(v1.3.0.9016) mo_uncertainties() overhaul

2025-07-08 12:31:58 +02:00 · 2020-09-12 08:49:01 +02:00
parent 68e9cb78e9
commit 3ff871afeb
71 changed files with 820 additions and 169 deletions
--- a/docs/reference/WHONET.html
+++ b/docs/reference/WHONET.html
@ -49,7 +49,7 @@
  <script src="../extra.js"></script>

 <meta property="og:title" content="Data set with 500 isolates - WHONET example — WHONET" />
-<meta property="og:description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are based on our example_isolates data set. All patient names are created using online surname generators and are only in place for practice purposes." />
+<meta property="og:description" content="This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our example_isolates data set. All patient names are created using online surname generators and are only in place for practice purposes." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />


@ -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">1.3.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
      </span>
    </div>

@ -239,7 +239,7 @@
    </div>

    <div class="ref-description">
-    <p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are based on our <a href='example_isolates.html'>example_isolates</a> data set. All patient names are created using online surname generators and are only in place for practice purposes.</p>
+    <p>This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our <a href='example_isolates.html'>example_isolates</a> data set. All patient names are created using online surname generators and are only in place for practice purposes.</p>
    </div>

    <pre class="usage"><span class='kw'>WHONET</span></pre>
--- a/docs/reference/ab_property.html
+++ b/docs/reference/ab_property.html
@ -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">1.3.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
      </span>
    </div>

@ -384,7 +384,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='fu'>ab_atc</span>(<span class='st'>"ceftriaxon"</span>)
 <span class='fu'>ab_atc</span>(<span class='st'>"cephtriaxone"</span>)
 <span class='fu'>ab_atc</span>(<span class='st'>"cephthriaxone"</span>)
-<span class='fu'>ab_atc</span>(<span class='st'>"seephthriaaksone"</span>)</pre>
+<span class='fu'>ab_atc</span>(<span class='st'>"seephthriaaksone"</span>)
+</pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top">
--- a/docs/reference/as.ab.html
+++ b/docs/reference/as.ab.html
@ -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">1.3.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
      </span>
    </div>

@ -344,7 +344,8 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
 <span class='co'># use ab_* functions to get a specific properties (see ?ab_property);</span>
 <span class='co'># they use as.ab() internally:</span>
 <span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"J01FA01"</span>)    <span class='co'># "Erythromycin"</span>
-<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>)       <span class='co'># "Erythromycin"</span></pre>
+<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>)       <span class='co'># "Erythromycin"</span>
+</pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top">
--- a/docs/reference/as.disk.html
+++ b/docs/reference/as.disk.html
@ -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">1.3.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
      </span>
    </div>

@ -300,7 +300,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
       guideline = <span class='st'>"EUCAST"</span>)
       
 <span class='fu'><a href='as.rsi.html'>as.rsi</a></span>(<span class='kw'>df</span>)
-}</pre>
+}
+</pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top">
--- a/docs/reference/as.mic.html
+++ b/docs/reference/as.mic.html
@ -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">1.3.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
      </span>
    </div>

@ -298,8 +298,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
       ab = <span class='st'>"AMX"</span>,
       guideline = <span class='st'>"EUCAST"</span>)

-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span>(<span class='kw'>mic_data</span>)
-<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='kw'>mic_data</span>)</pre>
+<span class='fu'><a href='plot.html'>plot</a></span>(<span class='kw'>mic_data</span>)
+<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='kw'>mic_data</span>)
+</pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top">
--- a/docs/reference/as.mo.html
+++ b/docs/reference/as.mo.html
@ -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">1.3.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
      </span>
    </div>

@ -347,7 +347,7 @@
 </ul>

 <p>There are three helper functions that can be run after using the <code>as.mo()</code> function:</p><ul>
-<li><p>Use <code>mo_uncertainties()</code> to get a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with all values that were coerced to a valid value, but with uncertainty. The output contains a score, that is calculated as \((n - 0.5 * L) / n\), where <em>n</em> is the number of characters of the full taxonomic name of the microorganism, and <em>L</em> is the <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> between that full name and the user input.</p></li>
+<li><p>Use <code>mo_uncertainties()</code> to get a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> that prints in a pretty format with all taxonomic names that were guessed. The output contains a score that is based on the human pathogenic prevalence and the <a href='https://en.wikipedia.org/wiki/Levenshtein_distance'>Levenshtein distance</a> between the full taxonomic name and the user input.</p></li>
 <li><p>Use <code>mo_failures()</code> to get a <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> with all values that could not be coerced to a valid value.</p></li>
 <li><p>Use <code>mo_renamed()</code> to get a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with all values that could be coerced based on old, previously accepted taxonomic names.</p></li>
 </ul>
@ -456,7 +456,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 <span class='co'># although this works easier and does the same:</span>
 <span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='kw'>df</span> <span class='op'>%&gt;%</span>
  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(mo = <span class='fu'>as.mo</span>(<span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='kw'>genus</span>, <span class='kw'>species</span>)))
-}</pre>
+}
+</pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top">
--- a/docs/reference/as.rsi.html
+++ b/docs/reference/as.rsi.html
@ -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">1.3.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
      </span>
    </div>

@ -340,12 +340,14 @@
 <li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is unclear.</p></li>
 <li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href='as.mic.html'>as.mic()</a></code>, that also gives your columns the new data class <code><a href='as.mic.html'>mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> parameter.</p><ul>
 <li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='kw'>is.mic</span>, <span class='kw'>as.rsi</span>)             <span class='co'># until dplyr 1.0.0</span>
-<span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.mic</span>), <span class='kw'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span></pre></li>
+<span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.mic</span>), <span class='kw'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span>
+</pre></li>
 <li><p>Operators like "&lt;=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers "&gt;2" to be lower than "&gt;=4" and might in this case return "S" or "I".</p></li>
 </ul></li>
 <li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href='as.disk.html'>as.disk()</a></code>, that also gives your columns the new data class <code><a href='as.disk.html'>disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> parameter.</p><ul>
 <li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='kw'>is.disk</span>, <span class='kw'>as.rsi</span>)             <span class='co'># until dplyr 1.0.0</span>
-<span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.disk</span>), <span class='kw'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span></pre></li>
+<span class='kw'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span>(<span class='fu'>where</span>(<span class='kw'>is.disk</span>), <span class='kw'>as.rsi</span>)) <span class='co'># since dplyr 1.0.0</span>
+</pre></li>
 </ul></li>
 <li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.rsi(data)</code>.</p></li>
 </ol>
@ -468,7 +470,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s

 <span class='kw'>rsi_data</span> <span class='op'>&lt;-</span> <span class='fu'>as.rsi</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"S"</span>, <span class='fl'>474</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"I"</span>, <span class='fl'>36</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='st'>"R"</span>, <span class='fl'>370</span>)))
 <span class='fu'>is.rsi</span>(<span class='kw'>rsi_data</span>)
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span>(<span class='kw'>rsi_data</span>)    <span class='co'># for percentages</span>
+<span class='fu'><a href='plot.html'>plot</a></span>(<span class='kw'>rsi_data</span>)    <span class='co'># for percentages</span>
 <span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(<span class='kw'>rsi_data</span>) <span class='co'># for frequencies</span>

 <span class='co'>if</span> (<span class='fl'>FALSE</span>) {
@ -487,7 +489,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='co'># default threshold of `is.rsi.eligible` is 5%.</span>
 <span class='fu'>is.rsi.eligible</span>(<span class='kw'>WHONET</span><span class='op'>$</span><span class='kw'>`First name`</span>) <span class='co'># fails, &gt;80% is invalid</span>
 <span class='fu'>is.rsi.eligible</span>(<span class='kw'>WHONET</span><span class='op'>$</span><span class='kw'>`First name`</span>, threshold = <span class='fl'>0.99</span>) <span class='co'># succeeds</span>
-}</pre>
+}
+</pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top">
--- a/docs/reference/atc_online.html
+++ b/docs/reference/atc_online.html
@ -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">1.3.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
      </span>
    </div>

@ -333,7 +333,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='co'># [2] "ANTIBACTERIALS FOR SYSTEMIC USE"</span>
 <span class='co'># [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"</span>
 <span class='co'># [4] "Penicillins with extended spectrum"</span>
-}</pre>
+}
+</pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top">
--- a/docs/reference/bug_drug_combinations.html
+++ b/docs/reference/bug_drug_combinations.html
@ -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">1.3.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
      </span>
    </div>

@ -355,7 +355,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
                           FUN = <span class='fu'>function</span>(<span class='kw'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='kw'>x</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span>(<span class='st'>"E. coli"</span>),
                                                    <span class='st'>"E. coli"</span>,
                                                    <span class='st'>"Others"</span>))
-<span class='co'># }</span></pre>
+<span class='co'># }</span>
+</pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top">
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@ -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">1.3.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
      </span>
    </div>

@ -444,6 +444,12 @@
          <p><code><a href="eucast_rules.html">eucast_rules()</a></code> </p>
        </td>
        <td><p>Apply EUCAST rules</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">barplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">barplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Plotting for classes <code>rsi</code> and <code>disk</code></p></td>
      </tr>
    </tbody><tbody>
      <tr>
--- a/docs/reference/like.html
+++ b/docs/reference/like.html
@ -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">1.3.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
      </span>
    </div>

@ -317,7 +317,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
 <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></span>)
 <span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
  <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='kw'>mo</span>) <span class='op'>%like%</span> <span class='st'>"^ent"</span>)
-}</pre>
+}
+</pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top">
--- a/docs/reference/microorganisms.codes.html
+++ b/docs/reference/microorganisms.codes.html
@ -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">1.3.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
      </span>
    </div>

--- a/docs/reference/mo_property.html
+++ b/docs/reference/mo_property.html
@ -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">1.3.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
      </span>
    </div>

@ -461,7 +461,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 <span class='fu'>mo_taxonomy</span>(<span class='st'>"E. coli"</span>)
 <span class='co'># get a list with the taxonomy, the authors, Gram-stain and URL to the online database</span>
 <span class='fu'>mo_info</span>(<span class='st'>"E. coli"</span>)
-<span class='co'># }</span></pre>
+<span class='co'># }</span>
+</pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top">
--- a/docs/reference/plot.html
+++ b/docs/reference/plot.html
@ -0,0 +1,390 @@
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+<meta property="og:description" content="Functions to print classes of the AMR package." />
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+        <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">1.3.0.9016</span>
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+    <li>
+      <a href="../articles/AMR.html">
+        <span class="fa fa-directions"></span>
+         
+        Conduct AMR analysis
+      </a>
+    </li>
+    <li>
+      <a href="../articles/resistance_predict.html">
+        <span class="fa fa-dice"></span>
+         
+        Predict antimicrobial resistance
+      </a>
+    </li>
+    <li>
+      <a href="../articles/datasets.html">
+        <span class="fa fa-database"></span>
+         
+        Data sets for download / own use
+      </a>
+    </li>
+    <li>
+      <a href="../articles/PCA.html">
+        <span class="fa fa-compress"></span>
+         
+        Conduct principal component analysis for AMR
+      </a>
+    </li>
+    <li>
+      <a href="../articles/MDR.html">
+        <span class="fa fa-skull-crossbones"></span>
+         
+        Determine multi-drug resistance (MDR)
+      </a>
+    </li>
+    <li>
+      <a href="../articles/WHONET.html">
+        <span class="fa fa-globe-americas"></span>
+         
+        Work with WHONET data
+      </a>
+    </li>
+    <li>
+      <a href="../articles/SPSS.html">
+        <span class="fa fa-file-upload"></span>
+         
+        Import data from SPSS/SAS/Stata
+      </a>
+    </li>
+    <li>
+      <a href="../articles/EUCAST.html">
+        <span class="fa fa-exchange-alt"></span>
+         
+        Apply EUCAST rules
+      </a>
+    </li>
+    <li>
+      <a href="../reference/mo_property.html">
+        <span class="fa fa-bug"></span>
+         
+        Get properties of a microorganism
+      </a>
+    </li>
+    <li>
+      <a href="../reference/ab_property.html">
+        <span class="fa fa-capsules"></span>
+         
+        Get properties of an antibiotic
+      </a>
+    </li>
+    <li>
+      <a href="../articles/benchmarks.html">
+        <span class="fa fa-shipping-fast"></span>
+         
+        Other: benchmarks
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+    <span class="fa fa-clipboard-list"></span>
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+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header>
+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Plotting for classes <code>rsi</code> and <code>disk</code></h1>
+    <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a>, <a href='https://github.com/msberends/AMR/blob/master/R/mic.R'><code>R/mic.R</code></a>, <a href='https://github.com/msberends/AMR/blob/master/R/rsi.R'><code>R/rsi.R</code></a></small>
+    <div class="hidden name"><code>plot.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Functions to print classes of the <code>AMR</code> package.</p>
+    </div>
+
+    <pre class="usage"><span class='co'># S3 method for mic</span>
+<span class='fu'>plot</span>(
+  <span class='kw'>x</span>,
+  main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></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='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>x</span>))),
+  ylab = <span class='st'>"Frequency"</span>,
+  xlab = <span class='st'>"MIC value"</span>,
+  axes = <span class='fl'>FALSE</span>,
+  <span class='kw'>...</span>
+)
+
+<span class='co'># S3 method for mic</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(
+  <span class='kw'>height</span>,
+  main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></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='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>height</span>))),
+  ylab = <span class='st'>"Frequency"</span>,
+  xlab = <span class='st'>"MIC value"</span>,
+  axes = <span class='fl'>FALSE</span>,
+  <span class='kw'>...</span>
+)
+
+<span class='co'># S3 method for rsi</span>
+<span class='fu'>plot</span>(
+  <span class='kw'>x</span>,
+  lwd = <span class='fl'>2</span>,
+  ylim = <span class='kw'>NULL</span>,
+  ylab = <span class='st'>"Percentage"</span>,
+  xlab = <span class='st'>"Antimicrobial Interpretation"</span>,
+  main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></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='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>x</span>))),
+  axes = <span class='fl'>FALSE</span>,
+  <span class='kw'>...</span>
+)
+
+<span class='co'># S3 method for rsi</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/barplot.html'>barplot</a></span>(
+  <span class='kw'>height</span>,
+  col = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"chartreuse4"</span>, <span class='st'>"chartreuse3"</span>, <span class='st'>"brown3"</span>),
+  xlab = <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='kw'>beside</span>, <span class='st'>"Antimicrobial Interpretation"</span>, <span class='st'>""</span>),
+  main = <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></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='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span>(<span class='kw'>height</span>))),
+  ylab = <span class='st'>"Frequency"</span>,
+  beside = <span class='fl'>TRUE</span>,
+  axes = <span class='kw'>beside</span>,
+  <span class='kw'>...</span>
+)</pre>
+
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>x</th>
+      <td><p>the coordinates of points in the plot. Alternatively, a
+      single plotting structure, function or <em>any <span style="R">R</span> object with a
+        <code>plot</code> method</em> can be provided.</p></td>
+    </tr>
+    <tr>
+      <th>main</th>
+      <td><p>overall and sub title for the plot.</p></td>
+    </tr>
+    <tr>
+      <th>ylab</th>
+      <td><p>a label for the y axis.</p></td>
+    </tr>
+    <tr>
+      <th>xlab</th>
+      <td><p>a label for the x axis.</p></td>
+    </tr>
+    <tr>
+      <th>axes</th>
+      <td><p>logical.  If <code>TRUE</code>, a vertical (or horizontal, if
+    <code>horiz</code> is true) axis is drawn.</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>Parameters passed on to functions</p></td>
+    </tr>
+    <tr>
+      <th>height</th>
+      <td><p>either a vector or matrix of values describing the
+    bars which make up the plot.  If <code>height</code> is a vector, the
+    plot consists of a sequence of rectangular bars with heights
+    given by the values in the vector.  If <code>height</code> is a matrix
+    and <code>beside</code> is <code>FALSE</code> then each bar of the plot
+    corresponds to a column of <code>height</code>, with the values in the
+    column giving the heights of stacked sub-bars making up the
+    bar.  If <code>height</code> is a matrix and <code>beside</code> is
+    <code>TRUE</code>, then the values in each column are juxtaposed
+    rather than stacked.</p></td>
+    </tr>
+    <tr>
+      <th>ylim</th>
+      <td><p>limits for the y axis.</p></td>
+    </tr>
+    <tr>
+      <th>col</th>
+      <td><p>a vector of colors for the bars or bar components.
+    By default, grey is used if <code>height</code> is a vector, and a
+    gamma-corrected grey palette if <code>height</code> is a matrix.</p></td>
+    </tr>
+    <tr>
+      <th>beside</th>
+      <td><p>a logical value.  If <code>FALSE</code>, the columns of
+    <code>height</code> are portrayed as stacked bars, and if <code>TRUE</code>
+    the columns are portrayed as juxtaposed bars.</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
+
+    
+
+<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
+The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
+<p>If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
+    <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
+
+    
+
+<p>On our website <a href='https://msberends.github.io/AMR'>https://msberends.github.io/AMR</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
+
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
+</div>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
+</div>
+
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+
+  
+
+
+  </body>
+</html>
+
+
--- a/docs/reference/translate.html
+++ b/docs/reference/translate.html
@ -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">1.3.0.9015</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9016</span>
      </span>
    </div>

@ -291,7 +291,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s

 <span class='co'># Portuguese</span>
 <span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"CoNS"</span>, language = <span class='st'>"pt"</span>)
-<span class='co'>#&gt; "Staphylococcus coagulase negativo (CoNS)"</span></pre>
+<span class='co'>#&gt; "Staphylococcus coagulase negativo (CoNS)"</span>
+</pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top">