event names give output rather peculiar formatting. Checking field names validity also added.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-23121","dir":"Changelog","previous_headings":"","what":"REDCapCAST 23.12.1","title":"REDCapCAST 23.12.1","text":"CRAN release: 2023-12-20 One new function ease secure dataset retrieval bug fixes.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-23-12-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 23.12.1","text":"New: easy_redcap() function ease retrieval dataset read_redcap_tables() keyring-package based key storage, handles secure API set, storage retrieval. Relies small helper function, get_api_key(), wraps relevant keyring-functions. Includes option cast data wide format flag widen.data. Fix: REDCap_split(): using function , supplying data set check boxes fail metadata supplied tibble. Metadata now converted data.frame. Fixed. Fix: read_redcap_tables(): fixed bug supplying events.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2362","dir":"Changelog","previous_headings":"","what":"REDCapCAST 23.6.2","title":"REDCapCAST 23.6.2","text":"CRAN release: 2023-07-04 version marks introduction helper functions handle database creation.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-23-6-2","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 23.6.2","text":"New: ds2dd() function migrating stRoke-package. Assists building data dictionary REDCap dataset. New: strsplitx() function ease string splitting extension base::strsplit(). Inspiration https://stackoverflow.com//11014253/21019325 https://www.r-bloggers.com/2018/04/strsplit--keeping--delimiter/. New: d2n() function converts single digits written numbers. Used sanitize variable form names REDCap database creation. universal number word suggest english::word() xfun::numbers_to_words(), though testing .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2361","dir":"Changelog","previous_headings":"","what":"REDCapCAST 23.6.1","title":"REDCapCAST 23.6.1","text":"CRAN release: 2023-06-06","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-23-6-1","dir":"Changelog","previous_headings":"","what":"Documentation:","title":"REDCapCAST 23.6.1","text":"Updated description. Look! hex icon! Heading CRAN.","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-23-4-1","dir":"Changelog","previous_headings":"","what":"Documentation:","title":"REDCapCAST 23.4.1","text":"Aiming CRAN","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-23-3-2","dir":"Changelog","previous_headings":"","what":"Documentation:","title":"REDCapCAST 23.3.2","text":"Page added. Vignettes follow. GithubActions tests added code coverage assessed. Badge galore..","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"new-name-redcapcast-23-3-1","dir":"Changelog","previous_headings":"","what":"New name: REDCapCAST","title":"REDCapCAST 23.3.1","text":"reflect new functions limitation working R, changed naming fork, still, course, maintaining status fork. versioning moved monthly naming convention. main goal package keep option export defined subset whole dataset REDCap server made possible REDCapR::redcap_read() function, combine work put REDCapRITS package handling longitudinal projects /projects repeated instruments.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-23-3-1","dir":"Changelog","previous_headings":"","what":"Functions:","title":"REDCapCAST 23.3.1","text":"read_redcap_tables() NEW: function mainly implementation combined use REDCapR::readcap_read() REDCap_split() maintain focused nature REDCapR::readcap_read(), download specified data. Also implements tests valid form names event names. usual fall-back solution get data. redcap_wider() NEW: function pivots long data frames read_redcap_tables() using tidyr::pivot_wider(). focused_metadata() NEW: hidden helper function enable focused data acquisition approach handle subset metadata corresponding focused dataset.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"notes-23-3-1","dir":"Changelog","previous_headings":"","what":"Notes:","title":"REDCapCAST 23.3.1","text":"metadata handling IMPROVED: improved handling different column names matadata (DataDictionary) REDCap dependent whether acquired thorugh api og downloaded server.","code":""}]