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(v1.3.0.9001) website update

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dr. M.S. (Matthijs) Berends
2020-08-10 12:46:03 +02:00
parent 0d9602a6a9
commit 7d16bec21f
79 changed files with 2221 additions and 1974 deletions
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docs/reference/eucast_rules.html
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@ -83,7 +83,7 @@ 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="Latest development version">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@ -238,12 +238,12 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
<span class='kw'>rules</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR.eucast_rules"</span>, <span class='kw'>default</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>)),
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='no'>...</span>
<span class='kw'>x</span>,
col_mo = <span class='kw'>NULL</span>,
info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
rules = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR.eucast_rules"</span>, default = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>)),
verbose = <span class='fl'>FALSE</span>,
<span class='kw'>...</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@ -407,21 +407,21 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># \donttest{</span>
<span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Staphylococcus aureus"</span>,
<span class='kw'>a</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(mo = <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Staphylococcus aureus"</span>,
<span class='st'>"Enterococcus faecalis"</span>,
<span class='st'>"Escherichia coli"</span>,
<span class='st'>"Klebsiella pneumoniae"</span>,
<span class='st'>"Pseudomonas aeruginosa"</span>),
<span class='kw'>VAN</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Vancomycin</span>
<span class='kw'>AMX</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Amoxicillin</span>
<span class='kw'>COL</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Colistin</span>
<span class='kw'>CAZ</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span>
<span class='kw'>CXM</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span>
<span class='kw'>PEN</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Penicillin G</span>
<span class='kw'>FOX</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
<span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
VAN = <span class='st'>"-"</span>, <span class='co'># Vancomycin</span>
AMX = <span class='st'>"-"</span>, <span class='co'># Amoxicillin</span>
COL = <span class='st'>"-"</span>, <span class='co'># Colistin</span>
CAZ = <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span>
CXM = <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span>
PEN = <span class='st'>"S"</span>, <span class='co'># Penicillin G</span>
FOX = <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
stringsAsFactors = <span class='fl'>FALSE</span>)
<span class='no'>a</span>
<span class='kw'>a</span>
<span class='co'># mo VAN AMX COL CAZ CXM PEN FOX</span>
<span class='co'># 1 Staphylococcus aureus - - - - - S S</span>
<span class='co'># 2 Enterococcus faecalis - - - - - S S</span>
@ -431,9 +431,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='co'># apply EUCAST rules: 18 results are forced as R or S</span>
<span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>)
<span class='kw'>b</span> <span class='op'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='kw'>a</span>)
<span class='no'>b</span>
<span class='kw'>b</span>
<span class='co'># mo VAN AMX COL CAZ CXM PEN FOX</span>
<span class='co'># 1 Staphylococcus aureus - S R R S S S</span>
<span class='co'># 2 Enterococcus faecalis - - R R R S R</span>
@ -444,7 +444,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='co'># do not apply EUCAST rules, but rather get a data.frame</span>
<span class='co'># with 18 rows, containing all details about the transformations:</span>
<span class='no'>c</span> <span class='kw'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='kw'>c</span> <span class='op'>&lt;-</span> <span class='fu'>eucast_rules</span>(<span class='kw'>a</span>, verbose = <span class='fl'>TRUE</span>)
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@ -461,7 +461,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
</div>
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