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<img src="../logo.png" class="logo" alt=""><h1>Shiny-app</h1>
<small class="dont-index">Source: <a href="https://github.com/agdamsbo/REDCapCAST/blob/main/vignettes/Shiny-app.Rmd" class="external-link"><code>vignettes/Shiny-app.Rmd</code></a></small>
<div class="d-none name"><code>Shiny-app.Rmd</code></div>
</div>
<p>To make the easiest possible transition from spreadsheet/dataset to
REDCap, I have created a small app, which adds a graphical interface to
the casting of a data dictionary and data upload. Install the package
and launch the app as follows:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu">REDCapCAST</span><span class="fu">::</span><span class="fu"><a href="../reference/shiny_cast.html">shiny_cast</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>The app primarily wraps one function:
<code><a href="../reference/ds2dd_detailed.html">ds2dd_detailed()</a></code>.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/agdamsbo/REDCapCAST" class="external-link">REDCapCAST</a></span><span class="op">)</span></span>
<span><span class="va">ds</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/REDCap_split.html">REDCap_split</a></span><span class="op">(</span></span>
<span> records <span class="op">=</span> <span class="va">redcapcast_data</span>,</span>
<span> metadata <span class="op">=</span> <span class="va">redcapcast_meta</span>,</span>
<span> forms <span class="op">=</span> <span class="st">"all"</span></span>
<span> <span class="op">)</span> <span class="op">|&gt;</span> </span>
<span> <span class="fu"><a href="../reference/sanitize_split.html">sanitize_split</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span>
<span> <span class="fu"><a href="../reference/redcap_wider.html">redcap_wider</a></span><span class="op">(</span><span class="op">)</span> </span>
<span><span class="co">#&gt; Joining with `by = join_by(record_id)`</span></span>
<span><span class="co">#&gt; Joining with `by = join_by(record_id)`</span></span>
<span><span class="co">#&gt; Joining with `by = join_by(record_id)`</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span></span>
<span><span class="co">#&gt; 'data.frame': 6 obs. of 52 variables:</span></span>
<span><span class="co">#&gt; $ record_id : num 1 2 3 4 5 6</span></span>
<span><span class="co">#&gt; $ cpr : chr "1203401OB4" "0102342303" "2301569823" "0204051342" ...</span></span>
<span><span class="co">#&gt; $ inclusion : Date, format: "2023-03-13" "2023-03-01" ...</span></span>
<span><span class="co">#&gt; $ inclusion_time : 'hms' num 12:38:49 10:38:57 12:01:07 20:39:19 ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "units")= chr "secs"</span></span>
<span><span class="co">#&gt; $ dob : Date, format: "1940-03-12" "1934-02-01" ...</span></span>
<span><span class="co">#&gt; $ age : num 83 89.1 66.1 117.9 126.2 ...</span></span>
<span><span class="co">#&gt; $ age_integer : num 83 89 66 117 126 91</span></span>
<span><span class="co">#&gt; $ sex : chr "female" "male" "male" "female" ...</span></span>
<span><span class="co">#&gt; $ cohabitation : chr "Yes" "Yes" "No" NA ...</span></span>
<span><span class="co">#&gt; $ hypertension : chr "No" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ diabetes : chr "Yes" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ region : chr "East" "South" "North" NA ...</span></span>
<span><span class="co">#&gt; $ baseline_data_start_complete: chr "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_inclusion : chr "Yes" "Yes" NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_follow1 : chr NA "Yes" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_follow2 : chr NA NA "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_date_inclusion : Date, format: "2023-03-13" "2023-03-07" ...</span></span>
<span><span class="co">#&gt; $ mrs_date_follow1 : Date, format: NA "2023-03-09" ...</span></span>
<span><span class="co">#&gt; $ mrs_date_follow2 : Date, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_score_inclusion : num 1 1 NA NA NA NA</span></span>
<span><span class="co">#&gt; $ mrs_score_follow1 : num NA 3 2 NA NA NA</span></span>
<span><span class="co">#&gt; $ mrs_score_follow2 : num NA NA 1 NA NA NA</span></span>
<span><span class="co">#&gt; $ mrs_complete_inclusion : chr "Incomplete" "Incomplete" NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete_follow1 : chr NA "Incomplete" "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete_follow2 : chr NA NA "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ con_mrs : logi NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; $ con_calc : logi NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; $ consensus_complete : chr NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_1_follow1 : POSIXct, format: NA "2024-01-18 12:49:42" ...</span></span>
<span><span class="co">#&gt; $ event_datetime_1_follow2 : POSIXct, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age_1_follow1 : num NA NA NA 96 127 NA</span></span>
<span><span class="co">#&gt; $ event_age_1_follow2 : num NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; $ event_type_1_follow1 : chr NA "TIA" "AIS" "TIA" ...</span></span>
<span><span class="co">#&gt; $ event_type_1_follow2 : chr NA NA "ICH" "AIS" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_1_follow1: chr NA "Incomplete" "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_1_follow2: chr NA NA "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ event_datetime_2_follow1 : POSIXct, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_2_follow2 : POSIXct, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_3_follow1 : POSIXct, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_3_follow2 : POSIXct, format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age_2_follow1 : num NA NA NA 105 127 NA</span></span>
<span><span class="co">#&gt; $ event_age_2_follow2 : num NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; $ event_age_3_follow1 : num NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; $ event_age_3_follow2 : num NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; $ event_type_2_follow1 : chr NA NA "ICH" "TIA" ...</span></span>
<span><span class="co">#&gt; $ event_type_2_follow2 : chr NA NA "TIA" "ICH" ...</span></span>
<span><span class="co">#&gt; $ event_type_3_follow1 : chr NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ event_type_3_follow2 : chr NA NA "AIS" "Unknown" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_2_follow1: chr NA NA "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_2_follow2: chr NA NA "Incomplete" "Incomplete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_3_follow1: chr NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_3_follow2: chr NA NA "Incomplete" "Complete" ...</span></span></code></pre></div>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">ds</span><span class="op">|&gt;</span> </span>
<span> <span class="fu"><a href="../reference/ds2dd_detailed.html">ds2dd_detailed</a></span><span class="op">(</span><span class="op">)</span><span class="op">|&gt;</span> </span>
<span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/pluck.html" class="external-link">pluck</a></span><span class="op">(</span><span class="st">"data"</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
<span> <span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; tibble [6 × 52] (S3: tbl_df/tbl/data.frame)</span></span>
<span><span class="co">#&gt; $ record_id : num [1:6] 1 2 3 4 5 6</span></span>
<span><span class="co">#&gt; $ cpr : chr [1:6] "1203401OB4" "0102342303" "2301569823" "0204051342" ...</span></span>
<span><span class="co">#&gt; $ inclusion : Date[1:6], format: "2023-03-13" "2023-03-01" ...</span></span>
<span><span class="co">#&gt; $ inclusion_time : chr [1:6] "12:38:49" "10:38:57" "12:01:07" "20:39:19" ...</span></span>
<span><span class="co">#&gt; $ dob : Date[1:6], format: "1940-03-12" "1934-02-01" ...</span></span>
<span><span class="co">#&gt; $ age : num [1:6] 83 89.1 66.1 117.9 126.2 ...</span></span>
<span><span class="co">#&gt; $ age_integer : num [1:6] 83 89 66 117 126 91</span></span>
<span><span class="co">#&gt; $ sex : chr [1:6] "female" "male" "male" "female" ...</span></span>
<span><span class="co">#&gt; $ cohabitation : chr [1:6] "Yes" "Yes" "No" NA ...</span></span>
<span><span class="co">#&gt; $ hypertension : chr [1:6] "No" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ diabetes : chr [1:6] "Yes" "No" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ region : chr [1:6] "East" "South" "North" NA ...</span></span>
<span><span class="co">#&gt; $ baseline_data_start_complete: chr [1:6] "Incomplete" "Incomplete" "Incomplete" "Incomplete" ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_inclusion : chr [1:6] "Yes" "Yes" NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_follow1 : chr [1:6] NA "Yes" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed_follow2 : chr [1:6] NA NA "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_date_inclusion : Date[1:6], format: "2023-03-13" "2023-03-07" ...</span></span>
<span><span class="co">#&gt; $ mrs_date_follow1 : Date[1:6], format: NA "2023-03-09" ...</span></span>
<span><span class="co">#&gt; $ mrs_date_follow2 : Date[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_score_inclusion : num [1:6] 1 1 NA NA NA NA</span></span>
<span><span class="co">#&gt; $ mrs_score_follow1 : num [1:6] NA 3 2 NA NA NA</span></span>
<span><span class="co">#&gt; $ mrs_score_follow2 : num [1:6] NA NA 1 NA NA NA</span></span>
<span><span class="co">#&gt; $ mrs_complete_inclusion : chr [1:6] "Incomplete" "Incomplete" NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete_follow1 : chr [1:6] NA "Incomplete" "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete_follow2 : chr [1:6] NA NA "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ con_mrs : Factor w/ 2 levels "FALSE","TRUE": NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; $ con_calc : Factor w/ 2 levels "FALSE","TRUE": NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; $ consensus_complete : chr [1:6] NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_1_follow1 : POSIXct[1:6], format: NA "2024-01-18 12:49:42" ...</span></span>
<span><span class="co">#&gt; $ event_datetime_1_follow2 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age_1_follow1 : num [1:6] NA NA NA 96 127 NA</span></span>
<span><span class="co">#&gt; $ event_age_1_follow2 : num [1:6] NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; $ event_type_1_follow1 : chr [1:6] NA "TIA" "AIS" "TIA" ...</span></span>
<span><span class="co">#&gt; $ event_type_1_follow2 : chr [1:6] NA NA "ICH" "AIS" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_1_follow1: chr [1:6] NA "Incomplete" "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_1_follow2: chr [1:6] NA NA "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ event_datetime_2_follow1 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_2_follow2 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_3_follow1 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime_3_follow2 : POSIXct[1:6], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age_2_follow1 : num [1:6] NA NA NA 105 127 NA</span></span>
<span><span class="co">#&gt; $ event_age_2_follow2 : num [1:6] NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; $ event_age_3_follow1 : num [1:6] NA NA NA NA NA NA</span></span>
<span><span class="co">#&gt; $ event_age_3_follow2 : num [1:6] NA NA NA 118 NA NA</span></span>
<span><span class="co">#&gt; $ event_type_2_follow1 : chr [1:6] NA NA "ICH" "TIA" ...</span></span>
<span><span class="co">#&gt; $ event_type_2_follow2 : chr [1:6] NA NA "TIA" "ICH" ...</span></span>
<span><span class="co">#&gt; $ event_type_3_follow1 : chr [1:6] NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ event_type_3_follow2 : chr [1:6] NA NA "AIS" "Unknown" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_2_follow1: chr [1:6] NA NA "Incomplete" "Complete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_2_follow2: chr [1:6] NA NA "Incomplete" "Incomplete" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_3_follow1: chr [1:6] NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ new_event_complete_3_follow2: chr [1:6] NA NA "Incomplete" "Complete" ...</span></span></code></pre></div>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">ds</span><span class="op">|&gt;</span> </span>
<span> <span class="fu"><a href="../reference/ds2dd_detailed.html">ds2dd_detailed</a></span><span class="op">(</span><span class="op">)</span><span class="op">|&gt;</span> </span>
<span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/pluck.html" class="external-link">pluck</a></span><span class="op">(</span><span class="st">"meta"</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
<span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 10 × 18</span></span></span>
<span><span class="co">#&gt; field_name form_name section_header field_type field_label </span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> record_id data <span style="color: #BB0000;">NA</span> text record_id </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> cpr data <span style="color: #BB0000;">NA</span> text cpr </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> inclusion data <span style="color: #BB0000;">NA</span> text inclusion </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> inclusion_time data <span style="color: #BB0000;">NA</span> text inclusion_time</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> dob data <span style="color: #BB0000;">NA</span> text dob </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> age data <span style="color: #BB0000;">NA</span> text age </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> age_integer data <span style="color: #BB0000;">NA</span> text age_integer </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> sex data <span style="color: #BB0000;">NA</span> text sex </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> cohabitation data <span style="color: #BB0000;">NA</span> text cohabitation </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> hypertension data <span style="color: #BB0000;">NA</span> text hypertension </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 13 more variables: select_choices_or_calculations &lt;chr&gt;, field_note &lt;lgl&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># text_validation_type_or_show_slider_number &lt;chr&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># text_validation_min &lt;lgl&gt;, text_validation_max &lt;lgl&gt;, identifier &lt;lgl&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># branching_logic &lt;lgl&gt;, required_field &lt;lgl&gt;, custom_alignment &lt;lgl&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># question_number &lt;lgl&gt;, matrix_group_name &lt;lgl&gt;, matrix_ranking &lt;lgl&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># field_annotation &lt;lgl&gt;</span></span></span></code></pre></div>
<p>Different data formats are accepted, which all mostly implements the
<code><a href="https://readr.tidyverse.org/reference/parse_guess.html" class="external-link">readr::col_guess()</a></code> functionality to parse column
classes.</p>
<p>To ensure uniformity in data import this parsing has been implemented
on its own to use with <code><a href="../reference/ds2dd_detailed.html">ds2dd_detailed()</a></code> or any other data
set for that matter:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">ds_parsed</span> <span class="op">&lt;-</span> <span class="va">redcapcast_data</span> <span class="op">|&gt;</span> </span>
<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/everything.html" class="external-link">everything</a></span><span class="op">(</span><span class="op">)</span>,<span class="va">as.character</span><span class="op">)</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
<span> <span class="fu"><a href="../reference/parse_data.html">parse_data</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="va">ds_parsed</span><span class="op">)</span></span>
<span><span class="co">#&gt; tibble [25 × 27] (S3: tbl_df/tbl/data.frame)</span></span>
<span><span class="co">#&gt; $ record_id : num [1:25] 1 2 2 2 3 3 3 3 3 3 ...</span></span>
<span><span class="co">#&gt; $ redcap_event_name : chr [1:25] "inclusion" "inclusion" "follow1" "follow1" ...</span></span>
<span><span class="co">#&gt; $ redcap_repeat_instrument : chr [1:25] NA NA NA "New Event (?)" ...</span></span>
<span><span class="co">#&gt; $ redcap_repeat_instance : num [1:25] NA NA NA 1 NA NA NA 1 2 1 ...</span></span>
<span><span class="co">#&gt; $ cpr : chr [1:25] "1203401OB4" "0102342303" NA NA ...</span></span>
<span><span class="co">#&gt; $ inclusion : Date[1:25], format: "2023-03-13" "2023-03-01" ...</span></span>
<span><span class="co">#&gt; $ inclusion_time : 'hms' num [1:25] 12:38:49 10:38:57 NA NA ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "units")= chr "secs"</span></span>
<span><span class="co">#&gt; $ dob : Date[1:25], format: "1940-03-12" "1934-02-01" ...</span></span>
<span><span class="co">#&gt; $ age : num [1:25] 83 89.1 NA NA 66.1 ...</span></span>
<span><span class="co">#&gt; $ age_integer : num [1:25] 83 89 NA NA 66 NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ sex : chr [1:25] "female" "male" NA NA ...</span></span>
<span><span class="co">#&gt; $ cohabitation : chr [1:25] "Yes" "Yes" NA NA ...</span></span>
<span><span class="co">#&gt; $ hypertension : chr [1:25] "No" "No" NA NA ...</span></span>
<span><span class="co">#&gt; $ diabetes : chr [1:25] "Yes" "No" NA NA ...</span></span>
<span><span class="co">#&gt; $ region : chr [1:25] "East" "South" NA NA ...</span></span>
<span><span class="co">#&gt; $ baseline_data_start_complete: chr [1:25] "Incomplete" "Incomplete" NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed : chr [1:25] "Yes" "Yes" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_date : Date[1:25], format: "2023-03-13" "2023-03-07" ...</span></span>
<span><span class="co">#&gt; $ mrs_score : num [1:25] 1 1 3 NA NA 2 1 NA NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete : chr [1:25] "Incomplete" "Incomplete" "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ con_mrs : logi [1:25] NA NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ con_calc : logi [1:25] NA NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ consensus_complete : chr [1:25] NA NA "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime : POSIXct[1:25], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age : num [1:25] NA NA NA NA NA NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ event_type : chr [1:25] NA NA NA "TIA" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete : chr [1:25] NA NA NA "Incomplete" ...</span></span>
<span><span class="co">#&gt; - attr(*, "problems")=&lt;externalptr&gt;</span></span></code></pre></div>
<p>It will ignore specified columns, which is neat for numeric-looking
strings like cpr-with a leading 0:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">redcapcast_data</span> <span class="op">|&gt;</span> </span>
<span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/everything.html" class="external-link">everything</a></span><span class="op">(</span><span class="op">)</span>,<span class="va">as.character</span><span class="op">)</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
<span> <span class="fu"><a href="../reference/parse_data.html">parse_data</a></span><span class="op">(</span>ignore.vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"record_id"</span>,<span class="st">"cpr"</span><span class="op">)</span><span class="op">)</span> <span class="op">|&gt;</span> </span>
<span> <span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; tibble [25 × 27] (S3: tbl_df/tbl/data.frame)</span></span>
<span><span class="co">#&gt; $ record_id : chr [1:25] "1" "2" "2" "2" ...</span></span>
<span><span class="co">#&gt; $ redcap_event_name : chr [1:25] "inclusion" "inclusion" "follow1" "follow1" ...</span></span>
<span><span class="co">#&gt; $ redcap_repeat_instrument : chr [1:25] NA NA NA "New Event (?)" ...</span></span>
<span><span class="co">#&gt; $ redcap_repeat_instance : num [1:25] NA NA NA 1 NA NA NA 1 2 1 ...</span></span>
<span><span class="co">#&gt; $ cpr : chr [1:25] "1203401OB4" "0102342303" NA NA ...</span></span>
<span><span class="co">#&gt; $ inclusion : Date[1:25], format: "2023-03-13" "2023-03-01" ...</span></span>
<span><span class="co">#&gt; $ inclusion_time : 'hms' num [1:25] 12:38:49 10:38:57 NA NA ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "units")= chr "secs"</span></span>
<span><span class="co">#&gt; $ dob : Date[1:25], format: "1940-03-12" "1934-02-01" ...</span></span>
<span><span class="co">#&gt; $ age : num [1:25] 83 89.1 NA NA 66.1 ...</span></span>
<span><span class="co">#&gt; $ age_integer : num [1:25] 83 89 NA NA 66 NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ sex : chr [1:25] "female" "male" NA NA ...</span></span>
<span><span class="co">#&gt; $ cohabitation : chr [1:25] "Yes" "Yes" NA NA ...</span></span>
<span><span class="co">#&gt; $ hypertension : chr [1:25] "No" "No" NA NA ...</span></span>
<span><span class="co">#&gt; $ diabetes : chr [1:25] "Yes" "No" NA NA ...</span></span>
<span><span class="co">#&gt; $ region : chr [1:25] "East" "South" NA NA ...</span></span>
<span><span class="co">#&gt; $ baseline_data_start_complete: chr [1:25] "Incomplete" "Incomplete" NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed : chr [1:25] "Yes" "Yes" "Yes" NA ...</span></span>
<span><span class="co">#&gt; $ mrs_date : Date[1:25], format: "2023-03-13" "2023-03-07" ...</span></span>
<span><span class="co">#&gt; $ mrs_score : num [1:25] 1 1 3 NA NA 2 1 NA NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete : chr [1:25] "Incomplete" "Incomplete" "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ con_mrs : logi [1:25] NA NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ con_calc : logi [1:25] NA NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ consensus_complete : chr [1:25] NA NA "Incomplete" NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime : POSIXct[1:25], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age : num [1:25] NA NA NA NA NA NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ event_type : chr [1:25] NA NA NA "TIA" ...</span></span>
<span><span class="co">#&gt; $ new_event_complete : chr [1:25] NA NA NA "Incomplete" ...</span></span>
<span><span class="co">#&gt; - attr(*, "problems")=&lt;externalptr&gt;</span></span></code></pre></div>
<p>Column classes can be passed to <code><a href="../reference/parse_data.html">parse_data()</a></code>.</p>
<p>Making a few crude assumption for factorising data,
<code><a href="../reference/numchar2fct.html">numchar2fct()</a></code> factorises numerical and character vectors
based on a set threshold for unique values:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">mtcars</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; 'data.frame': 32 obs. of 11 variables:</span></span>
<span><span class="co">#&gt; $ mpg : num 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ...</span></span>
<span><span class="co">#&gt; $ cyl : num 6 6 4 6 8 6 8 4 4 6 ...</span></span>
<span><span class="co">#&gt; $ disp: num 160 160 108 258 360 ...</span></span>
<span><span class="co">#&gt; $ hp : num 110 110 93 110 175 105 245 62 95 123 ...</span></span>
<span><span class="co">#&gt; $ drat: num 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ...</span></span>
<span><span class="co">#&gt; $ wt : num 2.62 2.88 2.32 3.21 3.44 ...</span></span>
<span><span class="co">#&gt; $ qsec: num 16.5 17 18.6 19.4 17 ...</span></span>
<span><span class="co">#&gt; $ vs : num 0 0 1 1 0 1 0 1 1 1 ...</span></span>
<span><span class="co">#&gt; $ am : num 1 1 1 0 0 0 0 0 0 0 ...</span></span>
<span><span class="co">#&gt; $ gear: num 4 4 4 3 3 3 3 4 4 4 ...</span></span>
<span><span class="co">#&gt; $ carb: num 4 4 1 1 2 1 4 2 2 4 ...</span></span>
<span><span class="va">mtcars</span> <span class="op">|&gt;</span></span>
<span> <span class="fu"><a href="../reference/numchar2fct.html">numchar2fct</a></span><span class="op">(</span>numeric.threshold <span class="op">=</span> <span class="fl">6</span><span class="op">)</span> <span class="op">|&gt;</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; 'data.frame': 32 obs. of 11 variables:</span></span>
<span><span class="co">#&gt; $ mpg : num 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ...</span></span>
<span><span class="co">#&gt; $ cyl : Factor w/ 3 levels "4","6","8": 2 2 1 2 3 2 3 1 1 2 ...</span></span>
<span><span class="co">#&gt; $ disp: num 160 160 108 258 360 ...</span></span>
<span><span class="co">#&gt; $ hp : num 110 110 93 110 175 105 245 62 95 123 ...</span></span>
<span><span class="co">#&gt; $ drat: num 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ...</span></span>
<span><span class="co">#&gt; $ wt : num 2.62 2.88 2.32 3.21 3.44 ...</span></span>
<span><span class="co">#&gt; $ qsec: num 16.5 17 18.6 19.4 17 ...</span></span>
<span><span class="co">#&gt; $ vs : Factor w/ 2 levels "0","1": 1 1 2 2 1 2 1 2 2 2 ...</span></span>
<span><span class="co">#&gt; $ am : Factor w/ 2 levels "0","1": 2 2 2 1 1 1 1 1 1 1 ...</span></span>
<span><span class="co">#&gt; $ gear: Factor w/ 3 levels "3","4","5": 2 2 2 1 1 1 1 2 2 2 ...</span></span>
<span><span class="co">#&gt; $ carb: Factor w/ 6 levels "1","2","3","4",..: 4 4 1 1 2 1 4 2 2 4 ...</span></span></code></pre></div>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">ds_parsed</span><span class="op">|&gt;</span></span>
<span> <span class="fu"><a href="../reference/numchar2fct.html">numchar2fct</a></span><span class="op">(</span>numeric.threshold <span class="op">=</span> <span class="fl">2</span><span class="op">)</span> <span class="op">|&gt;</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; Warning: There were 13 warnings in `dplyr::mutate()`.</span></span>
<span><span class="co">#&gt; The first warning was:</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> In argument: `dplyr::across(...)`.</span></span>
<span><span class="co">#&gt; Caused by warning in `.roman2numeric()`:</span></span>
<span><span class="co">#&gt; <span style="color: #BBBB00;">!</span> invalid roman numerals: inclusion inclusion follow1 follow1 inclusion follow1 follow2 follow1 follow1 follow2 follow2 follow2 inclusion follow1 follow2 follow1 follow1 follow2 follow2 follow2 inclusion follow1 follow1 follow1 inclusion</span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 12 remaining warnings.</span></span>
<span><span class="co">#&gt; tibble [25 × 27] (S3: tbl_df/tbl/data.frame)</span></span>
<span><span class="co">#&gt; $ record_id : num [1:25] 1 2 2 2 3 3 3 3 3 3 ...</span></span>
<span><span class="co">#&gt; $ redcap_event_name : Factor w/ 3 levels "inclusion","follow1",..: 1 1 2 2 1 2 3 2 2 3 ...</span></span>
<span><span class="co">#&gt; $ redcap_repeat_instrument : Factor w/ 1 level "New Event (?)": NA NA NA 1 NA NA NA 1 1 1 ...</span></span>
<span><span class="co">#&gt; $ redcap_repeat_instance : num [1:25] NA NA NA 1 NA NA NA 1 2 1 ...</span></span>
<span><span class="co">#&gt; $ cpr : chr [1:25] "1203401OB4" "0102342303" NA NA ...</span></span>
<span><span class="co">#&gt; $ inclusion : Date[1:25], format: "2023-03-13" "2023-03-01" ...</span></span>
<span><span class="co">#&gt; $ inclusion_time : 'hms' num [1:25] 12:38:49 10:38:57 NA NA ...</span></span>
<span><span class="co">#&gt; ..- attr(*, "units")= chr "secs"</span></span>
<span><span class="co">#&gt; $ dob : Date[1:25], format: "1940-03-12" "1934-02-01" ...</span></span>
<span><span class="co">#&gt; $ age : num [1:25] 83 89.1 NA NA 66.1 ...</span></span>
<span><span class="co">#&gt; $ age_integer : num [1:25] 83 89 NA NA 66 NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ sex : Factor w/ 2 levels "female","male": 1 2 NA NA 2 NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ cohabitation : Factor w/ 2 levels "Yes","No": 1 1 NA NA 2 NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ hypertension : Factor w/ 2 levels "No","Yes": 1 1 NA NA 2 NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ diabetes : Factor w/ 2 levels "Yes","No": 1 2 NA NA 1 NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ region : Factor w/ 3 levels "East","South",..: 1 2 NA NA 3 NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ baseline_data_start_complete: Factor w/ 2 levels "Incomplete","Complete": 1 1 NA NA 1 NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_assessed : Factor w/ 1 level "Yes": 1 1 1 NA NA 1 1 NA NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_date : Date[1:25], format: "2023-03-13" "2023-03-07" ...</span></span>
<span><span class="co">#&gt; $ mrs_score : num [1:25] 1 1 3 NA NA 2 1 NA NA NA ...</span></span>
<span><span class="co">#&gt; $ mrs_complete : Factor w/ 1 level "Incomplete": 1 1 1 NA 1 1 1 NA NA NA ...</span></span>
<span><span class="co">#&gt; $ con_mrs : logi [1:25] NA NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ con_calc : logi [1:25] NA NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ consensus_complete : Factor w/ 1 level "Incomplete": NA NA 1 NA NA 1 1 NA NA NA ...</span></span>
<span><span class="co">#&gt; $ event_datetime : POSIXct[1:25], format: NA NA ...</span></span>
<span><span class="co">#&gt; $ event_age : num [1:25] NA NA NA NA NA NA NA NA NA NA ...</span></span>
<span><span class="co">#&gt; $ event_type : Factor w/ 4 levels "TIA","AIS","ICH",..: NA NA NA 1 NA NA NA 2 3 3 ...</span></span>
<span><span class="co">#&gt; $ new_event_complete : Factor w/ 2 levels "Incomplete","Complete": NA NA NA 1 NA NA NA 1 1 1 ...</span></span>
<span><span class="co">#&gt; - attr(*, "problems")=&lt;externalptr&gt;</span></span></code></pre></div>
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