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48 changes: 28 additions & 20 deletions tlf-ae-summary.html
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Expand Up @@ -412,14 +412,15 @@ <h1 class="title"><span id="sec-aesummary" class="quarto-section-identifier"><sp
<span id="cb4-9"><a href="#cb4-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(USUBJID, TRTAN, all, drug, ser, drug_ser, die) <span class="sc">%&gt;%</span></span>
<span id="cb4-10"><a href="#cb4-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">pivot_longer</span>(<span class="at">cols =</span> <span class="fu">c</span>(all, drug, ser, drug_ser, die))</span>
<span id="cb4-11"><a href="#cb4-11" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-12"><a href="#cb4-12" aria-hidden="true" tabindex="-1"></a>tidy_ae <span class="sc">%&gt;%</span> <span class="fu">head</span>(<span class="dv">4</span>)</span>
<span id="cb4-13"><a href="#cb4-13" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; # A tibble: 4 × 4</span></span>
<span id="cb4-12"><a href="#cb4-12" aria-hidden="true" tabindex="-1"></a>tidy_ae</span>
<span id="cb4-13"><a href="#cb4-13" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; # A tibble: 5,955 × 4</span></span>
<span id="cb4-14"><a href="#cb4-14" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; USUBJID TRTAN name value</span></span>
<span id="cb4-15"><a href="#cb4-15" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; &lt;lgl&gt;</span></span>
<span id="cb4-16"><a href="#cb4-16" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1 01-701-1015 0 all TRUE </span></span>
<span id="cb4-17"><a href="#cb4-17" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 2 01-701-1015 0 drug TRUE </span></span>
<span id="cb4-18"><a href="#cb4-18" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 3 01-701-1015 0 ser FALSE</span></span>
<span id="cb4-19"><a href="#cb4-19" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 4 01-701-1015 0 drug_ser FALSE</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span id="cb4-19"><a href="#cb4-19" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 4 01-701-1015 0 drug_ser FALSE</span></span>
<span id="cb4-20"><a href="#cb4-20" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; # ℹ 5,951 more rows</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>We summarize the number and percentage of participants who meet each AE criteria.</p>
<div class="cell">
Expand All @@ -444,15 +445,23 @@ <h1 class="title"><span id="sec-aesummary" class="quarto-section-identifier"><sp
<span id="cb6-9"><a href="#cb6-9" aria-hidden="true" tabindex="-1"></a> <span class="at">pct =</span> <span class="fu">paste0</span>(<span class="st">"("</span>, pct, <span class="st">")"</span>)</span>
<span id="cb6-10"><a href="#cb6-10" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb6-11"><a href="#cb6-11" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-12"><a href="#cb6-12" aria-hidden="true" tabindex="-1"></a>ana <span class="sc">%&gt;%</span> <span class="fu">head</span>(<span class="dv">4</span>)</span>
<span id="cb6-13"><a href="#cb6-13" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; # A tibble: 4 × 5</span></span>
<span id="cb6-14"><a href="#cb6-14" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; # Groups: TRTAN [2]</span></span>
<span id="cb6-15"><a href="#cb6-15" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; TRTAN name n tot pct </span></span>
<span id="cb6-16"><a href="#cb6-16" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;dbl&gt; &lt;chr&gt; &lt;chr&gt; &lt;int&gt; &lt;chr&gt; </span></span>
<span id="cb6-17"><a href="#cb6-17" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1 0 all " 69" 86 ( 80.2)</span></span>
<span id="cb6-18"><a href="#cb6-18" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 2 0 die " 2" 86 ( 2.3)</span></span>
<span id="cb6-19"><a href="#cb6-19" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 3 0 drug " 44" 86 ( 51.2)</span></span>
<span id="cb6-20"><a href="#cb6-20" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 4 54 all " 77" 84 ( 91.7)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span id="cb6-12"><a href="#cb6-12" aria-hidden="true" tabindex="-1"></a>ana</span>
<span id="cb6-13"><a href="#cb6-13" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; # A tibble: 12 × 5</span></span>
<span id="cb6-14"><a href="#cb6-14" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; # Groups: TRTAN [3]</span></span>
<span id="cb6-15"><a href="#cb6-15" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; TRTAN name n tot pct </span></span>
<span id="cb6-16"><a href="#cb6-16" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;dbl&gt; &lt;chr&gt; &lt;chr&gt; &lt;int&gt; &lt;chr&gt; </span></span>
<span id="cb6-17"><a href="#cb6-17" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1 0 all " 69" 86 ( 80.2)</span></span>
<span id="cb6-18"><a href="#cb6-18" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 2 0 die " 2" 86 ( 2.3)</span></span>
<span id="cb6-19"><a href="#cb6-19" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 3 0 drug " 44" 86 ( 51.2)</span></span>
<span id="cb6-20"><a href="#cb6-20" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 4 54 all " 77" 84 ( 91.7)</span></span>
<span id="cb6-21"><a href="#cb6-21" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 5 54 die " 1" 84 ( 1.2)</span></span>
<span id="cb6-22"><a href="#cb6-22" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 6 54 drug " 73" 84 ( 86.9)</span></span>
<span id="cb6-23"><a href="#cb6-23" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 7 54 drug_ser " 1" 84 ( 1.2)</span></span>
<span id="cb6-24"><a href="#cb6-24" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 8 54 ser " 1" 84 ( 1.2)</span></span>
<span id="cb6-25"><a href="#cb6-25" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 9 81 all " 79" 84 ( 94.0)</span></span>
<span id="cb6-26"><a href="#cb6-26" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 10 81 drug " 70" 84 ( 83.3)</span></span>
<span id="cb6-27"><a href="#cb6-27" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 11 81 drug_ser " 1" 84 ( 1.2)</span></span>
<span id="cb6-28"><a href="#cb6-28" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 12 81 ser " 2" 84 ( 2.4)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>We prepare reporting-ready dataset for each AE group.</p>
<div class="cell">
Expand Down Expand Up @@ -508,14 +517,13 @@ <h1 class="title"><span id="sec-aesummary" class="quarto-section-identifier"><sp
<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a>tbl_ae_summary</span>
<span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; # A tibble: 6 × 7</span></span>
<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; name n_0 pct_0 n_54 pct_54 n_81 pct_81</span></span>
<span id="cb9-7"><a href="#cb9-7" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; </span></span>
<span id="cb9-8"><a href="#cb9-8" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1 Participants in population " 8… &lt;NA&gt; " 8… &lt;NA&gt; " 8… &lt;NA&gt; </span></span>
<span id="cb9-9"><a href="#cb9-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 2 With one or more adverse events " 6… ( 80… " 7… ( 91.… " 7… ( 94.…</span></span>
<span id="cb9-10"><a href="#cb9-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 3 With drug-related adverse events " 4… ( 51… " 7… ( 86.… " 7… ( 83.…</span></span>
<span id="cb9-11"><a href="#cb9-11" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 4 With serious adverse events " … ( 0… " … ( 1.… " … ( 2.…</span></span>
<span id="cb9-12"><a href="#cb9-12" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 5 With serious drug-related adverse events " … ( 0… " … ( 1.… " … ( 1.…</span></span>
<span id="cb9-13"><a href="#cb9-13" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 6 Who died " … ( 2… " … ( 1.… " … ( 0.…</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; name n_0 pct_0 n_54 pct_54 n_81 pct_81 </span></span>
<span id="cb9-7"><a href="#cb9-7" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; </span></span>
<span id="cb9-8"><a href="#cb9-8" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1 Participants in population " 86" &lt;NA&gt; " 84" &lt;NA&gt; " 84" &lt;NA&gt; </span></span>
<span id="cb9-9"><a href="#cb9-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 2 With one or more adverse events " 69" ( 80.2) " 77" ( 91.7) " 79" ( 94.0)</span></span>
<span id="cb9-10"><a href="#cb9-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 3 With drug-related adverse events " 44" ( 51.2) " 73" ( 86.9) " 70" ( 83.3)</span></span>
<span id="cb9-11"><a href="#cb9-11" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 4 With serious adverse events " 0" ( 0.0) " 1" ( 1.2) " 2" ( 2.4)</span></span>
<span id="cb9-12"><a href="#cb9-12" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; # ℹ 2 more rows</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>We define the format of the output using code below:</p>
<div class="cell">
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Expand Up @@ -508,19 +508,13 @@ <h1 class="title"><span class="chapter-number">4</span>&nbsp; <span class="chapt
<span id="cb4-10"><a href="#cb4-10" aria-hidden="true" tabindex="-1"></a><span class="fu">names</span>(tbl_base) <span class="ot">&lt;-</span> <span class="fu">str_replace_all</span>(<span class="fu">names</span>(tbl_base), <span class="fu">intToUtf8</span>(<span class="dv">160</span>), <span class="st">" "</span>)</span>
<span id="cb4-11"><a href="#cb4-11" aria-hidden="true" tabindex="-1"></a>tbl_base</span>
<span id="cb4-12"><a href="#cb4-12" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; # A tibble: 11 × 5</span></span>
<span id="cb4-13"><a href="#cb4-13" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ` ` Placebo `Xanomeline High Dose` `Xanomeline Low Dose` Overall</span></span>
<span id="cb4-14"><a href="#cb4-14" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; </span></span>
<span id="cb4-15"><a href="#cb4-15" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1 "" "(N=86… "(N=84)" "(N=84)" "(N=25…</span></span>
<span id="cb4-16"><a href="#cb4-16" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 2 "SEX" "" "" "" "" </span></span>
<span id="cb4-17"><a href="#cb4-17" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 3 " Female" "53 (6… "40 (47.6%)" "50 (59.5%)" "143 (…</span></span>
<span id="cb4-18"><a href="#cb4-18" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 4 " Male" "33 (3… "44 (52.4%)" "34 (40.5%)" "111 (…</span></span>
<span id="cb4-19"><a href="#cb4-19" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 5 "Age" "" "" "" "" </span></span>
<span id="cb4-20"><a href="#cb4-20" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 6 " Mean (SD)" "75.2 … "74.4 (7.89)" "75.7 (8.29)" "75.1 …</span></span>
<span id="cb4-21"><a href="#cb4-21" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 7 " Median [Min,… "76.0 … "76.0 [56.0, 88.0]" "77.5 [51.0, 88.0]" "77.0 …</span></span>
<span id="cb4-22"><a href="#cb4-22" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 8 "RACE" "" "" "" "" </span></span>
<span id="cb4-23"><a href="#cb4-23" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 9 " Black or Afr… "8 (9.… "9 (10.7%)" "6 (7.1%)" "23 (9…</span></span>
<span id="cb4-24"><a href="#cb4-24" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 10 " White" "78 (9… "74 (88.1%)" "78 (92.9%)" "230 (…</span></span>
<span id="cb4-25"><a href="#cb4-25" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 11 " American Ind… "0 (0%… "1 (1.2%)" "0 (0%)" "1 (0.…</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span id="cb4-13"><a href="#cb4-13" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ` ` Placebo `Xanomeline High Dose` `Xanomeline Low Dose` Overall </span></span>
<span id="cb4-14"><a href="#cb4-14" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; </span></span>
<span id="cb4-15"><a href="#cb4-15" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1 "" "(N=86)" "(N=84)" "(N=84)" "(N=254)"</span></span>
<span id="cb4-16"><a href="#cb4-16" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 2 "SEX" "" "" "" "" </span></span>
<span id="cb4-17"><a href="#cb4-17" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 3 " Female" "53 (61.6%)" "40 (47.6%)" "50 (59.5%)" "143 (56…</span></span>
<span id="cb4-18"><a href="#cb4-18" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 4 " Male" "33 (38.4%)" "44 (52.4%)" "34 (40.5%)" "111 (43…</span></span>
<span id="cb4-19"><a href="#cb4-19" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; # ℹ 7 more rows</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>We define the format of the output. We highlight items that are not discussed in previous discussion.</p>
<p><code>text_indent_first</code> and <code>text_indent_left</code> are used to control the indent space of text. They are helpful when you need to control the white space of a long phrase, “AMERICAN INDIAN OR ALASKA NATIVE” in the table provides an example.</p>
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