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(v0.7.0.9005) ab algorithm update

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dr. M.S. (Matthijs) Berends
2019-06-11 14:18:25 +02:00
parent f6c47c8c88
commit 8f674e19bb
36 changed files with 274 additions and 248 deletions
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11
docs/reference/antibiotics.html
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@ -80,7 +80,7 @@
</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">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
@ -252,7 +245,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 454 observations and 13 variables:</p><dl class='dl-horizontal'>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 453 observations and 13 variables:</p><dl class='dl-horizontal'>
<dt><code>ab</code></dt><dd><p>Antibiotic ID as used in this package (like <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></dd>
<dt><code>atc</code></dt><dd><p>ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></dd>
<dt><code>cid</code></dt><dd><p>Compound ID as found in PubChem</p></dd>

15
docs/reference/catalogue_of_life.html
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@ -80,7 +80,7 @@
</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">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
@ -307,9 +300,9 @@ Function <code><a href='as.mo.html'>as.mo</a>()</code> to use the data for intel
<span class='co'># [1] "Castellani et al., 1919"</span>
<span class='co'># Do not get mistaken - the package only includes microorganisms</span>
<span class='fu'><a href='mo_property.html'>mo_phylum</a></span>(<span class='st'>"C. elegans"</span>)
<span class='co'># [1] "Cyanobacteria" # Bacteria?!</span>
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"C. elegans"</span>)
<span class='fu'><a href='mo_property.html'>mo_kingdom</a></span>(<span class='st'>"C. elegans"</span>)
<span class='co'># [1] "Bacteria" # Bacteria?!</span>
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"C. elegans"</span>)
<span class='co'># [1] "Chroococcus limneticus elegans" # Because a microorganism was found</span>
<span class='co'># }</span></pre>
</div>

16
docs/reference/catalogue_of_life_version.html
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@ -47,7 +47,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Version info of included Catalogue of Life — catalogue_of_life_version" />
<meta property="og:description" content="This function returns information about the included data from the Catalogue of Life. It also shows if the included version is their latest annual release. The Catalogue of Life releases their annual release in March each year." />
<meta property="og:description" content="This function returns information about the included data from the Catalogue of Life." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -80,7 +80,7 @@
</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">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
@ -244,7 +237,7 @@
<div class="ref-description">
<p>This function returns information about the included data from the Catalogue of Life. It also shows if the included version is their latest annual release. The Catalogue of Life releases their annual release in March each year.</p>
<p>This function returns information about the included data from the Catalogue of Life.</p>
</div>
@ -256,8 +249,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The list item <code>...$catalogue_of_life$is_latest_annual_release</code> is based on the system date.</p>
<p>For DSMZ, see <code><a href='microorganisms.html'>?microorganisms</a></code>.</p>
<p>For DSMZ, see <code><a href='microorganisms.html'>?microorganisms</a></code>.</p>
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>

4
docs/reference/index.html
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@ -78,7 +78,7 @@
</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">0.7.0.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
</span>
</div>
@ -373,7 +373,7 @@
</tr><tr>
<td>
<p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
<p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
</td>
<td><p>Property of a microorganism</p></td>
</tr><tr>

51
docs/reference/key_antibiotics.html
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@ -80,7 +80,7 @@
</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">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
</span>
</div>
@ -165,13 +165,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
@ -248,19 +241,22 @@
</div>
<pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"AMX"</span>),
<span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"AMC"</span>), <span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
<span class='st'>"CXM"</span>), <span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"TZP"</span>),
<span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"CIP"</span>), <span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
<span class='st'>"SXT"</span>), <span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"VAN"</span>),
<span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"TEC"</span>), <span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
<span class='st'>"TCY"</span>), <span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"ERY"</span>),
<span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"OXA"</span>), <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
<span class='st'>"RIF"</span>), <span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"GEN"</span>),
<span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"TOB"</span>), <span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
<span class='st'>"COL"</span>), <span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"CTX"</span>),
<span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"CAZ"</span>), <span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
<span class='st'>"MEM"</span>), <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
<pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
<span class='st'>"amoxicillin"</span>), <span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
<span class='st'>"amoxicillin/clavulanic acid"</span>), <span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
<span class='st'>"cefuroxime"</span>), <span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
<span class='st'>"piperacillin/tazobactam"</span>), <span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
<span class='st'>"ciprofloxacin"</span>), <span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
<span class='st'>"trimethoprim/sulfamethoxazole"</span>), <span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
<span class='st'>"vancomycin"</span>), <span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"teicoplanin"</span>),
<span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"tetracycline"</span>),
<span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"erythromycin"</span>),
<span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"oxacillin"</span>), <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
<span class='st'>"rifampin"</span>), <span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"gentamicin"</span>),
<span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"tobramycin"</span>),
<span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"colistin"</span>), <span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
<span class='st'>"cefotaxime"</span>), <span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"ceftazidime"</span>),
<span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"meropenem"</span>), <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
<span class='fu'>key_antibiotics_equal</span>(<span class='no'>y</span>, <span class='no'>z</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
<span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
@ -282,11 +278,11 @@
</tr>
<tr>
<th>GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6</th>
<td><p>column names of antibiotics for <strong>Gram positives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td>
<td><p>column names of antibiotics for <strong>Gram-positives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td>
</tr>
<tr>
<th>GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6</th>
<td><p>column names of antibiotics for <strong>Gram negatives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td>
<td><p>column names of antibiotics for <strong>Gram-negatives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td>
</tr>
<tr>
<th>warnings</th>
@ -321,10 +317,10 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The function <code>key_antibiotics</code> returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>). The <code><a href='first_isolate.html'>first_isolate</a></code> function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible <em>S. aureus</em> (MSSA) found within the same episode (see <code>episode</code> parameter of <code><a href='first_isolate.html'>first_isolate</a></code>). Without key antibiotic comparison it would not.</p>
<p>At default, the antibiotics that are used for <strong>Gram positive bacteria</strong> are (colum names): <br />
<code>"amox"</code>, <code>"amcl"</code>, <code>"cfur"</code>, <code>"pita"</code>, <code>"cipr"</code>, <code>"trsu"</code> (until here is universal), <code>"vanc"</code>, <code>"teic"</code>, <code>"tetr"</code>, <code>"eryt"</code>, <code>"oxac"</code>, <code>"rifa"</code>.</p>
<p>At default, the antibiotics that are used for <strong>Gram negative bacteria</strong> are (colum names): <br />
<code>"amox"</code>, <code>"amcl"</code>, <code>"cfur"</code>, <code>"pita"</code>, <code>"cipr"</code>, <code>"trsu"</code> (until here is universal), <code>"gent"</code>, <code>"tobr"</code>, <code>"coli"</code>, <code>"cfot"</code>, <code>"cfta"</code>, <code>"mero"</code>.</p>
<p>At default, the antibiotics that are used for <strong>Gram-positive bacteria</strong> are: <br />
amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampin.</p>
<p>At default, the antibiotics that are used for <strong>Gram-negative bacteria</strong> are: <br />
amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem.</p>
<p>The function <code>key_antibiotics_equal</code> checks the characters returned by <code>key_antibiotics</code> for equality, and returns a logical vector.</p>
<h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key antibiotics</h2>
@ -350,6 +346,7 @@
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># septic_patients is a dataset available in the AMR package</span>
?<span class='no'>septic_patients</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># set key antibiotics to a new variable</span>
<span class='no'>my_patients</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>

19
docs/reference/mo_property.html
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@ -80,7 +80,7 @@
</button>
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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">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
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@ -165,13 +165,6 @@
Create frequency tables
</a>
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<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
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<a href="../articles/benchmarks.html">
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@ -284,6 +277,8 @@
<span class='fu'>mo_taxonomy</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_info</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_url</span>(<span class='no'>x</span>, <span class='kw'>open</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
<span class='fu'>mo_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"fullname"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)</pre>
@ -378,8 +373,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'>mo_shortname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "E. coli"</span>
<span class='co'>## other properties</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gram negative"</span>
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" (equal to kingdom)</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gram-negative"</span>
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" (equal to kingdom, but may be translated)</span>
<span class='fu'>mo_rank</span>(<span class='st'>"E. coli"</span>) <span class='co'># "species"</span>
<span class='fu'>mo_url</span>(<span class='st'>"E. coli"</span>) <span class='co'># get the direct url to the online database entry</span>
@ -393,7 +388,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'>mo_genus</span>(<span class='st'>"MRSA"</span>) <span class='co'># "Staphylococcus"</span>
<span class='fu'>mo_species</span>(<span class='st'>"MRSA"</span>) <span class='co'># "aureus"</span>
<span class='fu'>mo_shortname</span>(<span class='st'>"MRSA"</span>) <span class='co'># "S. aureus"</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"MRSA"</span>) <span class='co'># "Gram positive"</span>
<span class='fu'>mo_gramstain</span>(<span class='st'>"MRSA"</span>) <span class='co'># "Gram-positive"</span>
<span class='fu'>mo_genus</span>(<span class='st'>"VISA"</span>) <span class='co'># "Staphylococcus"</span>
<span class='fu'>mo_species</span>(<span class='st'>"VISA"</span>) <span class='co'># "aureus"</span>
@ -442,6 +437,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='co'># get a list with the complete taxonomy (from kingdom to subspecies)</span>
<span class='fu'>mo_taxonomy</span>(<span class='st'>"E. coli"</span>)
<span class='co'># get a list with the taxonomy, the authors and the URL to the online database</span>
<span class='fu'>mo_info</span>(<span class='st'>"E. coli"</span>)
<span class='co'># }</span></pre>
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