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(v0.7.0.9008) T. vaginalis, rsi_df
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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
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</span>
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</div>
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@ -166,13 +166,6 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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Create frequency tables
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</a>
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</li>
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<li>
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<a href="../reference/g.test.html">
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<span class="fa fa-clipboard-check"></span>
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Use the G-test
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</a>
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</li>
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<li>
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<a href="../articles/benchmarks.html">
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<span class="fa fa-shipping-fast"></span>
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@ -311,8 +304,9 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>These functions are meant to count isolates. Use the <code><a href='portion.html'>portion</a>_*</code> functions to calculate microbial resistance.</p>
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<p><code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
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<p><code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p>
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<p>The function <code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
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<p>The function <code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of S, I and R. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p>
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<p>The function <code>rsi_df</code> works exactly like <code>count_df</code>, but add the percentage of S, I and R.</p>
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<h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>
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@ -80,7 +80,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
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</span>
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</div>
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@ -165,13 +165,6 @@
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Create frequency tables
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</a>
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</li>
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<li>
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<a href="../reference/g.test.html">
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<span class="fa fa-clipboard-check"></span>
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Use the G-test
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</a>
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</li>
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<li>
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<a href="../articles/benchmarks.html">
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<span class="fa fa-shipping-fast"></span>
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@ -248,8 +241,8 @@
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</div>
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<pre class="usage"><span class='fu'>ggplot_rsi</span>(<span class='no'>data</span>, <span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>,
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<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"Interpretation"</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
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<pre class="usage"><span class='fu'>ggplot_rsi</span>(<span class='no'>data</span>, <span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
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<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"interpretation"</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
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<span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
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<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>,
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<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>colours</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>S</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>SI</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>I</span> <span class='kw'>=</span>
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@ -258,12 +251,12 @@
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<span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>caption</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x.title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>y.title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
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<span class='no'>...</span>)
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<span class='fu'>geom_rsi</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Antibiotic"</span>, <span class='st'>"Interpretation"</span>),
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<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"Interpretation"</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
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<span class='fu'>geom_rsi</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"antibiotic"</span>, <span class='st'>"interpretation"</span>),
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<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"interpretation"</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
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<span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
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<span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>, <span class='no'>...</span>)
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<span class='fu'>facet_rsi</span>(<span class='kw'>facet</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Interpretation"</span>, <span class='st'>"Antibiotic"</span>), <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
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<span class='fu'>facet_rsi</span>(<span class='kw'>facet</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"interpretation"</span>, <span class='st'>"antibiotic"</span>), <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
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<span class='fu'>scale_y_percent</span>(<span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>), <span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
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@ -272,7 +265,7 @@
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<span class='fu'>theme_rsi</span>()
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<span class='fu'>labels_rsi_count</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>,
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<span class='fu'>labels_rsi_count</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
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<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
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<span class='kw'>datalabels.size</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"gray15"</span>)</pre>
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@ -289,15 +282,15 @@
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</tr>
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<tr>
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<th>x</th>
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<td><p>variable to show on x axis, either <code>"Antibiotic"</code> (default) or <code>"Interpretation"</code> or a grouping variable</p></td>
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<td><p>variable to show on x axis, either <code>"antibiotic"</code> (default) or <code>"interpretation"</code> or a grouping variable</p></td>
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</tr>
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<tr>
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<th>fill</th>
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<td><p>variable to categorise using the plots legend, either <code>"Antibiotic"</code> (default) or <code>"Interpretation"</code> or a grouping variable</p></td>
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<td><p>variable to categorise using the plots legend, either <code>"antibiotic"</code> (default) or <code>"interpretation"</code> or a grouping variable</p></td>
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</tr>
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<tr>
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<th>facet</th>
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<td><p>variable to split plots by, either <code>"Interpretation"</code> (default) or <code>"Antibiotic"</code> or a grouping variable</p></td>
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<td><p>variable to split plots by, either <code>"interpretation"</code> (default) or <code>"antibiotic"</code> or a grouping variable</p></td>
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</tr>
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<tr>
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<th>breaks</th>
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@ -458,7 +451,7 @@
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"hospital_id"</span>,
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<span class='kw'>facet</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>,
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<span class='kw'>facet</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
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<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>,
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<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
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<span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Hospital"</span>,
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@ -479,7 +472,7 @@
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<span class='co'># group by MO</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>bug</span>) <span class='kw'>%>%</span>
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<span class='co'># plot the thing, putting MOs on the facet</span>
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<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>,
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<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
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<span class='kw'>facet</span> <span class='kw'>=</span> <span class='st'>"bug"</span>,
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<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
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<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>,
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
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</span>
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</div>
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@ -435,7 +435,7 @@
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</tr><tr>
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<td>
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<p><code><a href="portion.html">portion_R()</a></code> <code><a href="portion.html">portion_IR()</a></code> <code><a href="portion.html">portion_I()</a></code> <code><a href="portion.html">portion_SI()</a></code> <code><a href="portion.html">portion_S()</a></code> <code><a href="portion.html">portion_df()</a></code> </p>
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<p><code><a href="portion.html">portion_R()</a></code> <code><a href="portion.html">portion_IR()</a></code> <code><a href="portion.html">portion_I()</a></code> <code><a href="portion.html">portion_SI()</a></code> <code><a href="portion.html">portion_S()</a></code> <code><a href="portion.html">portion_df()</a></code> <code><a href="portion.html">rsi_df()</a></code> </p>
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</td>
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<td><p>Calculate resistance of isolates</p></td>
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</tr><tr>
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@ -80,7 +80,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
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</span>
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</div>
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@ -165,13 +165,6 @@
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Create frequency tables
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</a>
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</li>
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<li>
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<a href="../reference/g.test.html">
|
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<span class="fa fa-clipboard-check"></span>
|
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|
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Use the G-test
|
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</a>
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</li>
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<li>
|
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<a href="../articles/benchmarks.html">
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<span class="fa fa-shipping-fast"></span>
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@ -252,7 +245,7 @@
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<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
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<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 67,903 observations and 16 variables:</p><dl class='dl-horizontal'>
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<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 67,906 observations and 16 variables:</p><dl class='dl-horizontal'>
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<dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd>
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<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
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<dt><code>fullname</code></dt><dd><p>Full name, like <code>"Escherichia coli"</code></p></dd>
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@ -272,9 +265,10 @@
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
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<p>Manually added were:</p><ul>
|
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<li><p>9 species of <em>Streptococcus</em> (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)</p></li>
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<li><p>2 species of <em>Staphylococcus</em> (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li>
|
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<li><p>3 other undefined (unknown, unknown Gram negatives and unknown Gram positives)</p></li>
|
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<li><p>9 entries of <em>Streptococcus</em> (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)</p></li>
|
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<li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li>
|
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<li><p>3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)</p></li>
|
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<li><p>3 other 'undefined' entries (unknown, unknown Gram negatives and unknown Gram positives)</p></li>
|
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<li><p>8,830 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life</p></li>
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</ul>
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@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
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</button>
|
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<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
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</span>
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</div>
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@ -166,13 +166,6 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
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Create frequency tables
|
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</a>
|
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</li>
|
||||
<li>
|
||||
<a href="../reference/g.test.html">
|
||||
<span class="fa fa-clipboard-check"></span>
|
||||
|
||||
Use the G-test
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
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@ -266,6 +259,10 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
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<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
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|
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<span class='fu'>portion_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
|
||||
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
||||
|
||||
<span class='fu'>rsi_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
|
||||
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
|
||||
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
|
||||
|
||||
@ -323,7 +320,8 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
||||
|
||||
<p><strong>Remember that you should filter your table to let it contain only first isolates!</strong> Use <code><a href='first_isolate.html'>first_isolate</a></code> to determine them in your data set.</p>
|
||||
<p>These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the <code><a href='count.html'>count</a></code> functions to count isolates. <em>Low counts can infuence the outcome - these <code>portion</code> functions may camouflage this, since they only return the portion albeit being dependent on the <code>minimum</code> parameter.</em></p>
|
||||
<p><code>portion_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and calculates the portions R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.
|
||||
<p>The function <code>portion_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and calculates the portions R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each group and each variable with class <code>"rsi"</code>.</p>
|
||||
<p>The function <code>rsi_df</code> works exactly like <code>portion_df</code>, but add the number of isolates.
|
||||
<br /><br />
|
||||
To calculate the probability (<em>p</em>) of susceptibility of one antibiotic, we use this formula:
|
||||
<div style="text-align: center;"><img src='figures/combi_therapy_2.png' alt='' /></div>
|
||||
|
||||
Reference in New Issue
Block a user