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@ -157,10 +157,7 @@
<table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2">
<h2 id="preparing-data-microorganisms">Preparing data: microorganisms <a href="#preparing-data-microorganisms" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>These functions are meant to get taxonomically valid properties of
microorganisms from any input. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach
this package how to translate your own codes to valid microorganism
codes.</p>
<p class="section-desc"></p><p>These functions are meant to get taxonomically valid properties of microorganisms from any input. Use <code><a href="../reference/mo_source.html">mo_source()</a></code> to teach this package how to translate your own codes to valid microorganism codes.</p>
</th>
</tr></tbody><tbody><tr><td>
<p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p>
@ -176,9 +173,7 @@ codes.</p>
<td><p>User-Defined Reference Data Set for Microorganisms</p></td>
</tr></tbody><tbody><tr><th colspan="2">
<h2 id="preparing-data-antibiotics">Preparing data: antibiotics <a href="#preparing-data-antibiotics" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>Use these functions to get valid properties of antibiotics from any
input or to clean your input. You can even retrieve drug names and doses
from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p>
<p class="section-desc"></p><p>Use these functions to get valid properties of antibiotics from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>.</p>
</th>
</tr></tbody><tbody><tr><td>
<p><code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> </p>
@ -198,13 +193,7 @@ from clinical text records, using <code><a href="../reference/ab_from_text.html"
<td><p>Get ATC Properties from WHOCC Website</p></td>
</tr></tbody><tbody><tr><th colspan="2">
<h2 id="preparing-data-antimicrobial-resistance">Preparing data: antimicrobial resistance <a href="#preparing-data-antimicrobial-resistance" class="anchor" aria-hidden="true"></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.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>
</th>
</tr></tbody><tbody><tr><td>
<p><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> </p>
@ -228,14 +217,7 @@ rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a>
<td><p>Define Custom EUCAST Rules</p></td>
</tr></tbody><tbody><tr><th colspan="2">
<h2 id="analysing-data-antimicrobial-resistance">Analysing data: antimicrobial resistance <a href="#analysing-data-antimicrobial-resistance" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>Use these function for the analysis part. You can use
<code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any
antibiotic column. Be sure to first select the isolates that are
appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or
<code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain
resistance in certain antibiotic classes (<code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>,
<code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant
microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p>
<p class="section-desc"></p><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p>
</th>
</tr></tbody><tbody><tr><td>
<p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</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> </p>
@ -287,9 +269,7 @@ microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).
<td><p>Guess Antibiotic Column</p></td>
</tr></tbody><tbody><tr><th colspan="2">
<h2 id="background-information-on-included-data">Background information on included data <a href="#background-information-on-included-data" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>Some pages about our package and its external sources. Be sure to
read our <a href="./../articles/index.html">How To’s</a> for more
information about how to work with functions in this package.</p>
<p class="section-desc"></p><p>Some pages about our package and its external sources. Be sure to read our <a href="./../articles/index.html">How To’s</a> for more information about how to work with functions in this package.</p>
</th>
</tr></tbody><tbody><tr><td>
<p><code><a href="AMR.html">AMR</a></code> </p>
@ -353,9 +333,7 @@ information about how to work with functions in this package.</p>
<td><p>Data Set with 500 Isolates - WHONET Example</p></td>
</tr></tbody><tbody><tr><th colspan="2">
<h2 id="other-miscellaneous-functions">Other: miscellaneous functions <a href="#other-miscellaneous-functions" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>These functions are mostly for internal use, but some of them may
also be suitable for your analysis. Especially the ‘like’ function can
be useful: <code>if (x %like% y) {...}</code>.</p>
<p class="section-desc"></p><p>These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: <code>if (x %like% y) {...}</code>.</p>
</th>
</tr></tbody><tbody><tr><td>
<p><code><a href="age_groups.html">age_groups()</a></code> </p>
@ -403,8 +381,7 @@ be useful: <code>if (x %like% y) {...}</code>.</p>
<td><p>Random MIC Values/Disk Zones/RSI Generation</p></td>
</tr></tbody><tbody><tr><th colspan="2">
<h2 id="other-statistical-tests">Other: statistical tests <a href="#other-statistical-tests" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>Some statistical tests or methods are not part of base R and were
added to this package for convenience.</p>
<p class="section-desc"></p><p>Some statistical tests or methods are not part of base R and were added to this package for convenience.</p>
</th>
</tr></tbody><tbody><tr><td>
<p><code><a href="g.test.html">g.test()</a></code> </p>
@ -420,9 +397,7 @@ added to this package for convenience.</p>
<td><p>Skewness of the Sample</p></td>
</tr></tbody><tbody><tr><th colspan="2">
<h2 id="other-deprecated-functions">Other: deprecated functions <a href="#other-deprecated-functions" class="anchor" aria-hidden="true"></a></h2>
<p class="section-desc"></p><p>These functions are deprecated, meaning that they will still work but
show a warning with every use and will be removed in a future
version.</p>
<p class="section-desc"></p><p>These functions are deprecated, meaning that they will still work but show a warning with every use and will be removed in a future version.</p>
</th>
</tr></tbody><tbody><tr><td>
<p><code><a href="AMR-deprecated.html">AMR-deprecated</a></code> </p>
@ -437,13 +412,11 @@ version.</p>
<footer><div class="copyright">
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
Erwin E. A. Hassing.</p>
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a>
2.0.2.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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