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(v1.4.0.9000) more extensive unit tests
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@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
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</span>
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</div>
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@ -244,16 +244,16 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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<p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details.</p>
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</div>
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<pre class="usage"><span class='fu'>eucast_rules</span>(
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<span class='kw'>x</span>,
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col_mo = <span class='kw'>NULL</span>,
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info = <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
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rules = <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR_eucastrules"</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>)),
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verbose = <span class='fl'>FALSE</span>,
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version_breakpoints = <span class='fl'>10</span>,
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version_expertrules = <span class='fl'>3.2</span>,
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<span class='kw'>...</span>
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)</pre>
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<pre class="usage"><span class='fu'>eucast_rules</span><span class='op'>(</span>
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<span class='va'>x</span>,
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col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
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info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
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rules <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"AMR_eucastrules"</span>, default <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span><span class='op'>)</span><span class='op'>)</span>,
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verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
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version_breakpoints <span class='op'>=</span> <span class='fl'>10</span>,
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version_expertrules <span class='op'>=</span> <span class='fl'>3.2</span>,
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<span class='va'>...</span>
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<span class='op'>)</span></pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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@ -311,7 +311,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<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 />
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<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>
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<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p><h3>'Other' rules</h3>
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<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>'Other' rules</h3>
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<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol>
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@ -349,21 +349,21 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># \donttest{</span>
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<span class='kw'>a</span> <span class='op'><-</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>,
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<span class='va'>a</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"Staphylococcus aureus"</span>,
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<span class='st'>"Enterococcus faecalis"</span>,
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<span class='st'>"Escherichia coli"</span>,
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<span class='st'>"Klebsiella pneumoniae"</span>,
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<span class='st'>"Pseudomonas aeruginosa"</span>),
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VAN = <span class='st'>"-"</span>, <span class='co'># Vancomycin</span>
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AMX = <span class='st'>"-"</span>, <span class='co'># Amoxicillin</span>
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COL = <span class='st'>"-"</span>, <span class='co'># Colistin</span>
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CAZ = <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span>
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CXM = <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span>
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PEN = <span class='st'>"S"</span>, <span class='co'># Benzylpenicillin</span>
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FOX = <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
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stringsAsFactors = <span class='fl'>FALSE</span>)
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<span class='st'>"Pseudomonas aeruginosa"</span><span class='op'>)</span>,
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VAN <span class='op'>=</span> <span class='st'>"-"</span>, <span class='co'># Vancomycin</span>
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AMX <span class='op'>=</span> <span class='st'>"-"</span>, <span class='co'># Amoxicillin</span>
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COL <span class='op'>=</span> <span class='st'>"-"</span>, <span class='co'># Colistin</span>
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CAZ <span class='op'>=</span> <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span>
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CXM <span class='op'>=</span> <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span>
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PEN <span class='op'>=</span> <span class='st'>"S"</span>, <span class='co'># Benzylpenicillin</span>
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FOX <span class='op'>=</span> <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
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stringsAsFactors <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
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<span class='kw'>a</span>
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<span class='va'>a</span>
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<span class='co'># mo VAN AMX COL CAZ CXM PEN FOX</span>
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<span class='co'># 1 Staphylococcus aureus - - - - - S S</span>
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<span class='co'># 2 Enterococcus faecalis - - - - - S S</span>
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@ -373,9 +373,9 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<span class='co'># apply EUCAST rules: some results wil be changed</span>
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<span class='kw'>b</span> <span class='op'><-</span> <span class='fu'>eucast_rules</span>(<span class='kw'>a</span>)
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<span class='va'>b</span> <span class='op'><-</span> <span class='fu'>eucast_rules</span><span class='op'>(</span><span class='va'>a</span><span class='op'>)</span>
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<span class='kw'>b</span>
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<span class='va'>b</span>
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<span class='co'># mo VAN AMX COL CAZ CXM PEN FOX</span>
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<span class='co'># 1 Staphylococcus aureus - S R R S S S</span>
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<span class='co'># 2 Enterococcus faecalis - - R R R S R</span>
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@ -386,7 +386,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<span class='co'># do not apply EUCAST rules, but rather get a data.frame</span>
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<span class='co'># containing all details about the transformations:</span>
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<span class='kw'>c</span> <span class='op'><-</span> <span class='fu'>eucast_rules</span>(<span class='kw'>a</span>, verbose = <span class='fl'>TRUE</span>)
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<span class='va'>c</span> <span class='op'><-</span> <span class='fu'>eucast_rules</span><span class='op'>(</span><span class='va'>a</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
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<span class='co'># }</span>
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</pre>
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</div>
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@ -404,7 +404,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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</div>
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<div class="pkgdown">
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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</div>
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</footer>
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