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(v0.7.0.9013) mo_synonym fix

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dr. M.S. (Matthijs) Berends
2019-06-22 14:49:12 +02:00
parent 409397a337
commit c9156c004a
75 changed files with 465 additions and 507 deletions
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2
docs/reference/AMR-deprecated.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/AMR.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/WHOCC.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/WHONET.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/ab_property.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/age.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/age_groups.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/antibiotics.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/as.ab.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/as.atc.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/as.disk.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/as.mic.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

9
docs/reference/as.mo.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>
@ -385,9 +385,10 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
<span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"Staphylococcus aureus (MRSA)"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"Sthafilokkockus aaureuz"</span>) <span class='co'># handles incorrect spelling</span>
<span class='fu'>as.mo</span>(<span class='st'>"MRSA"</span>) <span class='co'># Methicillin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VISA"</span>) <span class='co'># Vancomycin Intermediate S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VRSA"</span>) <span class='co'># Vancomycin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"MRSA"</span>) <span class='co'># Methicillin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VISA"</span>) <span class='co'># Vancomycin Intermediate S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VRSA"</span>) <span class='co'># Vancomycin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='fl'>22242419</span>) <span class='co'># Catalogue of Life ID</span>
<span class='co'># Dyslexia is no problem - these all work:</span>
<span class='fu'>as.mo</span>(<span class='st'>"Ureaplasma urealyticum"</span>)

2
docs/reference/as.rsi.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/atc_online.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/availability.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/catalogue_of_life.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/catalogue_of_life_version.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/count.html
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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</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">0.7.0.9012</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/eucast_rules.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/extended-functions.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/filter_ab_class.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/first_isolate.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/freq.html
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@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/g.test.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

16
docs/reference/ggplot_rsi.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>
@ -237,7 +237,7 @@
<div class="ref-description">
<p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a>2</code> functions.</p>
<p>Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a>2</code> functions.</p>
</div>
@ -371,11 +371,11 @@
<p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name</a></code>. This can be set with the <code>translate_ab</code> parameter. See <code><a href='count.html'>count_df</a></code>.</p>
<p><strong>The functions</strong><br />
<code>geom_rsi</code> will take any variable from the data that has an <code>rsi</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) using <code>fun</code> (<code><a href='count.html'>count_df</a></code> at default, can also be <code><a href='portion.html'>portion_df</a></code>) and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
<p><code>facet_rsi</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/facet_wrap'>facet_wrap</a></code>.</p>
<p><code>facet_rsi</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://ggplot2.tidyverse.org/reference/facet_wrap.html'>facet_wrap</a></code>.</p>
<p><code>scale_y_percent</code> transforms the y axis to a 0 to 100% range using <code>scale_continuous</code>.</p>
<p><code>scale_rsi_colours</code> sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using <code>scale_brewer</code>.</p>
<p><code>theme_rsi</code> is a <code>ggplot <a href='https://www.rdocumentation.org/packages/ggplot2/topics/theme'>theme</a></code> with minimal distraction.</p>
<p><code>labels_rsi_count</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://www.rdocumentation.org/packages/ggplot2/topics/geom_text'>geom_text</a></code></p>
<p><code>theme_rsi</code> is a <code>ggplot <a href='https://ggplot2.tidyverse.org/reference/theme.html'>theme</a></code> with minimal distraction.</p>
<p><code>labels_rsi_count</code> print datalabels on the bars with percentage and amount of isolates using <code><a href='https://ggplot2.tidyverse.org/reference/geom_text.html'>geom_text</a></code></p>
<p><code>ggplot_rsi</code> is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (<code>%&gt;%</code>). See Examples.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -390,12 +390,12 @@
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>ggplot2</span>)
<span class='co'># get antimicrobial results for drugs against a UTI:</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>)) +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>)) +
<span class='fu'>geom_rsi</span>()
<span class='co'># prettify the plot using some additional functions:</span>
<span class='no'>df</span> <span class='kw'>&lt;-</span> <span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>df</span>) +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>df</span>) +
<span class='fu'>geom_rsi</span>() +
<span class='fu'>scale_y_percent</span>() +
<span class='fu'>scale_rsi_colours</span>() +
@ -439,7 +439,7 @@
<span class='co'># for colourblind mode, use divergent colours from the viridis package:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>() + <span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/scale_viridis'>scale_fill_viridis_d</a></span>()
<span class='fu'>ggplot_rsi</span>() + <span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_viridis.html'>scale_fill_viridis_d</a></span>()
<span class='co'># a shorter version which also adjusts data label colours:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>

2
docs/reference/guess_ab_col.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/index.html
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@ -78,7 +78,7 @@
</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">0.7.0.9012</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/join.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/key_antibiotics.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/kurtosis.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/like.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/mdro.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/microorganisms.codes.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/microorganisms.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/microorganisms.old.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/mo_property.html
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@ -80,7 +80,7 @@
</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">0.7.0.9012</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/mo_source.html
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@ -81,7 +81,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/p.symbol.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/portion.html
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@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
</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">0.7.0.9012</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/read.4D.html
View File

@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

16
docs/reference/resistance_predict.html
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@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>
@ -379,21 +379,21 @@
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>15</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggplot'>ggplot</a></span>(<span class='no'>data</span>,
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/aes'>aes</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>year</span>)) +
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/geom_bar'>geom_col</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/aes'>aes</a></span>(<span class='kw'>y</span> <span class='kw'>=</span> <span class='no'>value</span>),
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span>(<span class='no'>data</span>,
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='no'>year</span>)) +
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_bar.html'>geom_col</a></span>(<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(<span class='kw'>y</span> <span class='kw'>=</span> <span class='no'>value</span>),
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"grey75"</span>) +
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/geom_linerange'>geom_errorbar</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/aes'>aes</a></span>(<span class='kw'>ymin</span> <span class='kw'>=</span> <span class='no'>se_min</span>,
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/geom_linerange.html'>geom_errorbar</a></span>(<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/aes.html'>aes</a></span>(<span class='kw'>ymin</span> <span class='kw'>=</span> <span class='no'>se_min</span>,
<span class='kw'>ymax</span> <span class='kw'>=</span> <span class='no'>se_max</span>),
<span class='kw'>colour</span> <span class='kw'>=</span> <span class='st'>"grey50"</span>) +
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/scale_continuous'>scale_y_continuous</a></span>(<span class='kw'>limits</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>),
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/scale_continuous.html'>scale_y_continuous</a></span>(<span class='kw'>limits</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>),
<span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
<span class='kw'>labels</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste0</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>, <span class='fl'>10</span>), <span class='st'>"%"</span>)) +
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/labs'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/expression'>expression</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Forecast of amoxicillin resistance in "</span>,
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/labs.html'>labs</a></span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/expression'>expression</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Forecast of amoxicillin resistance in "</span>,
<span class='fu'><a href='https://www.rdocumentation.org/packages/grDevices/topics/plotmath'>italic</a></span>(<span class='st'>"E. coli"</span>))),
<span class='kw'>y</span> <span class='kw'>=</span> <span class='st'>"%IR"</span>,
<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Year"</span>) +
<span class='fu'><a href='https://www.rdocumentation.org/packages/ggplot2/topics/ggtheme'>theme_minimal</a></span>(<span class='kw'>base_size</span> <span class='kw'>=</span> <span class='fl'>13</span>)
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggtheme.html'>theme_minimal</a></span>(<span class='kw'>base_size</span> <span class='kw'>=</span> <span class='fl'>13</span>)
}
<span class='co'># }</span></pre>
</div>

2
docs/reference/rsi_translation.html
View File

@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/septic_patients.html
View File

@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/skewness.html
View File

@ -81,7 +81,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>

2
docs/reference/translate.html
View File

@ -80,7 +80,7 @@
</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">0.7.0.9009</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
</span>
</div>