mirror of
https://github.com/msberends/AMR.git
synced 2025-07-19 01:03:17 +02:00
Built site for AMR: 1.8.2.9096@98e62c9
This commit is contained in:
github-actions
@ -10,7 +10,7 @@
|
||||
|
||||
<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="">1.8.2.9095</small>
|
||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</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">
|
||||
@ -200,7 +200,7 @@
|
||||
</dl></div><div class="section level2">
|
||||
<h2 id="preparing-data-antimicrobial-resistance">Preparing data: antimicrobial resistance<a class="anchor" aria-label="anchor" href="#preparing-data-antimicrobial-resistance"></a></h2>
|
||||
|
||||
<p class="section-desc"></p><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p>
|
||||
<p class="section-desc"></p><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.sir.html">as.sir()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as SIR based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p>
|
||||
|
||||
|
||||
</div><div id="" class="section level2">
|
||||
@ -210,9 +210,9 @@
|
||||
|
||||
<dl><dt>
|
||||
|
||||
<code><a href="as.rsi.html">as.rsi()</a></code> <code><a href="as.rsi.html">NA_rsi_</a></code> <code><a href="as.rsi.html">is.rsi()</a></code> <code><a href="as.rsi.html">is.rsi.eligible()</a></code> <code><a href="as.rsi.html">rsi_interpretation_history()</a></code>
|
||||
<code><a href="as.sir.html">as.sir()</a></code> <code><a href="as.sir.html">NA_sir_</a></code> <code><a href="as.sir.html">is.sir()</a></code> <code><a href="as.sir.html">is_sir_eligible()</a></code> <code><a href="as.sir.html">sir_interpretation_history()</a></code>
|
||||
</dt>
|
||||
<dd>Interpret MIC and Disk Values, or Clean Raw R/SI Data</dd>
|
||||
<dd>Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<code><a href="as.mic.html">as.mic()</a></code> <code><a href="as.mic.html">NA_mic_</a></code> <code><a href="as.mic.html">is.mic()</a></code> <code><a href="as.mic.html">droplevels(<i><mic></i>)</a></code>
|
||||
@ -246,12 +246,12 @@
|
||||
|
||||
<dl><dt>
|
||||
|
||||
<code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">rsi_confidence_interval()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">rsi_df()</a></code>
|
||||
<code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">sir_confidence_interval()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">sir_df()</a></code>
|
||||
</dt>
|
||||
<dd>Calculate Microbial Resistance</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<code><a href="count.html">count_resistant()</a></code> <code><a href="count.html">count_susceptible()</a></code> <code><a href="count.html">count_R()</a></code> <code><a href="count.html">count_IR()</a></code> <code><a href="count.html">count_I()</a></code> <code><a href="count.html">count_SI()</a></code> <code><a href="count.html">count_S()</a></code> <code><a href="count.html">count_all()</a></code> <code><a href="count.html">n_rsi()</a></code> <code><a href="count.html">count_df()</a></code>
|
||||
<code><a href="count.html">count_resistant()</a></code> <code><a href="count.html">count_susceptible()</a></code> <code><a href="count.html">count_R()</a></code> <code><a href="count.html">count_IR()</a></code> <code><a href="count.html">count_I()</a></code> <code><a href="count.html">count_SI()</a></code> <code><a href="count.html">count_S()</a></code> <code><a href="count.html">count_all()</a></code> <code><a href="count.html">n_sir()</a></code> <code><a href="count.html">count_df()</a></code>
|
||||
</dt>
|
||||
<dd>Count Available Isolates</dd>
|
||||
</dl><dl><dt>
|
||||
@ -276,12 +276,12 @@
|
||||
<dd>Determine Multidrug-Resistant Organisms (MDRO)</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<code><a href="plot.html">plot(<i><mic></i>)</a></code> <code><a href="plot.html">autoplot(<i><mic></i>)</a></code> <code><a href="plot.html">fortify(<i><mic></i>)</a></code> <code><a href="plot.html">plot(<i><disk></i>)</a></code> <code><a href="plot.html">autoplot(<i><disk></i>)</a></code> <code><a href="plot.html">fortify(<i><disk></i>)</a></code> <code><a href="plot.html">plot(<i><rsi></i>)</a></code> <code><a href="plot.html">autoplot(<i><rsi></i>)</a></code> <code><a href="plot.html">fortify(<i><rsi></i>)</a></code>
|
||||
<code><a href="plot.html">plot(<i><mic></i>)</a></code> <code><a href="plot.html">autoplot(<i><mic></i>)</a></code> <code><a href="plot.html">fortify(<i><mic></i>)</a></code> <code><a href="plot.html">plot(<i><disk></i>)</a></code> <code><a href="plot.html">autoplot(<i><disk></i>)</a></code> <code><a href="plot.html">fortify(<i><disk></i>)</a></code> <code><a href="plot.html">plot(<i><sir></i>)</a></code> <code><a href="plot.html">autoplot(<i><sir></i>)</a></code> <code><a href="plot.html">fortify(<i><sir></i>)</a></code>
|
||||
</dt>
|
||||
<dd>Plotting for Classes <code>rsi</code>, <code>mic</code> and <code>disk</code></dd>
|
||||
<dd>Plotting for Classes <code>sir</code>, <code>mic</code> and <code>disk</code></dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<code><a href="ggplot_rsi.html">ggplot_rsi()</a></code> <code><a href="ggplot_rsi.html">geom_rsi()</a></code> <code><a href="ggplot_rsi.html">facet_rsi()</a></code> <code><a href="ggplot_rsi.html">scale_y_percent()</a></code> <code><a href="ggplot_rsi.html">scale_rsi_colours()</a></code> <code><a href="ggplot_rsi.html">theme_rsi()</a></code> <code><a href="ggplot_rsi.html">labels_rsi_count()</a></code>
|
||||
<code><a href="ggplot_sir.html">ggplot_sir()</a></code> <code><a href="ggplot_sir.html">geom_sir()</a></code> <code><a href="ggplot_sir.html">facet_sir()</a></code> <code><a href="ggplot_sir.html">scale_y_percent()</a></code> <code><a href="ggplot_sir.html">scale_sir_colours()</a></code> <code><a href="ggplot_sir.html">theme_sir()</a></code> <code><a href="ggplot_sir.html">labels_sir_count()</a></code>
|
||||
</dt>
|
||||
<dd>AMR Plots with <code>ggplot2</code></dd>
|
||||
</dl><dl><dt>
|
||||
@ -301,7 +301,7 @@
|
||||
<dd>Calculate the Mean AMR Distance</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i><resistance_predict></i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> <code><a href="resistance_predict.html">autoplot(<i><resistance_predict></i>)</a></code>
|
||||
<code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">sir_predict()</a></code> <code><a href="resistance_predict.html">plot(<i><resistance_predict></i>)</a></code> <code><a href="resistance_predict.html">ggplot_sir_predict()</a></code> <code><a href="resistance_predict.html">autoplot(<i><resistance_predict></i>)</a></code>
|
||||
</dt>
|
||||
<dd>Predict Antimicrobial Resistance</dd>
|
||||
</dl><dl><dt>
|
||||
@ -393,9 +393,9 @@
|
||||
<dd>Data Set with Unclean Data</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<code><a href="rsi_translation.html">rsi_translation</a></code>
|
||||
<code><a href="clinical_breakpoints.html">clinical_breakpoints</a></code>
|
||||
</dt>
|
||||
<dd>Data Set for R/SI Interpretation</dd>
|
||||
<dd>Data Set with Clinical Breakpoints for SIR Interpretation</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<code><a href="WHONET.html">WHONET</a></code>
|
||||
@ -464,9 +464,9 @@
|
||||
<dd>Principal Component Analysis (for AMR)</dd>
|
||||
</dl><dl><dt>
|
||||
|
||||
<code><a href="random.html">random_mic()</a></code> <code><a href="random.html">random_disk()</a></code> <code><a href="random.html">random_rsi()</a></code>
|
||||
<code><a href="random.html">random_mic()</a></code> <code><a href="random.html">random_disk()</a></code> <code><a href="random.html">random_sir()</a></code>
|
||||
</dt>
|
||||
<dd>Random MIC Values/Disk Zones/RSI Generation</dd>
|
||||
<dd>Random MIC Values/Disk Zones/SIR Generation</dd>
|
||||
</dl></div><div class="section level2">
|
||||
<h2 id="other-statistical-tests">Other: statistical tests<a class="anchor" aria-label="anchor" href="#other-statistical-tests"></a></h2>
|
||||
|
||||
@ -506,7 +506,7 @@
|
||||
|
||||
<dl><dt>
|
||||
|
||||
<code><a href="AMR-deprecated.html">AMR-deprecated</a></code>
|
||||
<code><a href="AMR-deprecated.html">NA_rsi_</a></code> <code><a href="AMR-deprecated.html">as.rsi()</a></code> <code><a href="AMR-deprecated.html">facet_rsi()</a></code> <code><a href="AMR-deprecated.html">geom_rsi()</a></code> <code><a href="AMR-deprecated.html">ggplot_rsi()</a></code> <code><a href="AMR-deprecated.html">ggplot_rsi_predict()</a></code> <code><a href="AMR-deprecated.html">is.rsi()</a></code> <code><a href="AMR-deprecated.html">is.rsi.eligible()</a></code> <code><a href="AMR-deprecated.html">labels_rsi_count()</a></code> <code><a href="AMR-deprecated.html">n_rsi()</a></code> <code><a href="AMR-deprecated.html">random_rsi()</a></code> <code><a href="AMR-deprecated.html">rsi_df()</a></code> <code><a href="AMR-deprecated.html">rsi_predict()</a></code> <code><a href="AMR-deprecated.html">scale_rsi_colours()</a></code> <code><a href="AMR-deprecated.html">theme_rsi()</a></code>
|
||||
</dt>
|
||||
<dd>Deprecated Functions</dd>
|
||||
</dl></div>
|
||||
|
||||
Reference in New Issue
Block a user