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website update

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dr. M.S. (Matthijs) Berends
2019-06-02 19:50:22 +02:00
parent bd73988f15
commit 702da574c0
62 changed files with 390 additions and 379 deletions
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2
docs/reference/AMR-deprecated.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

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docs/reference/WHOCC.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

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docs/reference/WHONET.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/ab_property.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/age.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

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docs/reference/age_groups.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

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docs/reference/antibiotics.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/as.ab.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/as.atc.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

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docs/reference/as.disk.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

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docs/reference/as.mic.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/as.mo.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/as.rsi.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/atc_online.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/availability.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/catalogue_of_life_version.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

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docs/reference/count.html
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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/filter_ab_class.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/first_isolate.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/freq.html
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@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/g.test.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/ggplot_rsi.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/guess_ab_col.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/join.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="Latest development version">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
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="Latest development version">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/kurtosis.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="Latest development version">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/like.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="Latest development version">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/mdro.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

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docs/reference/microorganisms.html
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<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>An object of class <code>data.frame</code> with 67903 rows and 16 columns.</p>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 67,903 observations and 16 variables:</p><dl class='dl-horizontal'>
<dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>fullname</code></dt><dd><p>Full name, like <code>"Escherichia coli"</code></p></dd>
<dt><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code></dt><dd><p>Taxonomic rank of the microorganism</p></dd>
<dt><code>rank</code></dt><dd><p>Text of the taxonomic rank of the microorganism, like <code>"species"</code> or <code>"genus"</code></p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning scientific publication</p></dd>
<dt><code>species_id</code></dt><dd><p>ID of the species as used by the Catalogue of Life</p></dd>
<dt><code>source</code></dt><dd><p>Either <code>"CoL"</code>, <code>"DSMZ"</code> (see source) or "manually added"</p></dd>
<dt><code>prevalence</code></dt><dd><p>Prevalence of the microorganism, see <code><a href='as.mo.html'>?as.mo</a></code></p></dd>
</dl>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>

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docs/reference/microorganisms.old.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/mo_property.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/mo_source.html
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@ -81,7 +81,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/p.symbol.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/portion.html
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@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/read.4D.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/resistance_predict.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

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docs/reference/rsi_translation.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

2
docs/reference/septic_patients.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

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docs/reference/skewness.html
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@ -81,7 +81,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>

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docs/reference/translate.html
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</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">0.6.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.6.1.9053</span>
</span>
</div>