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<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <ahref="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
<h5id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9100">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<aclass="anchor"aria-label="anchor"href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9100"></a></h5>
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <ahref="https://www.upei.ca/avc"class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
<ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li>
<ul><li>Function <code><ahref="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
<li>The CLSI VET09 guideline has been implemented to address cases where veterinary breakpoints are missing (only applies when <code>guideline</code> is set to CLSI)</li>
<li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <ahref="https://msberends.github.io/AMR/articles/datasets.html">download page</a>.</li>
<li>The <code>antibiotics</code> data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.</li>
<li>
<code><ahref="../reference/ab_property.html">ab_atc()</a></code> now supports ATC codes of veterinary antibiotics (that all start with “Q”)</li>
<strong>Major update to fungal taxonomy and tools for mycologists</strong>
<ul><li>MycoBank has now been integrated as the primary taxonomic source for fungi. The <code>microorganisms</code> data set has been enriched with new columns (<code>mycobank</code>, <code>mycobank_parent</code>, and <code>mycobank_renamed_to</code>) that provide detailed information for fungal species.</li>
<li>A remarkable addition of over 20,000 new fungal records</li>
<li>New function <code><ahref="../reference/mo_property.html">mo_mycobank()</a></code> to retrieve the MycoBank record number, analogous to existing functions such as <code><ahref="../reference/mo_property.html">mo_lpsn()</a></code> and <code><ahref="../reference/mo_property.html">mo_gbif()</a></code>.</li>
<li>The <code><ahref="../reference/as.mo.html">as.mo()</a></code> function and all <code>mo_*()</code> functions now include an <code>only_fungi</code> argument, allowing users to restrict results solely to fungal species. This ensures fungi are prioritised over bacteria during microorganism identification. This can also be set globally with the new <code>AMR_only_fungi</code> option.</li>
<li>Also updated other kingdoms, welcoming a total of 2,149 new records from 2023 and 927 from 2024.</li>
</ul></li>
<li>
<strong>Updated clinical breakpoints</strong>
<ul><li>EUCAST 2024 and CLSI 2024 are now supported, by adding all of their over 4,000 new clinical breakpoints to the <code>clinical_breakpoints</code> data set for usage in <code><ahref="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2024 is now the new default guideline for all MIC and disk diffusion interpretations.</li>
<code><ahref="../reference/as.sir.html">as.sir()</a></code> now brings additional factor levels: “NI” for non-interpretable and “SDD” for susceptible dose-dependent. Currently, the <code>clinical_breakpoints</code> data set contains 24 breakpoints that can return the value “SDD” instead of “I”.</li>
<ul><li>New function group <code>scale_*_mic()</code>, namely: <code><ahref="../reference/plot.html">scale_x_mic()</a></code>, <code><ahref="../reference/plot.html">scale_y_mic()</a></code>, <code><ahref="../reference/plot.html">scale_colour_mic()</a></code> and <code><ahref="../reference/plot.html">scale_fill_mic()</a></code>. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.</li>
<li>New function <code><ahref="../reference/as.mic.html">rescale_mic()</a></code>, which allows users to rescale MIC values to a manually set range. This is the powerhouse behind the <code>scale_*_mic()</code> functions, but it can be used independently to, for instance, compare equality in MIC distributions by rescaling them to the same range first.</li>
<ul><li>While using R for the heavy lifting, <ahref="https://pypi.org/project/AMR/"class="external-link">our ‘AMR’ Python Package</a> was developed to run the AMR R package natively in Python. The Python package will always have the same version number as the R package, as it is built automatically with every code change.</li>
<ul><li>New function <code><ahref="../reference/mo_property.html">mo_group_members()</a></code> to retrieve the member microorganisms of a microorganism group. For example, <code>mo_group_members("Strep group C")</code> returns a vector of all microorganisms that belong to that group.</li>
<ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
<li>To get quantitative values, <code><ahref="https://rdrr.io/r/base/double.html"class="external-link">as.double()</a></code> on a <code>sir</code> object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become <code>NA</code>). Other functions using <code>sir</code> classes (e.g., <code><ahref="https://rdrr.io/r/base/summary.html"class="external-link">summary()</a></code>) are updated to reflect the change to contain NI and SDD.</li>
<code><ahref="../reference/antibiogram.html">antibiogram()</a></code> function
<ul><li>New argument <code>formatting_type</code> to set any of the 12 options for the formatting of all ‘cells’. This defaults to <code>10</code>, changing the output of antibiograms to cells with <code>5% (15/300)</code> instead of the previous standard of just <code>5</code>.</li>
<li>For this reason, <code>add_total_n</code> is now <code>FALSE</code> at default since the denominators are added to the cells</li>
<li>The <code>ab_transform</code> argument now defaults to <code>"name"</code>, displaying antibiotic column names instead of codes</li>
<ul><li>Added “clindamycin inducible screening” as <code>CLI1</code>. Since clindamycin is a lincosamide, the antibiotic selector <code><ahref="../reference/antibiotic_class_selectors.html">lincosamides()</a></code> now contains the argument <code>only_treatable = TRUE</code> (similar to other antibiotic selectors that contain non-treatable drugs)</li>
<li>Added Amorolfine (<code>AMO</code>, D01AE16), which is now also part of the <code><ahref="../reference/antibiotic_class_selectors.html">antifungals()</a></code> selector</li>
<ul><li>Added selectors <code><ahref="../reference/antibiotic_class_selectors.html">nitrofurans()</a></code> and <code><ahref="../reference/antibiotic_class_selectors.html">rifamycins()</a></code>
</li>
<li>When using antibiotic selectors such as <code><ahref="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> that exclude non-treatable drugs like gentamicin-high, the function now always returns a warning that these can be included using <code>only_treatable = FALSE</code>
<li>Added new argument <code>keep_operators</code> to <code><ahref="../reference/as.mic.html">as.mic()</a></code>. This can be <code>"all"</code> (default), <code>"none"</code>, or <code>"edges"</code>. This argument is also available in the new <code><ahref="../reference/as.mic.html">rescale_mic()</a></code> and <code>scale_*_mic()</code> functions.</li>
<li>Comparisons of MIC values are now more strict. For example, <code>>32</code> is higher than (and never equal to) <code>32</code>. Thus, <code>as.mic(">32") == as.mic(32)</code> now returns <code>FALSE</code>, and <code>as.mic(">32") > as.mic(32)</code> now returns <code>TRUE</code>.</li>
<li>Sorting of MIC values (using <code><ahref="https://rdrr.io/r/base/sort.html"class="external-link">sort()</a></code>) was fixed in the same manner; <code><0.001</code> now gets sorted before <code>0.001</code>, and <code>>0.001</code> gets sorted after <code>0.001</code>.</li>
<li>Disks of 0 to 5 mm are now allowed, the newly allowed range for disk diffusion (<code><ahref="../reference/as.disk.html">as.disk()</a></code>) is now between 0 and 50 mm</li>
<code><ahref="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> now supports multiple antibiotics and antibiotic groups to be affected by a single rule</li>
<code><ahref="../reference/mo_property.html">mo_info()</a></code> now contains an extra element <code>rank</code> and <code>group_members</code> (with the contents of the new <code><ahref="../reference/mo_property.html">mo_group_members()</a></code> function)</li>
<li>Improved overall algorithm of <code><ahref="../reference/as.mo.html">as.mo()</a></code> for better performance and accuracy. Specifically:
<ul><li>More weight is given to genus and species combinations in cases where the subspecies is miswritten, so that the result will be the correct genus and species</li>
<li>Genera from the World Health Organization’s (WHO) Priority Pathogen List now have the highest prevalence</li>
<li>Updated the prevalence calculation to include genera from the World Health Organization’s (WHO) Priority Pathogen List</li>
<li>Improved algorithm of <code><ahref="../reference/first_isolate.html">first_isolate()</a></code> when using the phenotype-based method, to prioritise records with the highest availability of SIR values</li>
<ul><li>Greatly improved <code>vctrs</code> integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as <code>dplyr</code>’s <code><ahref="https://dplyr.tidyverse.org/reference/bind_rows.html"class="external-link">bind_rows()</a></code>, <code><ahref="https://dplyr.tidyverse.org/reference/rowwise.html"class="external-link">rowwise()</a></code> and <code><ahref="https://dplyr.tidyverse.org/reference/c_across.html"class="external-link">c_across()</a></code> are now supported for e.g.columns of class <code>mic</code>. Despite this, this <code>AMR</code> package is still zero-dependent on any other package, including <code>dplyr</code> and <code>vctrs</code>.</li>
<li>Greatly updated and expanded documentation</li>
<li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
<p><code>AMR</code> (for R). Free and open-source, licenced under the <atarget="_blank"href="https://github.com/msberends/AMR/blob/main/LICENSE"class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <atarget="_blank"href="https://www.rug.nl"class="external-link">University of Groningen</a> and <atarget="_blank"href="https://www.umcg.nl"class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
