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Built site for AMR@3.0.0.9010: 65ec098

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2025-07-17 17:19:09 +00:00
parent 7d4c4ecffc
commit eb889b5de5
85 changed files with 128 additions and 122 deletions
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reference/ggplot_sir.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9010</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -256,13 +256,11 @@
<span class="r-in"><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">age_group</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu">ggplot_sir</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"age_group"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">as.sir()</span>: 271 results in index 'age_group' truncated (100%) that were</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> invalid antimicrobial interpretations: "0-11", "12-24", "25-54", "55-74",</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> and "75+"</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in ggplot2::geom_col(data = function(x) { sir_df(data = x, translate_ab = translate_ab, language = language, minimum = minimum, combine_SI = combine_SI)}, mapping = utils::modifyList(ggplot2::aes(), list(x = str2lang(x), y = str2lang(y), fill = str2lang(fill))), position = position, ...):</span> Problem while computing layer data.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Error occurred in the 1st layer.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Caused by error in `sir_df()`:</span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> incorrect number of dimensions</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 6 rows containing missing values or values outside the scale range</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (`geom_col()`).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 6 rows containing missing values or values outside the scale range</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (`geom_text()`).</span>
<span class="r-plt img"><img src="ggplot_sir-8.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&amp;&amp;</span> <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># a shorter version which also adjusts data label colours:</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -290,12 +288,7 @@
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_is_gram_negative()</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">as.sir()</span>: 700 results in index 'ward' truncated (100%) that were</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> invalid antimicrobial interpretations: "Clinical" and "ICU"</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in ggplot2::geom_col(data = function(x) { sir_df(data = x, translate_ab = translate_ab, language = language, minimum = minimum, combine_SI = combine_SI)}, mapping = utils::modifyList(ggplot2::aes(), list(x = str2lang(x), y = str2lang(y), fill = str2lang(fill))), position = position, ...):</span> Problem while computing layer data.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Error occurred in the 1st layer.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Caused by error in `sir_df()`:</span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> incorrect number of dimensions</span>
<span class="r-plt img"><img src="ggplot_sir-9.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
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