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(v1.7.1.9067) Support for Swedish and Russian

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dr. M.S. (Matthijs) Berends
2021-12-12 09:42:03 +01:00
parent 5b5f70a103
commit 56f1ce328a
81 changed files with 1588 additions and 530 deletions
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18
docs/reference/ab_property.html
View File

@ -17,7 +17,7 @@
</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">1.7.1.9064</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>
@ -161,7 +161,7 @@
<p>Use these functions to return a specific property of an antibiotic from the <a href="antibiotics.html">antibiotics</a> data set. All input values will be evaluated internally with <code><a href="as.ab.html">as.ab()</a></code>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">ab_name</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, tolower <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">ab_name</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, tolower <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_cid</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span>
@ -169,13 +169,13 @@
<span class="fu">ab_tradenames</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_group</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_group</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_atc</span><span class="op">(</span><span class="va">x</span>, only_first <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_atc_group1</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_atc_group1</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_atc_group2</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_atc_group2</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_loinc</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span>
@ -183,17 +183,17 @@
<span class="fu">ab_ddd_units</span><span class="op">(</span><span class="va">x</span>, administration <span class="op">=</span> <span class="st">"oral"</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_info</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_info</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_url</span><span class="op">(</span><span class="va">x</span>, open <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_property</span><span class="op">(</span><span class="va">x</span>, property <span class="op">=</span> <span class="st">"name"</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">ab_property</span><span class="op">(</span><span class="va">x</span>, property <span class="op">=</span> <span class="st">"name"</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">set_ab_names</span><span class="op">(</span>
<span class="va">data</span>,
<span class="va">...</span>,
property <span class="op">=</span> <span class="st">"name"</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
snake_case <span class="op">=</span> <span class="cn">NULL</span>
<span class="op">)</span></code></pre></div></div>
@ -202,7 +202,7 @@
<dl><dt>x</dt>
<dd><p>any (vector of) text that can be coerced to a valid antibiotic code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_locale()</a></code>) and can also be set with <code>getOption("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with <code>getOption("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>tolower</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the first <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> of every output should be transformed to a lower case <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a>. This will lead to e.g. "polymyxin B" and not "polymyxin b".</p></dd>
<dt>...</dt>

2
docs/reference/antibiotic_class_selectors.html
View File

@ -17,7 +17,7 @@
</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">1.7.1.9063</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>

6
docs/reference/as.mo.html
View File

@ -17,7 +17,7 @@
</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">1.7.1.9062</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>
@ -168,7 +168,7 @@
allow_uncertain <span class="op">=</span> <span class="cn">TRUE</span>,
reference_df <span class="op">=</span> <span class="fu"><a href="mo_source.html">get_mo_source</a></span><span class="op">(</span><span class="op">)</span>,
ignore_pattern <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_ignore_pattern"</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,
<span class="va">...</span>
<span class="op">)</span>
@ -198,7 +198,7 @@
<dt>ignore_pattern</dt>
<dd><p>a regular expression (case-insensitive) of which all matches in <code>x</code> must return <code>NA</code>. This can be convenient to exclude known non-relevant input and can also be set with the option <code>AMR_ignore_pattern</code>, e.g. <code>options(AMR_ignore_pattern = "(not reported|contaminated flora)")</code>.</p></dd>
<dt>language</dt>
<dd><p>language to translate text like "no growth", which defaults to the system language (see <code><a href="translate.html">get_locale()</a></code>)</p></dd>
<dd><p>language to translate text like "no growth", which defaults to the system language (see <code><a href="translate.html">get_AMR_locale()</a></code>)</p></dd>
<dt>info</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if a progress bar should be printed if more than 25 items are to be coerced, defaults to <code>TRUE</code> only in interactive mode</p></dd>
<dt>...</dt>

4
docs/reference/as.rsi.html
View File

@ -17,7 +17,7 @@
</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">1.7.1.9064</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>
@ -254,7 +254,7 @@
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href="as.disk.html">as.disk()</a></code>, that also gives your columns the new data class <code><a href="as.disk.html">disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul><li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><div class="sourceCode"><pre><code><span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.disk</span>, <span class="va">as.rsi</span><span class="op">)</span> <span class="co"># until dplyr 1.0.0</span>
<span class="va">your_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.disk</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span> <span class="co"># since dplyr 1.0.0</span></code></pre></div></li>
</ul></li>
<li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.rsi(data)</code>.</p></li>
<li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.rsi(your_data)</code>.</p></li>
</ol></div>
<div class="section">

6
docs/reference/bug_drug_combinations.html
View File

@ -17,7 +17,7 @@
</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">1.7.1.9062</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>
@ -167,7 +167,7 @@
<span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span>
<span class="va">x</span>,
translate_ab <span class="op">=</span> <span class="st">"name (ab, atc)"</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
minimum <span class="op">=</span> <span class="fl">30</span>,
combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,
combine_IR <span class="op">=</span> <span class="cn">FALSE</span>,
@ -195,7 +195,7 @@
<dt>translate_ab</dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> of length 1 containing column names of the <a href="antibiotics.html">antibiotics</a> data set</p></dd>
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_locale()</a></code>) and can also be set with <code>getOption("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with <code>getOption("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>minimum</dt>
<dd><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see <em>Source</em>.</p></dd>
<dt>combine_SI</dt>

6
docs/reference/count.html
View File

@ -18,7 +18,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</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">1.7.1.9062</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>
@ -184,7 +184,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<span class="fu">count_df</span><span class="op">(</span>
<span class="va">data</span>,
translate_ab <span class="op">=</span> <span class="st">"name"</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,
combine_IR <span class="op">=</span> <span class="cn">FALSE</span>
<span class="op">)</span></code></pre></div></div>
@ -200,7 +200,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<dt>translate_ab</dt>
<dd><p>a column name of the <a href="antibiotics.html">antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_locale()</a></code>) and can also be set with <code>getOption("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with <code>getOption("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>combine_SI</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the argument <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is <code>TRUE</code>.</p></dd>
<dt>combine_IR</dt>

2
docs/reference/eucast_rules.html
View File

@ -18,7 +18,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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">1.7.1.9063</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>

10
docs/reference/ggplot_rsi.html
View File

@ -17,7 +17,7 @@
</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">1.7.1.9062</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>
@ -173,7 +173,7 @@
combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,
combine_IR <span class="op">=</span> <span class="cn">FALSE</span>,
minimum <span class="op">=</span> <span class="fl">30</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
nrow <span class="op">=</span> <span class="cn">NULL</span>,
colours <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SI <span class="op">=</span> <span class="st">"#3CAEA3"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, IR <span class="op">=</span> <span class="st">"#ED553B"</span>, R <span class="op">=</span>
<span class="st">"#ED553B"</span><span class="op">)</span>,
@ -194,7 +194,7 @@
fill <span class="op">=</span> <span class="st">"interpretation"</span>,
translate_ab <span class="op">=</span> <span class="st">"name"</span>,
minimum <span class="op">=</span> <span class="fl">30</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,
combine_IR <span class="op">=</span> <span class="cn">FALSE</span>,
<span class="va">...</span>
@ -213,7 +213,7 @@
x <span class="op">=</span> <span class="st">"antibiotic"</span>,
translate_ab <span class="op">=</span> <span class="st">"name"</span>,
minimum <span class="op">=</span> <span class="fl">30</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,
combine_IR <span class="op">=</span> <span class="cn">FALSE</span>,
datalabels.size <span class="op">=</span> <span class="fl">3</span>,
@ -245,7 +245,7 @@
<dt>minimum</dt>
<dd><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see <em>Source</em>.</p></dd>
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_locale()</a></code>) and can also be set with <code>getOption("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with <code>getOption("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>nrow</dt>
<dd><p>(when using <code>facet</code>) number of rows</p></dd>
<dt>colours</dt>

4
docs/reference/index.html
View File

@ -17,7 +17,7 @@
</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">1.7.1.9064</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>
@ -348,7 +348,7 @@
</td>
<td><p>Check Availability of Columns</p></td>
</tr><tr><td>
<p><code><a href="translate.html">get_locale()</a></code> </p>
<p><code><a href="translate.html">get_AMR_locale()</a></code> </p>
</td>
<td><p>Translate Strings from AMR Package</p></td>
</tr><tr><td>

2
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@ -17,7 +17,7 @@
</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">1.7.1.9064</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>

2
docs/reference/like.html
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@ -17,7 +17,7 @@
</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">1.7.1.9064</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>

2
docs/reference/mdro.html
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@ -17,7 +17,7 @@
</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">1.7.1.9064</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>

2
docs/reference/mo_matching_score.html
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@ -17,7 +17,7 @@
</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">1.7.1.9063</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>

62
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@ -17,7 +17,7 @@
</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">1.7.1.9064</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>
@ -161,70 +161,70 @@
<p>Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with <code><a href="as.mo.html">as.mo()</a></code>, which makes it possible to use microbial abbreviations, codes and names as input. See <em>Examples</em>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mo_name</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mo_name</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_fullname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_fullname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_shortname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_shortname</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_subspecies</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_subspecies</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_species</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_species</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_genus</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_genus</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_family</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_family</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_order</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_order</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_class</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_class</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_phylum</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_phylum</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_kingdom</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_kingdom</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_domain</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_domain</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_type</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_type</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_gramstain</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_gramstain</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_is_gram_negative</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_is_gram_negative</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_is_gram_positive</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_is_gram_positive</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_is_yeast</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_is_yeast</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span><span class="va">x</span>, <span class="va">ab</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span><span class="va">x</span>, <span class="va">ab</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_snomed</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_snomed</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_ref</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_ref</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_authors</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_authors</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_year</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_year</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_lpsn</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_lpsn</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_rank</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_rank</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_taxonomy</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_taxonomy</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_synonyms</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_synonyms</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_info</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_info</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_url</span><span class="op">(</span><span class="va">x</span>, open <span class="op">=</span> <span class="cn">FALSE</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_url</span><span class="op">(</span><span class="va">x</span>, open <span class="op">=</span> <span class="cn">FALSE</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">mo_property</span><span class="op">(</span><span class="va">x</span>, property <span class="op">=</span> <span class="st">"fullname"</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></code></pre></div></div>
<span class="fu">mo_property</span><span class="op">(</span><span class="va">x</span>, property <span class="op">=</span> <span class="st">"fullname"</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></code></pre></div></div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>x</dt>
<dd><p>any <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vector) that can be coerced to a valid microorganism code with <code><a href="as.mo.html">as.mo()</a></code>. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see <em>Examples</em>.</p></dd>
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_locale()</a></code>) and can be overwritten by setting the option <code>AMR_locale</code>, e.g. <code>options(AMR_locale = "de")</code>, see <a href="translate.html">translate</a>. Also used to translate text like "no growth". Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can be overwritten by setting the option <code>AMR_locale</code>, e.g. <code>options(AMR_locale = "de")</code>, see <a href="translate.html">translate</a>. Also used to translate text like "no growth". Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>...</dt>
<dd><p>other arguments passed on to <code><a href="as.mo.html">as.mo()</a></code>, such as 'allow_uncertain' and 'ignore_pattern'</p></dd>
<dt>ab</dt>

14
docs/reference/plot.html
View File

@ -17,7 +17,7 @@
</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">1.7.1.9062</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>
@ -171,7 +171,7 @@
ylab <span class="op">=</span> <span class="st">"Frequency"</span>,
xlab <span class="op">=</span> <span class="st">"Minimum Inhibitory Concentration (mg/L)"</span>,
colours_RSI <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#ED553B"</span>, <span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
expand <span class="op">=</span> <span class="cn">TRUE</span>,
<span class="va">...</span>
<span class="op">)</span>
@ -186,7 +186,7 @@
ylab <span class="op">=</span> <span class="st">"Frequency"</span>,
xlab <span class="op">=</span> <span class="st">"Minimum Inhibitory Concentration (mg/L)"</span>,
colours_RSI <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#ED553B"</span>, <span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
expand <span class="op">=</span> <span class="cn">TRUE</span>,
<span class="va">...</span>
<span class="op">)</span>
@ -204,7 +204,7 @@
ab <span class="op">=</span> <span class="cn">NULL</span>,
guideline <span class="op">=</span> <span class="st">"EUCAST"</span>,
colours_RSI <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#ED553B"</span>, <span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
expand <span class="op">=</span> <span class="cn">TRUE</span>,
<span class="va">...</span>
<span class="op">)</span>
@ -219,7 +219,7 @@
xlab <span class="op">=</span> <span class="st">"Disk diffusion diameter (mm)"</span>,
guideline <span class="op">=</span> <span class="st">"EUCAST"</span>,
colours_RSI <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#ED553B"</span>, <span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
expand <span class="op">=</span> <span class="cn">TRUE</span>,
<span class="va">...</span>
<span class="op">)</span>
@ -243,7 +243,7 @@
xlab <span class="op">=</span> <span class="st">"Antimicrobial Interpretation"</span>,
ylab <span class="op">=</span> <span class="st">"Frequency"</span>,
colours_RSI <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#ED553B"</span>, <span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
<span class="va">...</span>
<span class="op">)</span>
@ -267,7 +267,7 @@
<dt>colours_RSI</dt>
<dd><p>colours to use for filling in the bars, must be a vector of three values (in the order R, S and I). The default colours are colour-blind friendly.</p></dd>
<dt>language</dt>
<dd><p>language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see <code><a href="translate.html">get_locale()</a></code>) and can be overwritten by setting the option <code>AMR_locale</code>, e.g. <code>options(AMR_locale = "de")</code>, see <a href="translate.html">translate</a>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can be overwritten by setting the option <code>AMR_locale</code>, e.g. <code>options(AMR_locale = "de")</code>, see <a href="translate.html">translate</a>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>expand</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.</p></dd>
<dt>...</dt>

8
docs/reference/proportion.html
View File

@ -18,7 +18,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</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">1.7.1.9062</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>
@ -180,7 +180,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<span class="fu">proportion_df</span><span class="op">(</span>
<span class="va">data</span>,
translate_ab <span class="op">=</span> <span class="st">"name"</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
minimum <span class="op">=</span> <span class="fl">30</span>,
as_percent <span class="op">=</span> <span class="cn">FALSE</span>,
combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,
@ -190,7 +190,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<span class="fu">rsi_df</span><span class="op">(</span>
<span class="va">data</span>,
translate_ab <span class="op">=</span> <span class="st">"name"</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_locale</a></span><span class="op">(</span><span class="op">)</span>,
language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,
minimum <span class="op">=</span> <span class="fl">30</span>,
as_percent <span class="op">=</span> <span class="cn">FALSE</span>,
combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,
@ -216,7 +216,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<dt>translate_ab</dt>
<dd><p>a column name of the <a href="antibiotics.html">antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_locale()</a></code>) and can also be set with <code>getOption("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dd><p>language of the returned text, defaults to system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with <code>getOption("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>combine_SI</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the argument <code>combine_IR</code>, but this now follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is <code>TRUE</code>.</p></dd>
<dt>combine_IR</dt>

14
docs/reference/translate.html
View File

@ -17,7 +17,7 @@
</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">1.7.1.9062</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.7.1.9067</span>
</span>
</div>
@ -161,19 +161,19 @@
<p>For language-dependent output of AMR functions, like <code><a href="mo_property.html">mo_name()</a></code>, <code><a href="mo_property.html">mo_gramstain()</a></code>, <code><a href="mo_property.html">mo_type()</a></code> and <code><a href="ab_property.html">ab_name()</a></code>.</p>
</div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">get_locale</span><span class="op">(</span><span class="op">)</span></code></pre></div></div>
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">get_AMR_locale</span><span class="op">(</span><span class="op">)</span></code></pre></div></div>
<div id="details">
<h2>Details</h2>
<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://github.com/msberends/AMR/blob/main/data-raw/translations.tsv" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/translations.tsv</a>. This file will be read by all functions where a translated output can be desired, like all <code><a href="mo_property.html">mo_*</a></code> functions (such as <code><a href="mo_property.html">mo_name()</a></code>, <code><a href="mo_property.html">mo_gramstain()</a></code>, <code><a href="mo_property.html">mo_type()</a></code>, etc.) and <code><a href="ab_property.html">ab_*</a></code> functions (such as <code><a href="ab_property.html">ab_name()</a></code>, <code><a href="ab_property.html">ab_group()</a></code>, etc.).</p>
<p>Currently supported languages are: Danish, Dutch, English, French, German, Italian, Portuguese and Spanish. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.</p>
<p>Currently supported languages are: Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.</p>
<p>Please suggest your own translations <a href="https://github.com/msberends/AMR/issues/new?title=Translations" class="external-link">by creating a new issue on our repository</a>.</p><div class="section">
<h3 id="changing-the-default-language">Changing the Default Language<a class="anchor" aria-label="anchor" href="#changing-the-default-language"></a></h3>
<p>The system language will be used at default (as returned by <code>Sys.getenv("LANG")</code> or, if <code>LANG</code> is not set, <code><a href="https://rdrr.io/r/base/locales.html" class="external-link">Sys.getlocale()</a></code>), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:</p><ol><li><p>Setting the R option <code>AMR_locale</code>, e.g. by running <code>options(AMR_locale = "de")</code></p></li>
<li><p>Setting the system variable <code>LANGUAGE</code> or <code>LANG</code>, e.g. by adding <code>LANGUAGE="de_DE.utf8"</code> to your <code>.Renviron</code> file in your home directory</p></li>
</ol><p>So if the R option <code>AMR_locale</code> is set, the system variables <code>LANGUAGE</code> and <code>LANG</code> will be ignored.</p>
</ol><p>Thus, if the R option <code>AMR_locale</code> is set, the system variables <code>LANGUAGE</code> and <code>LANG</code> will be ignored.</p>
</div>
</div>
@ -196,15 +196,15 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># The 'language' argument of below functions</span>
<span class="co"># will be set automatically to your system language</span>
<span class="co"># with get_locale()</span>
<span class="co"># with get_AMR_locale()</span>
<span class="co"># English</span>
<span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"en"</span><span class="op">)</span>
<span class="co">#&gt; "Coagulase-negative Staphylococcus (CoNS)"</span>
<span class="co"># Danish</span>
<span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span>
<span class="co">#&gt; "Koagulase-negative stafylokokker (CoNS)"</span>
<span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"da"</span><span class="op">)</span>
<span class="co">#&gt; "Koagulase-negative stafylokokker (KNS)"</span>
<span class="co"># Dutch</span>
<span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"CoNS"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span>