P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-24 05:03:49 +02:00
Code Releases Activity

(v1.7.1.9002) ab class selectors update

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-06-14 22:04:04 +02:00
parent 683a0e748a
commit 99be4c7e7e
36 changed files with 416 additions and 198 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
docs/404.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>

2
docs/LICENSE-text.html
View File

@ -81,7 +81,7 @@
</button>
<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="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>

6
docs/articles/datasets.html
View File

@ -39,7 +39,7 @@
</button>
<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="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>
@ -187,12 +187,12 @@
</header><script src="datasets_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
</header><script src="datasets_files/header-attrs-2.7/header-attrs.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 class="date">05 June 2021</h4>
<h4 class="date">14 June 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>

2
docs/articles/index.html
View File

@ -81,7 +81,7 @@
</button>
<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="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>

2
docs/authors.html
View File

@ -81,7 +81,7 @@
</button>
<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="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>

4
docs/index.html
View File

@ -42,7 +42,7 @@
</button>
<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="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>
@ -213,7 +213,7 @@
<a href="#with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="anchor"></a>With <code>AMR</code> (for R), there’s always a knowledgeable microbiologist by your side!</h5>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/AMR">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
<span class="va">example_isolates</span> <span class="op">%&gt;%</span>

29
docs/news/index.html
View File

@ -81,7 +81,7 @@
</button>
<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="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>
@ -236,19 +236,24 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1719001" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9001">
<a href="#amr-1719001" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9001</h1>
<div id="last-updated-5-june-2021" class="section level2">
<div id="amr-1719002" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9002">
<a href="#amr-1719002" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9002</h1>
<div id="last-updated-14-june-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-5-june-2021" class="anchor"></a><small>Last updated: 5 June 2021</small>
<a href="#last-updated-14-june-2021" class="anchor"></a><small>Last updated: 14 June 2021</small>
</h2>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<li>Added more antibiotic class selectors, such as <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">lipoglycopeptides()</a></code>
<li>Added more antibiotic class selectors: <code><a href="../reference/antibiotic_class_selectors.html">aminopenicillins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lipoglycopeptides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">polymyxins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">quinolones()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">streptogramins()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">ureidopenicillins()</a></code>
</li>
<li>Added <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html">ggplot2::autoplot()</a></code> generic for classes <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code>, <code>&lt;rsi&gt;</code> and <code>&lt;resistance_predict&gt;</code>
</li>
<li>Fix to prevent introducing <code>NA</code>s for old MO codes when running <code><a href="../reference/as.mo.html">as.mo()</a></code> on them</li>
<li>Added more informative error messages when any of the <code>proportion_*()</code> and <code>count_*()</code> functions fail</li>
<li>Fix for using antibiotic selectors multiple times in one call (e.g., using in <code><a href="https://dplyr.tidyverse.org/reference/filter.html">dplyr::filter()</a></code> and immediately after in <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code>)</li>
</ul>
</div>
</div>
@ -302,7 +307,7 @@
</ul>
</li>
<li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code><a href="../reference/AMR-deprecated.html">filter_betalactams()</a></code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
</li>
</ul>
</div>
@ -403,7 +408,7 @@
<span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
</li>
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li>
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
@ -460,7 +465,7 @@
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
</ul>
</li>
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
@ -498,7 +503,7 @@
<a href="#other-1" class="anchor"></a>Other</h3>
<ul>
<li>Big documentation updates</li>
<li>Loading the package (i.e., <code><a href="https://msberends.github.io/AMR/">library(AMR)</a></code>) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)</li>
<li>Loading the package (i.e., <code><a href="https://github.com/msberends/AMR">library(AMR)</a></code>) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)</li>
</ul>
</div>
</div>
@ -629,7 +634,7 @@
<p>Curious about which enterococci are actually intrinsic resistant to vancomycin?</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/AMR">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
<span class="va">intrinsic_resistant</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span>, <span class="va">microorganism</span> <span class="op">%like%</span> <span class="st">"Enterococcus"</span><span class="op">)</span> <span class="op">%&gt;%</span>

2
docs/pkgdown.yml
View File

@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-06-05T13:10Z
last_built: 2021-06-14T20:03Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

2
docs/reference/AMR.html
View File

@ -82,7 +82,7 @@
</button>
<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="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>

8
docs/reference/count.html
View File

@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</button>
<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="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>
@ -409,6 +409,12 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
n1 <span class='op'>=</span> <span class='fu'>count_all</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>, <span class='co'># the actual total; sum of all three</span>
n2 <span class='op'>=</span> <span class='fu'>n_rsi</span><span class='op'>(</span><span class='va'>CIP</span><span class='op'>)</span>, <span class='co'># same - analogous to n_distinct</span>
total <span class='op'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># NOT the number of tested isolates!</span>
<span class='co'># Number of available isolates for a whole antibiotic class</span>
<span class='co'># (i.e., in this data set columns GEN, TOB, AMK, KAN)</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'><a href='antibiotic_class_selectors.html'>aminoglycosides</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>n_rsi</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>

6
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</button>
<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="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>
@ -508,7 +508,7 @@
</tr><tr>
<td>
<p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
<p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">ggplot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
</td>
<td><p>Plotting for Classes <code>rsi</code>, <code>mic</code> and <code>disk</code></p></td>
</tr><tr>
@ -532,7 +532,7 @@
</tr><tr>
<td>
<p><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>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> </p>
<p><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>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> <code><a href="resistance_predict.html">ggplot(<i>&lt;resistance_predict&gt;</i>)</a></code> <code><a href="resistance_predict.html">autoplot(<i>&lt;resistance_predict&gt;</i>)</a></code> </p>
</td>
<td><p>Predict antimicrobial resistance</p></td>
</tr><tr>

52
docs/reference/plot.html
View File

@ -82,7 +82,7 @@
</button>
<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="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>
@ -258,7 +258,23 @@
<span class='op'>)</span>
<span class='co'># S3 method for mic</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
<span class='fu'>ggplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
xlab <span class='op'>=</span> <span class='st'>"Minimum Inhibitory Concentration (mg/L)"</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
ab <span class='op'>=</span> <span class='cn'>NULL</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
expand <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for mic</span>
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
@ -289,7 +305,23 @@
<span class='op'>)</span>
<span class='co'># S3 method for disk</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
<span class='fu'>ggplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
xlab <span class='op'>=</span> <span class='st'>"Disk diffusion diameter (mm)"</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
ab <span class='op'>=</span> <span class='cn'>NULL</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
expand <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for disk</span>
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
@ -314,7 +346,19 @@
<span class='op'>)</span>
<span class='co'># S3 method for rsi</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
<span class='fu'>ggplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
xlab <span class='op'>=</span> <span class='st'>"Antimicrobial Interpretation"</span>,
ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</span>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for rsi</span>
<span class='fu'>autoplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,

12
docs/reference/resistance_predict.html
View File

@ -82,7 +82,7 @@
</button>
<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="Latest development version">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>
@ -275,10 +275,18 @@
<span class='co'># S3 method for resistance_predict</span>
<span class='fu'><a href='plot.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span>, main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ggplot_rsi_predict</span><span class='op'>(</span>
<span class='va'>x</span>,
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>,
ribbon <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for resistance_predict</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>x</span>, main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>, ribbon <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ggplot_rsi_predict</span><span class='op'>(</span>
<span class='co'># S3 method for resistance_predict</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span>
<span class='va'>x</span>,
main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Prediction of"</span>, <span class='va'>x_name</span><span class='op'>)</span>,
ribbon <span class='op'>=</span> <span class='cn'>TRUE</span>,

2
docs/survey.html
View File

@ -81,7 +81,7 @@
</button>
<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="Latest development version">1.7.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9002</span>
</span>
</div>