<p><em>(<helptitle="Too Long, Didn't Read">TLDR</help> - to find out how to conduct AMR analysis, please <ahref="./articles/AMR.html">continue reading here to get started</a>.</em></p>
<p><em>(<helptitle="Too Long, Didn't Read">TLDR</help> - to find out how to conduct AMR analysis, please <ahref="./articles/AMR.html">continue reading here to get started</a>.</em></p>
<hr>
<hr>
@ -238,15 +238,15 @@
<h4class="hasAnchor">
<h4class="hasAnchor">
<ahref="#latest-released-version"class="anchor"></a>Latest released version</h4>
<ahref="#latest-released-version"class="anchor"></a>Latest released version</h4>
<p>This package is available <ahref="https://cran.r-project.org/package=AMR">on the official R network (CRAN)</a>, which has a peer-reviewed submission process. Install this package in R with:</p>
<p>This package is available <ahref="https://cran.r-project.org/package=AMR">on the official R network (CRAN)</a>, which has a peer-reviewed submission process. Install this package in R with:</p>
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em>><em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em>><em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
<p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <ahref="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure and a WHONET export file. Furthermore, this package also contains a <ahref="./reference/antibiotics.html">data set <code>antibiotics</code></a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p>
<p>We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an <ahref="./reference/WHONET.html">example data set <code>WHONET</code></a> with the exact same structure and a WHONET export file. Furthermore, this package also contains a <ahref="./reference/antibiotics.html">data set <code>antibiotics</code></a> with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.</p>
<p>Read our tutorial about <ahref="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
<p>Read our tutorial about <ahref="./articles/WHONET.html">how to work with WHONET data here</a>.</p>
These functions use <code><ahref="../reference/as.atc.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><ahref="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><ahref="../reference/as.mo.html">as.mo()</a></code> and e.g.<code>mo_genus</code>.</li>
These functions use <code><ahref="../reference/as.atc.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><ahref="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><ahref="../reference/as.mo.html">as.mo()</a></code> and e.g.<code>mo_genus</code>.</li>
<li>New website: <ahref="https://msberends.gitlab.io/AMR"class="uri">https://msberends.gitlab.io/AMR</a> (built with the great <ahref="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)
<li>New website: <ahref="https://msberends.gitlab.io/AMR"class="uri">https://msberends.gitlab.io/AMR</a> (built with the great <ahref="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)
<ul>
<ul>
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
@ -269,20 +269,20 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<li>New function <code><ahref="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
<li>New function <code><ahref="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
<li>
<li>
<p>New function <code><ahref="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><ahref="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><ahref="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<p>New function <code><ahref="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><ahref="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><ahref="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<p>Functions <code><ahref="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><ahref="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
<p>Functions <code><ahref="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><ahref="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
<li>New function <code><ahref="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code>
<li>New function <code><ahref="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code>
</li>
</li>
@ -347,19 +347,19 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<ul>
<ul>
<li>
<li>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
<divclass="sourceCode"id="cb5"><preclass="sourceCode r"><codeclass="sourceCode r"><aclass="sourceLine"id="cb5-1"data-line-number="1"><spanclass="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
<divclass="sourceCode"id="cb5"><preclass="sourceCode r"><codeclass="sourceCode r"><aclass="sourceLine"id="cb5-1"title="1"><spanclass="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
<aclass="sourceLine"id="cb5-2"data-line-number="2"><spanclass="co"># OLD WAY</span></a>
<aclass="sourceLine"id="cb5-2"title="2"><spanclass="co"># OLD WAY</span></a>
<li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs.IR (susceptible vs.non-susceptible)</li>
<li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs.IR (susceptible vs.non-susceptible)</li>
<li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
<li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
@ -449,15 +449,15 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<aclass="sourceLine"id="cb8-3"data-line-number="3"><spanclass="st"></span><spanclass="kw">select</span>(<spanclass="op">-</span>count, <spanclass="op">-</span>cum_count) <spanclass="co"># only get item, percent, cum_percent</span></a></code></pre></div>
<aclass="sourceLine"id="cb8-3"title="3"><spanclass="st"></span><spanclass="kw">select</span>(<spanclass="op">-</span>count, <spanclass="op">-</span>cum_count) <spanclass="co"># only get item, percent, cum_percent</span></a></code></pre></div>
</li>
</li>
<li>Check for <code><ahref="https://www.rdocumentation.org/packages/hms/topics/hms">hms::is.hms</a></code>
<li>Check for <code><ahref="https://www.rdocumentation.org/packages/hms/topics/hms">hms::is.hms</a></code>
</li>
</li>
@ -516,9 +516,9 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates
<li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates
<ul>
<ul>
@ -559,18 +559,18 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
</li>
</li>
<li>
<li>
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using Artificial Intelligence (AI):</p>
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using Artificial Intelligence (AI):</p>
<aclass="sourceLine"id="cb11-5"data-line-number="5"><spanclass="kw"><ahref="../reference/as.mo.html">as.mo</a></span>(<spanclass="st">"S group A"</span>)</a>
<aclass="sourceLine"id="cb11-5"title="5"><spanclass="kw"><ahref="../reference/as.mo.html">as.mo</a></span>(<spanclass="st">"S group A"</span>)</a>
<li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li>
<li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li>
<li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:
<li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:
@ -598,12 +598,12 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
<li>
<li>
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
<li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li>
<li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li>
@ -614,13 +614,13 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
</li>
</li>
<li>
<li>
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
<li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li>
<li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li>
<li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
<li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
@ -634,12 +634,12 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
</li>
</li>
<li>
<li>
<p>Support for types (classes) list and matrix for <code>freq</code></p>
<p>Support for types (classes) list and matrix for <code>freq</code></p>
@ -758,7 +758,7 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
</li>
</li>
</ul>
</ul>
</li>
</li>
<li>Now possible to coerce MIC values with a space between operator and value, i.e.<code><ahref="../reference/as.mic.html">as.mic("<= 0.002")</a></code> now works</li>
<li>Now possible to coerce MIC values with a space between operator and value, i.e.<code><ahref="../reference/as.mic.html">as.mic("<= 0.002")</a></code> now works</li>
<li>Classes <code>rsi</code> and <code>mic</code> do not add the attribute <code>package.version</code> anymore</li>
<li>Classes <code>rsi</code> and <code>mic</code> do not add the attribute <code>package.version</code> anymore</li>
<li>Added <code>"groups"</code> option for <code><ahref="../reference/atc_property.html">atc_property(..., property)</a></code>. It will return a vector of the ATC hierarchy as defined by the <ahref="https://www.whocc.no/atc/structure_and_principles/">WHO</a>. The new function <code>atc_groups</code> is a convenient wrapper around this.</li>
<li>Added <code>"groups"</code> option for <code><ahref="../reference/atc_property.html">atc_property(..., property)</a></code>. It will return a vector of the ATC hierarchy as defined by the <ahref="https://www.whocc.no/atc/structure_and_principles/">WHO</a>. The new function <code>atc_groups</code> is a convenient wrapper around this.</li>
<li>Build-in host check for <code>atc_property</code> as it requires the host set by <code>url</code> to be responsive</li>
<li>Build-in host check for <code>atc_property</code> as it requires the host set by <code>url</code> to be responsive</li>
@ -788,9 +788,9 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
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