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https://github.com/msberends/AMR.git
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(v1.5.0.9027) website update
This commit is contained in:
@ -82,7 +82,7 @@
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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">1.5.0.9026</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9027</span>
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</span>
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</div>
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@ -274,7 +274,7 @@
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<span class='co'># S3 method for disk</span>
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<span class='fu'>plot</span><span class='op'>(</span>
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<span class='va'>x</span>,
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main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
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main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
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ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
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xlab <span class='op'>=</span> <span class='st'>"Disk diffusion diameter (mm)"</span>,
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mo <span class='op'>=</span> <span class='cn'>NULL</span>,
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@ -289,7 +289,7 @@
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<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
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<span class='va'>data</span>,
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mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
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title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
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title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
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ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
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xlab <span class='op'>=</span> <span class='st'>"Disk diffusion diameter (mm)"</span>,
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mo <span class='op'>=</span> <span class='cn'>NULL</span>,
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@ -307,6 +307,17 @@
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xlab <span class='op'>=</span> <span class='st'>"Antimicrobial Interpretation"</span>,
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main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
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<span class='va'>...</span>
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<span class='op'>)</span>
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<span class='co'># S3 method for rsi</span>
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<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
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<span class='va'>data</span>,
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mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
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title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
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xlab <span class='op'>=</span> <span class='st'>"Antimicrobial Interpretation"</span>,
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ylab <span class='op'>=</span> <span class='st'>"Frequency"</span>,
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colours_RSI <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'>"#ED553B"</span>, <span class='st'>"#3CAEA3"</span>, <span class='st'>"#F6D55C"</span><span class='op'>)</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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@ -378,9 +389,11 @@ 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='va'>some_mic_values</span> <span class='op'><-</span> <span class='fu'><a href='random.html'>random_mic</a></span><span class='op'>(</span>size <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>
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<span class='va'>some_disk_values</span> <span class='op'><-</span> <span class='fu'><a href='random.html'>random_disk</a></span><span class='op'>(</span>size <span class='op'>=</span> <span class='fl'>100</span>, mo <span class='op'>=</span> <span class='st'>"Escherichia coli"</span>, ab <span class='op'>=</span> <span class='st'>"cipro"</span><span class='op'>)</span>
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<span class='va'>some_rsi_values</span> <span class='op'><-</span> <span class='fu'><a href='random.html'>random_rsi</a></span><span class='op'>(</span><span class='fl'>50</span>, prob_RSI <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='fl'>0.30</span>, <span class='fl'>0.55</span>, <span class='fl'>0.05</span><span class='op'>)</span><span class='op'>)</span>
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<span class='fu'>plot</span><span class='op'>(</span><span class='va'>some_mic_values</span><span class='op'>)</span>
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<span class='fu'>plot</span><span class='op'>(</span><span class='va'>some_disk_values</span><span class='op'>)</span>
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<span class='fu'>plot</span><span class='op'>(</span><span class='va'>some_rsi_values</span><span class='op'>)</span>
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<span class='co'># when providing the microorganism and antibiotic, colours will show interpretations:</span>
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<span class='fu'>plot</span><span class='op'>(</span><span class='va'>some_mic_values</span>, mo <span class='op'>=</span> <span class='st'>"S. aureus"</span>, ab <span class='op'>=</span> <span class='st'>"ampicillin"</span><span class='op'>)</span>
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@ -389,6 +402,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='http://ggplot2.tidyverse.org'>"ggplot2"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
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<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_mic_values</span><span class='op'>)</span>
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<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_disk_values</span>, mo <span class='op'>=</span> <span class='st'>"Escherichia coli"</span>, ab <span class='op'>=</span> <span class='st'>"cipro"</span><span class='op'>)</span>
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<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span><span class='va'>some_rsi_values</span><span class='op'>)</span>
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<span class='op'>}</span>
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</pre>
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</div>
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