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(v0.6.1.9050) support staged install

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dr. M.S. (Matthijs) Berends
2019-06-01 20:40:49 +02:00
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commit 2667fff8a7
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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
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<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">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
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<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">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
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<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">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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<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">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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<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">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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docs/reference/catalogue_of_life.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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>
@ -249,9 +249,7 @@
</div>
<pre class="usage"><span class='fu'>eucast_rules</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>rules</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"breakpoints"</span>,
<span class='st'>"expert"</span>, <span class='st'>"other"</span>, <span class='st'>"all"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
<span class='fu'>eucast_rules_file</span>()</pre>
<span class='st'>"expert"</span>, <span class='st'>"other"</span>, <span class='st'>"all"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -293,7 +291,6 @@
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <br />
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx</a></p></li>
</ul>
<p>For editing the reference file (which is available with <code>eucast_rules_file</code>), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like AMC. They can be separated by comma: <code>"AMC, fluoroquinolones"</code>. The mo_property can be any column name from the <code><a href='microorganisms.html'>microorganisms</a></code> data set, or <code>genus_species</code> or <code>gramstain</code>. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180).</p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@ -303,9 +300,7 @@
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi</a></code> for that. <br />
<strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.</p>
<p>The file used for applying all EUCAST rules can be retrieved with <code>eucast_rules_file()</code>. It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by <code>eucast_rules()</code> can be found by running this command: <br />
<code>AMR::EUCAST_RULES_FILE_LOCATION</code> (without brackets).</p>
<p>In the source code the file containing all rules is located <a href='https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv'>here</a>.</p>
<p>The file containing all EUCAST rules is located here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9049</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
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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="Released version">0.6.1.9045</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
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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="Released version">0.6.1.9049</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>
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</tr><tr>
<td>
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">eucast_rules_file()</a></code> </p>
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> </p>
</td>
<td><p>EUCAST rules</p></td>
</tr><tr>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

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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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

2
docs/reference/septic_patients.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">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

2
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="Released version">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>

8
docs/reference/translate.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">0.6.1.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
</span>
</div>
@ -252,9 +252,9 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Strings will be translated to foreign languages if they are defined in a local translation file. This file comes with this package and can be found when running:</p>
<p><code><a href='https://www.rdocumentation.org/packages/base/topics/system.file'>system.file("translations.tsv", package = "AMR")</a></code></p>
<p>This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_property</a></code> functions (<code><a href='mo_property.html'>mo_fullname</a></code>, <code><a href='mo_property.html'>mo_type</a></code>, etc.). Please suggest your own translations <a href='https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation%20suggestion'>by creating a new issue on our repository</a>.</p>
<p>Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv'>https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv</a>.</p>
<p>Please suggest your own translations <a href='https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation%20suggestion'>by creating a new issue on our repository</a>.</p>
<p>This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_property</a></code> functions (<code><a href='mo_property.html'>mo_fullname</a></code>, <code><a href='mo_property.html'>mo_type</a></code>, etc.).</p>
<p>The system language will be used at default, if supported, using <code>get_locale</code>. The system language can be overwritten with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>.</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>