big website update, licence txt update

2025-07-25 03:35:38 +02:00 · 2019-01-02 23:24:07 +01:00
parent 4255707cb7
commit 6b2d464f8c
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--- a/docs/index.html
+++ b/docs/index.html
@ -22,7 +22,7 @@
 <meta property="og:description" content="Functions to simplify the analysis and prediction of Antimicrobial 
    Resistance (AMR) and to work with microbial and antimicrobial properties by
    using evidence-based methods.">
-<meta property="og:image" content="https://msberends.gitlab.io/logo.png">
+<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png">
 <meta name="twitter:card" content="summary">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@ -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="Released version">0.5.0.9008</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9009</span>
      </span>
    </div>

@ -55,12 +55,65 @@
    Home
  </a>
 </li>
-<li>
-  <a href="articles/AMR.html">
-    <span class="fa fa-directions"></span>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    <span class="fa fa-question-circle"></span>
     
-    Get Started
+    How to
+     
+    <span class="caret"></span>
  </a>
+  <ul class="dropdown-menu" role="menu">
+<li>
+      <a href="articles/AMR.html">
+        <span class="fa fa-directions"></span>
+         
+        Conduct AMR analysis
+      </a>
+    </li>
+    <li>
+      <a href="articles/Predict.html">
+        <span class="fa fa-dice"></span>
+         
+        Predict antimicrobial resistance
+      </a>
+    </li>
+    <li>
+      <a href="articles/EUCAST.html">
+        <span class="fa fa-exchange-alt"></span>
+         
+        Apply EUCAST rules
+      </a>
+    </li>
+    <li>
+      <a href="articles/mo_property.html">
+        <span class="fa fa-bug"></span>
+         
+        Get properties of a microorganism
+      </a>
+    </li>
+    <li>
+      <a href="articles/ab_property.html">
+        <span class="fa fa-capsules"></span>
+         
+        Get properties of an antibiotic
+      </a>
+    </li>
+    <li>
+      <a href="articles/freq.html">
+        <span class="fa fa-sort-amount-down"></span>
+         
+        Create frequency tables
+      </a>
+    </li>
+    <li>
+      <a href="articles/G_test.html">
+        <span class="fa fa-clipboard-check"></span>
+         
+        Use the G-test
+      </a>
+    </li>
+  </ul>
 </li>
 <li>
  <a href="reference/">
@ -83,6 +136,8 @@
    Changelog
  </a>
 </li>
+      </ul>
+<ul class="nav navbar-nav navbar-right">
 <li>
  <a href="https://gitlab.com/msberends/AMR">
    <span class="fab fa fab fa-gitlab"></span>
@ -90,8 +145,6 @@
    Source Code
  </a>
 </li>
-      </ul>
-<ul class="nav navbar-nav navbar-right">
 <li>
  <a href="LICENSE-text.html">
    <span class="fa fa-book"></span>
@ -162,13 +215,13 @@
 <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. 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.</p>
 </div>
 <div id="get-started" class="section level3">
 <h3 class="hasAnchor">
 <a href="#get-started" class="anchor"></a>Get started</h3>
-<p>To find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click the button ‘Get Started’ in the top menu.</p>
+<p>To find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click the links in the ‘How to’ menu.</p>
 </div>
 <div id="short-introduction" class="section level3">
 <h3 class="hasAnchor">
@ -178,17 +231,17 @@
 <p>All (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all 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. ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists.</p>
 <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” and “esccol”. Even <code><a href="reference/as.mo.html">as.mo("MRSA")</a></code> will return the ID of <em>S. aureus</em>. Moreover, it can group all coagulase negative and positive <em>Staphylococci</em>, and can transform <em>Streptococci</em> into Lancefield groups. To find bacteria based on your input, it uses Artificial Intelligence to look up values in the included ITIS data, consisting of more than 18,000 microorganisms.</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).
@ -200,9 +253,9 @@
 <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 <a href="https://dplyr.tidyverse.org/#usage">with the <code>dplyr</code> package</a> (e.g. in conjunction with <a href="https://dplyr.tidyverse.org/reference/summarise.html"><code>summarise</code></a>)</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>
@ -210,9 +263,9 @@
 <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:
@ -223,6 +276,8 @@
 </ul>
 </li>
 </ul>
+</li>
+</ol>
 <hr>
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 </div>