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fmtr-example1.html
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fmtr-example1.html
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.6.2</span>
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<h1 data-toc-skip>Complete Example</h1>
<small class="dont-index">Source: <a href="https://github.com/dbosak01/fmtr/blob/HEAD/vignettes/fmtr-example1.Rmd" class="external-link"><code>vignettes/fmtr-example1.Rmd</code></a></small>
<div class="hidden name"><code>fmtr-example1.Rmd</code></div>
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<div class="section level2">
<h2 id="program">Program<a class="anchor" aria-label="anchor" href="#program"></a>
</h2>
<p>The previous examples in the <strong>fmtr</strong> documentation were
intentionally simplified to focus on the workings of a particular
function. It is helpful to also view <strong>fmtr</strong> functions in
the context of a complete program. The following example shows a
complete program.</p>
<p>The data for this example has been included in the
<strong>fmtr</strong> package as an external data file. It may be
accessed using the <code><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file()</a></code> function as shown below,
or downloaded directly from the <strong>fmtr</strong> GitHub site <a href="https://raw.githubusercontent.com/dbosak01/fmtr/master/inst/extdata/DM.csv" class="external-link">here</a></p>
<div class="sourceCode" id="cb1"><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://tidyverse.tidyverse.org" class="external-link">tidyverse</a></span><span class="op">)</span></span>
<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://r-sassy.org" class="external-link">sassy</a></span><span class="op">)</span></span>
<span></span>
<span></span>
<span><span class="co"># Prepare Log -------------------------------------------------------------</span></span>
<span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span><span class="st">"logr.autolog"</span> <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> <span class="st">"logr.notes"</span> <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Get temp location for log and report output</span></span>
<span><span class="va">tmp</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir</a></span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Open log</span></span>
<span><span class="va">lf</span> <span class="op"><-</span> <span class="fu">log_open</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="va">tmp</span>, <span class="st">"example1.log"</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span></span>
<span><span class="co"># Load and Prepare Data ---------------------------------------------------</span></span>
<span></span>
<span><span class="fu">sep</span><span class="op">(</span><span class="st">"Prepare Data"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Get path to sample data</span></span>
<span><span class="va">pkg</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"extdata"</span>, package <span class="op">=</span> <span class="st">"fmtr"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Define data library</span></span>
<span><span class="fu">libname</span><span class="op">(</span><span class="va">sdtm</span>, <span class="va">pkg</span>, <span class="st">"csv"</span><span class="op">)</span> </span>
<span></span>
<span><span class="co"># Loads data into workspace</span></span>
<span><span class="fu">lib_load</span><span class="op">(</span><span class="va">sdtm</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Prepare data</span></span>
<span><span class="va">dm_mod</span> <span class="op"><-</span> <span class="va">sdtm.DM</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">USUBJID</span>, <span class="va">SEX</span>, <span class="va">AGE</span>, <span class="va">ARM</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">ARM</span> <span class="op">!=</span> <span class="st">"SCREEN FAILURE"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">put</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span></span>
<span><span class="fu">put</span><span class="op">(</span><span class="st">"Get ARM population counts"</span><span class="op">)</span></span>
<span><span class="va">arm_pop</span> <span class="op"><-</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/count.html" class="external-link">count</a></span><span class="op">(</span><span class="va">dm_mod</span>, <span class="va">ARM</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://tibble.tidyverse.org/reference/enframe.html" class="external-link">deframe</a></span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">put</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Create Format Catalog --------------------------------------------------</span></span>
<span><span class="fu">sep</span><span class="op">(</span><span class="st">"Create format catalog"</span><span class="op">)</span></span>
<span></span>
<span><span class="va">fmts</span> <span class="op"><-</span> <span class="fu"><a href="../reference/fcat.html">fcat</a></span><span class="op">(</span>AGECAT <span class="op">=</span> <span class="fu"><a href="../reference/value.html">value</a></span><span class="op">(</span><span class="fu"><a href="../reference/condition.html">condition</a></span><span class="op">(</span><span class="va">x</span> <span class="op">>=</span> <span class="fl">18</span> <span class="op">&</span> <span class="va">x</span> <span class="op"><=</span> <span class="fl">24</span>, <span class="st">"18 to 24"</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="../reference/condition.html">condition</a></span><span class="op">(</span><span class="va">x</span> <span class="op">>=</span> <span class="fl">25</span> <span class="op">&</span> <span class="va">x</span> <span class="op"><=</span> <span class="fl">44</span>, <span class="st">"25 to 44"</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="../reference/condition.html">condition</a></span><span class="op">(</span><span class="va">x</span> <span class="op">>=</span> <span class="fl">45</span> <span class="op">&</span> <span class="va">x</span> <span class="op"><=</span> <span class="fl">64</span>, <span class="st">"45 to 64"</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="../reference/condition.html">condition</a></span><span class="op">(</span><span class="va">x</span> <span class="op">>=</span> <span class="fl">65</span>, <span class="st">">= 65"</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="../reference/condition.html">condition</a></span><span class="op">(</span><span class="cn">TRUE</span>, <span class="st">"Other"</span><span class="op">)</span><span class="op">)</span>,</span>
<span> SEX <span class="op">=</span> <span class="fu"><a href="../reference/value.html">value</a></span><span class="op">(</span><span class="fu"><a href="../reference/condition.html">condition</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>, <span class="st">"Missing"</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="../reference/condition.html">condition</a></span><span class="op">(</span><span class="va">x</span> <span class="op">==</span> <span class="st">"M"</span>, <span class="st">"Male"</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="../reference/condition.html">condition</a></span><span class="op">(</span><span class="va">x</span> <span class="op">==</span> <span class="st">"F"</span>, <span class="st">"Female"</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="../reference/condition.html">condition</a></span><span class="op">(</span><span class="cn">TRUE</span>, <span class="st">"Other"</span><span class="op">)</span><span class="op">)</span>,</span>
<span> VAR <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">"AGE"</span> <span class="op">=</span> <span class="st">"Age"</span>, </span>
<span> <span class="st">"AGECAT"</span> <span class="op">=</span> <span class="st">"Age Group"</span>, </span>
<span> <span class="st">"SEX"</span> <span class="op">=</span> <span class="st">"Sex"</span><span class="op">)</span><span class="op">)</span> </span>
<span><span class="fu">put</span><span class="op">(</span><span class="va">fmts</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Age Summary Block -------------------------------------------------------</span></span>
<span></span>
<span><span class="fu">sep</span><span class="op">(</span><span class="st">"Create summary statistics for age"</span><span class="op">)</span></span>
<span></span>
<span><span class="va">age_block</span> <span class="op"><-</span> </span>
<span> <span class="va">dm_mod</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ARM</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span> N <span class="op">=</span> <span class="fu"><a href="../reference/fmt_n.html">fmt_n</a></span><span class="op">(</span><span class="va">AGE</span><span class="op">)</span>,</span>
<span> `Mean (SD)` <span class="op">=</span> <span class="fu"><a href="../reference/fmt_mean_sd.html">fmt_mean_sd</a></span><span class="op">(</span><span class="va">AGE</span><span class="op">)</span>,</span>
<span> Median <span class="op">=</span> <span class="fu"><a href="../reference/fmt_median.html">fmt_median</a></span><span class="op">(</span><span class="va">AGE</span><span class="op">)</span>,</span>
<span> `Q1 - Q3` <span class="op">=</span> <span class="fu"><a href="../reference/fmt_quantile_range.html">fmt_quantile_range</a></span><span class="op">(</span><span class="va">AGE</span><span class="op">)</span>,</span>
<span> Range <span class="op">=</span> <span class="fu"><a href="../reference/fmt_range.html">fmt_range</a></span><span class="op">(</span><span class="va">AGE</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
<span> <span class="fu"><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html" class="external-link">pivot_longer</a></span><span class="op">(</span><span class="op">-</span><span class="va">ARM</span>,</span>
<span> names_to <span class="op">=</span> <span class="st">"label"</span>,</span>
<span> values_to <span class="op">=</span> <span class="st">"value"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
<span> <span class="fu"><a href="https://tidyr.tidyverse.org/reference/pivot_wider.html" class="external-link">pivot_wider</a></span><span class="op">(</span>names_from <span class="op">=</span> <span class="va">ARM</span>,</span>
<span> values_from <span class="op">=</span> <span class="st">"value"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://tibble.tidyverse.org/reference/add_column.html" class="external-link">add_column</a></span><span class="op">(</span>var <span class="op">=</span> <span class="st">"AGE"</span>, .before <span class="op">=</span> <span class="st">"label"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">put</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span></span>
<span><span class="co"># Age Group Block ----------------------------------------------------------</span></span>
<span></span>
<span><span class="fu">sep</span><span class="op">(</span><span class="st">"Create frequency counts for Age Group"</span><span class="op">)</span></span>
<span></span>
<span></span>
<span><span class="fu">put</span><span class="op">(</span><span class="st">"Create age group frequency counts"</span><span class="op">)</span></span>
<span><span class="va">ageg_block</span> <span class="op"><-</span> </span>
<span> <span class="va">dm_mod</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>AGECAT <span class="op">=</span> <span class="fu"><a href="../reference/fapply.html">fapply</a></span><span class="op">(</span><span class="va">AGE</span>, <span class="va">fmts</span><span class="op">$</span><span class="va">AGECAT</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">ARM</span>, <span class="va">AGECAT</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ARM</span>, <span class="va">AGECAT</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>n <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://tidyr.tidyverse.org/reference/pivot_wider.html" class="external-link">pivot_wider</a></span><span class="op">(</span>names_from <span class="op">=</span> <span class="va">ARM</span>,</span>
<span> values_from <span class="op">=</span> <span class="va">n</span>, </span>
<span> values_fill <span class="op">=</span> <span class="fl">0</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/transmute.html" class="external-link">transmute</a></span><span class="op">(</span>var <span class="op">=</span> <span class="st">"AGECAT"</span>, </span>
<span> label <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">AGECAT</span>, levels <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">"18 to 24"</span>, </span>
<span> <span class="st">"25 to 44"</span>, </span>
<span> <span class="st">"45 to 64"</span>, </span>
<span> <span class="st">">= 65"</span><span class="op">)</span><span class="op">)</span>,</span>
<span> `ARM A` <span class="op">=</span> <span class="fu"><a href="../reference/fmt_cnt_pct.html">fmt_cnt_pct</a></span><span class="op">(</span><span class="va">`ARM A`</span>, <span class="va">arm_pop</span><span class="op">[</span><span class="st">"ARM A"</span><span class="op">]</span><span class="op">)</span>,</span>
<span> `ARM B` <span class="op">=</span> <span class="fu"><a href="../reference/fmt_cnt_pct.html">fmt_cnt_pct</a></span><span class="op">(</span><span class="va">`ARM B`</span>, <span class="va">arm_pop</span><span class="op">[</span><span class="st">"ARM B"</span><span class="op">]</span><span class="op">)</span>,</span>
<span> `ARM C` <span class="op">=</span> <span class="fu"><a href="../reference/fmt_cnt_pct.html">fmt_cnt_pct</a></span><span class="op">(</span><span class="va">`ARM C`</span>, <span class="va">arm_pop</span><span class="op">[</span><span class="st">"ARM C"</span><span class="op">]</span><span class="op">)</span>,</span>
<span> `ARM D` <span class="op">=</span> <span class="fu"><a href="../reference/fmt_cnt_pct.html">fmt_cnt_pct</a></span><span class="op">(</span><span class="va">`ARM D`</span>, <span class="va">arm_pop</span><span class="op">[</span><span class="st">"ARM D"</span><span class="op">]</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">label</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">put</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span></span>
<span><span class="co"># Sex Block ---------------------------------------------------------------</span></span>
<span></span>
<span><span class="fu">sep</span><span class="op">(</span><span class="st">"Create frequency counts for SEX"</span><span class="op">)</span></span>
<span></span>
<span></span>
<span><span class="co"># Create sex frequency counts </span></span>
<span><span class="va">sex_block</span> <span class="op"><-</span> </span>
<span> <span class="va">dm_mod</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">ARM</span>, <span class="va">SEX</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ARM</span>, <span class="va">SEX</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>n <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://tidyr.tidyverse.org/reference/pivot_wider.html" class="external-link">pivot_wider</a></span><span class="op">(</span>names_from <span class="op">=</span> <span class="va">ARM</span>,</span>
<span> values_from <span class="op">=</span> <span class="va">n</span>, </span>
<span> values_fill <span class="op">=</span> <span class="fl">0</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/transmute.html" class="external-link">transmute</a></span><span class="op">(</span>var <span class="op">=</span> <span class="st">"SEX"</span>, </span>
<span> label <span class="op">=</span> <span class="fu"><a href="https://forcats.tidyverse.org/reference/fct_relevel.html" class="external-link">fct_relevel</a></span><span class="op">(</span><span class="va">SEX</span>, <span class="st">"M"</span>, <span class="st">"F"</span><span class="op">)</span>, </span>
<span> `ARM A` <span class="op">=</span> <span class="fu"><a href="../reference/fmt_cnt_pct.html">fmt_cnt_pct</a></span><span class="op">(</span><span class="va">`ARM A`</span>, <span class="va">arm_pop</span><span class="op">[</span><span class="st">"ARM A"</span><span class="op">]</span><span class="op">)</span>,</span>
<span> `ARM B` <span class="op">=</span> <span class="fu"><a href="../reference/fmt_cnt_pct.html">fmt_cnt_pct</a></span><span class="op">(</span><span class="va">`ARM B`</span>, <span class="va">arm_pop</span><span class="op">[</span><span class="st">"ARM B"</span><span class="op">]</span><span class="op">)</span>,</span>
<span> `ARM C` <span class="op">=</span> <span class="fu"><a href="../reference/fmt_cnt_pct.html">fmt_cnt_pct</a></span><span class="op">(</span><span class="va">`ARM C`</span>, <span class="va">arm_pop</span><span class="op">[</span><span class="st">"ARM C"</span><span class="op">]</span><span class="op">)</span>,</span>
<span> `ARM D` <span class="op">=</span> <span class="fu"><a href="../reference/fmt_cnt_pct.html">fmt_cnt_pct</a></span><span class="op">(</span><span class="va">`ARM D`</span>, <span class="va">arm_pop</span><span class="op">[</span><span class="st">"ARM D"</span><span class="op">]</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">label</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>label <span class="op">=</span> <span class="fu"><a href="../reference/fapply.html">fapply</a></span><span class="op">(</span><span class="va">label</span>, <span class="va">fmts</span><span class="op">$</span><span class="va">SEX</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">put</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">put</span><span class="op">(</span><span class="st">"Combine blocks into final data frame"</span><span class="op">)</span></span>
<span><span class="va">final</span> <span class="op"><-</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows</a></span><span class="op">(</span><span class="va">age_block</span>, <span class="va">ageg_block</span>, <span class="va">sex_block</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">put</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Report ------------------------------------------------------------------</span></span>
<span></span>
<span></span>
<span><span class="fu">sep</span><span class="op">(</span><span class="st">"Create and print report"</span><span class="op">)</span></span>
<span></span>
<span></span>
<span><span class="co"># Create Table</span></span>
<span><span class="va">tbl</span> <span class="op"><-</span> <span class="fu">create_table</span><span class="op">(</span><span class="va">final</span>, first_row_blank <span class="op">=</span> <span class="cn">TRUE</span>, borders <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">"top"</span>, <span class="st">"bottom"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">column_defaults</span><span class="op">(</span>from <span class="op">=</span> <span class="va">`ARM A`</span>, to <span class="op">=</span> <span class="va">`ARM D`</span>, align <span class="op">=</span> <span class="st">"center"</span>, width <span class="op">=</span> <span class="fl">1.25</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">stub</span><span class="op">(</span>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">"var"</span>, <span class="st">"label"</span><span class="op">)</span>, <span class="st">"Variable"</span>, width <span class="op">=</span> <span class="fl">2.5</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">define</span><span class="op">(</span><span class="va">var</span>, blank_after <span class="op">=</span> <span class="cn">TRUE</span>, dedupe <span class="op">=</span> <span class="cn">TRUE</span>, label <span class="op">=</span> <span class="st">"Variable"</span>,</span>
<span> format <span class="op">=</span> <span class="va">fmts</span><span class="op">$</span><span class="va">VAR</span>,label_row <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">define</span><span class="op">(</span><span class="va">label</span>, indent <span class="op">=</span> <span class="fl">.25</span>, label <span class="op">=</span> <span class="st">"Demographic Category"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">define</span><span class="op">(</span><span class="va">`ARM A`</span>, label <span class="op">=</span> <span class="st">"Treatment Group 1"</span>, n <span class="op">=</span> <span class="va">arm_pop</span><span class="op">[</span><span class="st">"ARM A"</span><span class="op">]</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">define</span><span class="op">(</span><span class="va">`ARM B`</span>, label <span class="op">=</span> <span class="st">"Treatment Group 2"</span>, n <span class="op">=</span> <span class="va">arm_pop</span><span class="op">[</span><span class="st">"ARM B"</span><span class="op">]</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">define</span><span class="op">(</span><span class="va">`ARM C`</span>, label <span class="op">=</span> <span class="st">"Treatment Group 3"</span>, n <span class="op">=</span> <span class="va">arm_pop</span><span class="op">[</span><span class="st">"ARM C"</span><span class="op">]</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">define</span><span class="op">(</span><span class="va">`ARM D`</span>, label <span class="op">=</span> <span class="st">"Treatment Group 4"</span>, n <span class="op">=</span> <span class="va">arm_pop</span><span class="op">[</span><span class="st">"ARM D"</span><span class="op">]</span><span class="op">)</span> </span>
<span></span>
<span><span class="va">rpt</span> <span class="op"><-</span> <span class="fu">create_report</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="va">tmp</span>, <span class="st">"output/example1.rtf"</span><span class="op">)</span>, </span>
<span> output_type <span class="op">=</span> <span class="st">"RTF"</span>, font <span class="op">=</span> <span class="st">"Arial"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">set_margins</span><span class="op">(</span>top <span class="op">=</span> <span class="fl">1</span>, bottom <span class="op">=</span> <span class="fl">1</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">page_header</span><span class="op">(</span><span class="st">"Sponsor: Company"</span>, <span class="st">"Study: ABC"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">titles</span><span class="op">(</span><span class="st">"Table 1.0"</span>, bold <span class="op">=</span> <span class="cn">TRUE</span>, blank_row <span class="op">=</span> <span class="st">"none"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">titles</span><span class="op">(</span><span class="st">"Analysis of Demographic Characteristics"</span>, </span>
<span> <span class="st">"Safety Population"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">add_content</span><span class="op">(</span><span class="va">tbl</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">footnotes</span><span class="op">(</span><span class="st">"Program: DM_Table.R"</span>,</span>
<span> <span class="st">"NOTE: Denominator based on number of non-missing responses."</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span>
<span> <span class="fu">page_footer</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"Date Produced: "</span>, <span class="fu"><a href="../reference/fapply.html">fapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">"%d%b%y %H:%M"</span><span class="op">)</span><span class="op">)</span>, </span>
<span> right <span class="op">=</span> <span class="st">"Page [pg] of [tpg]"</span><span class="op">)</span></span>
<span></span>
<span><span class="va">res</span> <span class="op"><-</span> <span class="fu">write_report</span><span class="op">(</span><span class="va">rpt</span><span class="op">)</span></span>
<span></span>
<span></span>
<span><span class="co"># Clean Up ----------------------------------------------------------------</span></span>
<span><span class="fu">sep</span><span class="op">(</span><span class="st">"Clean Up"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Unload library from workspace</span></span>
<span><span class="fu">lib_unload</span><span class="op">(</span><span class="va">sdtm</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Close log</span></span>
<span><span class="fu">log_close</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># View log</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/writeLines.html" class="external-link">writeLines</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="va">lf</span>, encoding <span class="op">=</span> <span class="st">"UTF-8"</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># View report</span></span>
<span><span class="co"># file.show(res$modified_path)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="log">Log<a class="anchor" aria-label="anchor" href="#log"></a>
</h2>
<p>Here is the log produced by the above sample program:</p>
<pre><code>=========================================================================
Log Path: C:/Users/dbosa/AppData/Local/Temp/RtmpcV9Bys/log/example1.log
Program Path: C:\packages\Testing\fmtr_example1.R
Working Directory: C:/packages/Testing
User Name: dbosa
R Version: 4.1.2 (2021-11-01)
Machine: SOCRATES x86-64
Operating System: Windows 10 x64 build 19041
Base Packages: stats graphics grDevices utils datasets methods base
Other Packages: tidylog_1.0.2 reporter_1.2.6 libr_1.2.1 fmtr_1.5.3 logr_1.2.7
sassy_1.0.5 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
readr_2.0.2 tidyr_1.1.4 tibble_3.1.5 ggplot2_3.3.5 tidyverse_1.3.1
Log Start Time: 2021-11-17 10:32:36
=========================================================================
=========================================================================
Prepare Data
=========================================================================
# library 'sdtm': 1 items
- attributes: csv not loaded
- path: C:/Users/dbosa/Documents/R/win-library/4.1/fmtr/extdata
- items:
Name Extension Rows Cols Size LastModified
1 DM csv 87 24 45.4 Kb 2021-11-16 10:34:25
lib_load: library 'sdtm' loaded
select: dropped 20 variables (STUDYID, DOMAIN, SUBJID, RFSTDTC, RFENDTC, <U+0085>)
filter: removed 2 rows (2%), 85 rows remaining
# A tibble: 85 x 4
USUBJID SEX AGE ARM
<chr> <chr> <dbl> <chr>
1 ABC-01-049 M 39 ARM D
2 ABC-01-050 M 47 ARM B
3 ABC-01-051 M 34 ARM A
4 ABC-01-052 F 45 ARM C
5 ABC-01-053 F 26 ARM B
6 ABC-01-054 M 44 ARM D
7 ABC-01-055 F 47 ARM C
8 ABC-01-056 M 31 ARM A
9 ABC-01-113 M 74 ARM D
10 ABC-01-114 F 72 ARM B
# ... with 75 more rows
Get ARM population counts
count: now 4 rows and 2 columns, ungrouped
ARM A ARM B ARM C ARM D
20 21 21 23
=========================================================================
Create format catalog
=========================================================================
# A format catalog: 3 formats
- $AGECAT: type U, 5 conditions
- $SEX: type U, 4 conditions
- $VAR: type V, 3 elements
=========================================================================
Create summary statistics for age
=========================================================================
group_by: one grouping variable (ARM)
summarise: now 4 rows and 6 columns, ungrouped
pivot_longer: reorganized (N, Mean (SD), Median, Q1 - Q3, Range) into (label, value) [was 4x6, now 20x3]
pivot_wider: reorganized (ARM, value) into (ARM A, ARM B, ARM C, ARM D) [was 20x3, now 5x5]
# A tibble: 5 x 6
var label `ARM A` `ARM B` `ARM C` `ARM D`
<chr> <chr> <chr> <chr> <chr> <chr>
1 AGE N 20 21 21 23
2 AGE Mean (SD) 53.1 (11.9) 47.4 (16.3) 45.7 (14.4) 49.7 (14.3)
3 AGE Median 52.5 46.0 46.0 48.0
4 AGE Q1 - Q3 47.8 - 60.0 35.0 - 61.0 38.0 - 53.0 39.0 - 60.5
5 AGE Range 31 - 73 22 - 73 19 - 71 21 - 75
=========================================================================
Create frequency counts for Age Group
=========================================================================
Create age group frequency counts
mutate: new variable 'AGECAT' (character) with 4 unique values and 0% NA
select: dropped 3 variables (USUBJID, SEX, AGE)
group_by: 2 grouping variables (ARM, AGECAT)
summarize: now 15 rows and 3 columns, one group variable remaining (ARM)
pivot_wider: reorganized (ARM, n) into (ARM A, ARM B, ARM C, ARM D) [was 15x3, now 4x5]
transmute: dropped one variable (AGECAT)
new variable 'var' (character) with one unique value and 0% NA
new variable 'label' (factor) with 4 unique values and 0% NA
converted 'ARM A' from integer to character (0 new NA)
converted 'ARM B' from integer to character (0 new NA)
converted 'ARM C' from integer to character (0 new NA)
converted 'ARM D' from integer to character (0 new NA)
# A tibble: 4 x 6
var label `ARM A` `ARM B` `ARM C` `ARM D`
<chr> <fct> <chr> <chr> <chr> <chr>
1 AGECAT 18 to 24 0 ( 0.0%) 1 ( 4.8%) 3 ( 14.3%) 1 ( 4.3%)
2 AGECAT 25 to 44 4 ( 20.0%) 8 ( 38.1%) 4 ( 19.0%) 7 ( 30.4%)
3 AGECAT 45 to 64 13 ( 65.0%) 7 ( 33.3%) 12 ( 57.1%) 12 ( 52.2%)
4 AGECAT >= 65 3 ( 15.0%) 5 ( 23.8%) 2 ( 9.5%) 3 ( 13.0%)
=========================================================================
Create frequency counts for SEX
=========================================================================
select: dropped 2 variables (USUBJID, AGE)
group_by: 2 grouping variables (ARM, SEX)
summarize: now 8 rows and 3 columns, one group variable remaining (ARM)
pivot_wider: reorganized (ARM, n) into (ARM A, ARM B, ARM C, ARM D) [was 8x3, now 2x5]
transmute: dropped one variable (SEX)
new variable 'var' (character) with one unique value and 0% NA
new variable 'label' (factor) with 2 unique values and 0% NA
converted 'ARM A' from integer to character (0 new NA)
converted 'ARM B' from integer to character (0 new NA)
converted 'ARM C' from integer to character (0 new NA)
converted 'ARM D' from integer to character (0 new NA)
mutate: converted 'label' from factor to character (0 new NA)
# A tibble: 2 x 6
var label `ARM A` `ARM B` `ARM C` `ARM D`
<chr> <chr> <chr> <chr> <chr> <chr>
1 SEX Male 15 ( 75.0%) 10 ( 47.6%) 12 ( 57.1%) 16 ( 69.6%)
2 SEX Female 5 ( 25.0%) 11 ( 52.4%) 9 ( 42.9%) 7 ( 30.4%)
Combine blocks into final data frame
# A tibble: 11 x 6
var label `ARM A` `ARM B` `ARM C` `ARM D`
<chr> <chr> <chr> <chr> <chr> <chr>
1 AGE N 20 21 21 23
2 AGE Mean (SD) 53.1 (11.9) 47.4 (16.3) 45.7 (14.4) 49.7 (14.3)
3 AGE Median 52.5 46.0 46.0 48.0
4 AGE Q1 - Q3 47.8 - 60.0 35.0 - 61.0 38.0 - 53.0 39.0 - 60.5
5 AGE Range 31 - 73 22 - 73 19 - 71 21 - 75
6 AGECAT 18 to 24 0 ( 0.0%) 1 ( 4.8%) 3 ( 14.3%) 1 ( 4.3%)
7 AGECAT 25 to 44 4 ( 20.0%) 8 ( 38.1%) 4 ( 19.0%) 7 ( 30.4%)
8 AGECAT 45 to 64 13 ( 65.0%) 7 ( 33.3%) 12 ( 57.1%) 12 ( 52.2%)
9 AGECAT >= 65 3 ( 15.0%) 5 ( 23.8%) 2 ( 9.5%) 3 ( 13.0%)
10 SEX Male 15 ( 75.0%) 10 ( 47.6%) 12 ( 57.1%) 16 ( 69.6%)
11 SEX Female 5 ( 25.0%) 11 ( 52.4%) 9 ( 42.9%) 7 ( 30.4%)
=========================================================================
Create and print report
=========================================================================
# A report specification: 1 pages
- file_path: 'output/example1.rtf'
- output_type: RTF
- units: inches
- orientation: landscape
- margins: top 1 bottom 1 left 1 right 1
- line size/count: 9/40
- page_header: left=Sponsor: Company right=Study: ABC
- title 1: 'Table 1.0'
- title 2: 'Analysis of Demographic Characteristics'
- title 3: 'Safety Population'
- footnote 1: 'Program: DM_Table.R'
- footnote 2: 'NOTE: Denominator based on number of non-missing responses.'
- page_footer: left=Date Produced: 17Nov21 10:32 center= right=Page [pg] of [tpg]
- content:
# A table specification:
- data: tibble 'final' 11 rows 6 cols
- show_cols: all
- use_attributes: all
- stub: var label 'Variable' width=2.5 align='left'
- define: var 'Variable' dedupe='TRUE'
- define: label 'Demographic Category'
- define: ARM A 'Treatment Group 1'
- define: ARM B 'Treatment Group 2'
- define: ARM C 'Treatment Group 3'
- define: ARM D 'Treatment Group 4'
=========================================================================
Clean Up
=========================================================================
lib_sync: synchronized data in library 'sdtm'
lib_unload: library 'sdtm' unloaded
=========================================================================
Log End Time: 2021-11-17 10:32:36
Log Elapsed Time: 0 00:00:00
=========================================================================</code></pre>
</div>
<div class="section level2">
<h2 id="output">Output<a class="anchor" aria-label="anchor" href="#output"></a>
</h2>
<p>Here is the report produced by the above sample program:</p>
<p><img src="../man/images/example1.png"></p>
</div>
</div>
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