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(v1.6.0.9001) support Inf for episodes

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dr. M.S. (Matthijs) Berends
2021-04-12 12:35:13 +02:00
parent 7a3139f7cc
commit 6ff5448192
29 changed files with 144 additions and 104 deletions
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2
docs/reference/custom_eucast_rules.html
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@ -82,7 +82,7 @@
</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="Latest development version">1.6.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9001</span>
</span>
</div>

2
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">1.6.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9001</span>
</span>
</div>

4
docs/reference/first_isolate.html
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@ -82,7 +82,7 @@
</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="Latest development version">1.5.0.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9001</span>
</span>
</div>
@ -314,7 +314,7 @@
</tr>
<tr>
<th>col_keyantibiotics</th>
<td><p>column name of the key antibiotics to determine first (weighted) isolates, see <code><a href='key_antibiotics.html'>key_antibiotics()</a></code>. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use <code>col_keyantibiotics = FALSE</code> to prevent this.</p></td>
<td><p>column name of the key antibiotics to determine first (weighted) isolates, see <code><a href='key_antibiotics.html'>key_antibiotics()</a></code>. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use <code>col_keyantibiotics = FALSE</code> to prevent this. Can also be the output of <code><a href='key_antibiotics.html'>key_antibiotics()</a></code>.</p></td>
</tr>
<tr>
<th>episode_days</th>

6
docs/reference/get_episode.html
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@ -82,7 +82,7 @@
</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="Latest development version">1.5.0.9016</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9001</span>
</span>
</div>
@ -255,7 +255,7 @@
</tr>
<tr>
<th>episode_days</th>
<td><p>required episode length in days, can also be less than a day, see <em>Details</em></p></td>
<td><p>required episode length in days, can also be less than a day or <code>Inf</code>, see <em>Details</em></p></td>
</tr>
<tr>
<th>...</th>
@ -337,7 +337,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># grouping on patients and microorganisms leads to the same results</span>
<span class='co'># as first_isolate():</span>
<span class='va'>x</span> <span class='op'>&lt;-</span> <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span><span class='va'>.</span>, include_unknown <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span>
<span class='fu'><a href='first_isolate.html'>filter_first_isolate</a></span><span class='op'>(</span>include_unknown <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>y</span> <span class='op'>&lt;-</span> <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>patient_id</span>, <span class='va'>mo</span><span class='op'>)</span> <span class='op'>%&gt;%</span>

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</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="Latest development version">1.6.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9001</span>
</span>
</div>

2
docs/reference/like.html
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@ -82,7 +82,7 @@
</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="Latest development version">1.6.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9001</span>
</span>
</div>

2
docs/reference/mdro.html
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@ -82,7 +82,7 @@
</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="Latest development version">1.6.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9001</span>
</span>
</div>

8
docs/reference/plot.html
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@ -82,7 +82,7 @@
</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="Latest development version">1.6.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9001</span>
</span>
</div>
@ -258,7 +258,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for mic</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
<span class='fu'>ggplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
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'>"MIC 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>,
@ -289,7 +289,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for disk</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
<span class='fu'>ggplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
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>,
@ -314,7 +314,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for rsi</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
<span class='fu'>ggplot</span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
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>,