WHO update, antibiotics update

docs/index.html

@@ -42,7 +42,7 @@
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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="Released version">0.5.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9012</span>
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@@ -214,7 +214,7 @@
 <h3 class="hasAnchor">
 <a href="#get-this-package" class="anchor"></a>Get this package</h3>
 <p>This package is available on the official R network (CRAN), which has a peer-reviewed submission process. Install this package in R with:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"AMR"</span>)</code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"AMR"</span>)</a></code></pre></div>
 <p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
 </div>
 <div id="get-started" class="section level3">
@@ -225,30 +225,39 @@
 <div id="short-introduction" class="section level3">
 <h3 class="hasAnchor">
 <a href="#short-introduction" class="anchor"></a>Short introduction</h3>
-<div id="taxonomic-reference-data" class="section level4">
+<div id="microbial-taxonomic-reference-data" class="section level4">
 <h4 class="hasAnchor">
-<a href="#taxonomic-reference-data" class="anchor"></a>Taxonomic reference data</h4>
-<p><img src="reference/figures/itis_logo.jpg" height="60px"></p>
+<a href="#microbial-taxonomic-reference-data" class="anchor"></a>Microbial (taxonomic) reference data</h4>
+<p><img src="reference/figures/logo_itis.jpg" height="60px"></p>
 <p>This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href="https://www.itis.gov" class="uri">https://www.itis.gov</a>).</p>
-<p>All ~20,000 (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.</p>
-<p>Read more about ITIS <a href="./reference/ITIS.html">in our manual</a>.</p>
+<p>All ~20,000 (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.</p>
+<p>Read more about the data from ITIS <a href="./reference/ITIS.html">in our manual</a>.</p>
+</div>
+<div id="antimicrobial-reference-data" class="section level4">
+<h4 class="hasAnchor">
+<a href="#antimicrobial-reference-data" class="anchor"></a>Antimicrobial reference data</h4>
+<div>
+<img src="reference/figures/logo_who.png" height="75px" class="logo_img"><p class="logo_txt">WHO Collaborating Centre for Drug Statistics Methodology</p>
+</div>
+<p>This package contains <strong>all ~500 antimicrobial drugs and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD)</strong> from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href="https://www.whocc.no" class="uri">https://www.whocc.no</a>) and the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register of the European Commission</a>.</p>
+<p>Read more about the data from WHOCC <a href="./reference/WHOCC.html">in our manual</a>.</p>
 </div>
 <div id="overview-of-functions" class="section level4">
 <h4 class="hasAnchor">
 <a href="#overview-of-functions" class="anchor"></a>Overview of functions</h4>
 <p>The <code>AMR</code> package basically does four important things:</p>
 <ol>
-<li>It <strong>cleanses existing data</strong>, by transforming it to reproducible and profound <em>classes</em>, making the most efficient use of R. These functions all use artificial intelligence to guess results that you would expect:</li>
-</ol>
+<li>
+<p>It <strong>cleanses existing data</strong>, by transforming it to reproducible and profound <em>classes</em>, making the most efficient use of R. These functions all use artificial intelligence to guess results that you would expect:</p>
 <ul>
 <li>Use <code><a href="reference/as.mo.html">as.mo()</a></code> to get an ID of a microorganism. The IDs are human readable for the trained eye - the ID of <em>Klebsiella pneumoniae</em> is “B_KLBSL_PNE” (B stands for Bacteria) and the ID of <em>S. aureus</em> is “B_STPHY_AUR”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” or “esccol” and tries to find expected results using artificial intelligence (AI) on the included ITIS data set, consisting of almost 20,000 microorganisms. It is <em>very</em> fast, please see our <a href="./articles/benchmarks.html">benchmarks</a>. Moreover, it can group <em>Staphylococci</em> into coagulase negative and positive (CoNS and CoPS, see <a href="./reference/as.mo.html#source">source</a>) and can categorise <em>Streptococci</em> into Lancefield groups (like beta-haemolytic <em>Streptococcus</em> Group B, <a href="./reference/as.mo.html#source">source</a>).</li>
 <li>Use <code><a href="reference/as.rsi.html">as.rsi()</a></code> to transform values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “&lt;=0.002; S” (combined MIC/RSI) will result in “S”.</li>
 <li>Use <code><a href="reference/as.mic.html">as.mic()</a></code> to cleanse your MIC values. It produces a so-called factor (called <em>ordinal</em> in SPSS) with valid MIC values as levels. A value like “&lt;=0.002; S” (combined MIC/RSI) will result in “&lt;=0.002”.</li>
 <li>Use <code><a href="reference/as.atc.html">as.atc()</a></code> to get the ATC code of an antibiotic as defined by the WHO. This package contains a database with most LIS codes, official names, DDDs and even trade names of antibiotics. For example, the values “Furabid”, “Furadantin”, “nitro” all return the ATC code of Nitrofurantoine.</li>
 </ul>
-<ol>
-<li>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</li>
-</ol>
+</li>
+<li>
+<p>It <strong>enhances existing data</strong> and <strong>adds new data</strong> from data sets included in this package.</p>
 <ul>
 <li>Use <code><a href="reference/eucast_rules.html">eucast_rules()</a></code> to apply <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST expert rules to isolates</a>.</li>
 <li>Use <code><a href="reference/first_isolate.html">first_isolate()</a></code> to identify the first isolates of every patient <a href="https://clsi.org/standards/products/microbiology/documents/m39/">using guidelines from the CLSI</a> (Clinical and Laboratory Standards Institute).
@@ -260,9 +269,9 @@
 <li>The data set <code>microorganisms</code> contains the complete taxonomic tree of more than 18,000 microorganisms (bacteria, fungi/yeasts and protozoa). Furthermore, the colloquial name and Gram stain are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like <code><a href="reference/mo_property.html">mo_genus()</a></code>, <code><a href="reference/mo_property.html">mo_family()</a></code>, <code><a href="reference/mo_property.html">mo_gramstain()</a></code> or even <code><a href="reference/mo_property.html">mo_phylum()</a></code>. As they use <code><a href="reference/as.mo.html">as.mo()</a></code> internally, they also use artificial intelligence. For example, <code><a href="reference/mo_property.html">mo_genus("MRSA")</a></code> and <code><a href="reference/mo_property.html">mo_genus("S. aureus")</a></code> will both return <code>"Staphylococcus"</code>. They also come with support for German, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.</li>
 <li>The data set <code>antibiotics</code> contains the ATC code, LIS codes, official name, trivial name and DDD of both oral and parenteral administration. It also contains a total of 298 trade names. Use functions like <code><a href="reference/ab_property.html">ab_name()</a></code> and <code><a href="reference/ab_property.html">ab_tradenames()</a></code> to look up values. The <code>ab_*</code> functions use <code><a href="reference/as.atc.html">as.atc()</a></code> internally so they support AI to guess your expected result. For example, <code><a href="reference/ab_property.html">ab_name("Fluclox")</a></code>, <code><a href="reference/ab_property.html">ab_name("Floxapen")</a></code> and <code><a href="reference/ab_property.html">ab_name("J01CF05")</a></code> will all return <code>"Flucloxacillin"</code>. These functions can again be used to add new variables to your data.</li>
 </ul>
-<ol>
-<li>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</li>
-</ol>
+</li>
+<li>
+<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
 <ul>
 <li>Calculate the resistance (and even co-resistance) of microbial isolates with the <code><a href="reference/portion.html">portion_R()</a></code>, <code><a href="reference/portion.html">portion_IR()</a></code>, <code><a href="reference/portion.html">portion_I()</a></code>, <code><a href="reference/portion.html">portion_SI()</a></code> and <code><a href="reference/portion.html">portion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_R()</a></code>, <code><a href="reference/count.html">count_IR()</a></code>, <code><a href="reference/count.html">count_I()</a></code>, <code><a href="reference/count.html">count_SI()</a></code> and <code><a href="reference/count.html">count_S()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code>summarise()</code>)</li>
 <li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
@@ -270,9 +279,9 @@
 <li>Conduct descriptive statistics to enhance base R: calculate <code><a href="reference/kurtosis.html">kurtosis()</a></code>, <code><a href="reference/skewness.html">skewness()</a></code> and create frequency tables with <code><a href="reference/freq.html">freq()</a></code>
 </li>
 </ul>
-<ol>
-<li>It <strong>teaches the user</strong> how to use all the above actions.</li>
-</ol>
+</li>
+<li>
+<p>It <strong>teaches the user</strong> how to use all the above actions.</p>
 <ul>
 <li>The package contains extensive help pages with many examples.</li>
 <li>It also contains an example data set called <code>septic_patients</code>. This data set contains:
@@ -283,6 +292,8 @@
 </ul>
 </li>
 </ul>
+</li>
+</ol>
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