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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9081</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9083</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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</div>
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<div class="section level2">
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<h2 class="pkg-version" data-toc-text="2.1.1.9081" id="amr-2119081">AMR 2.1.1.9081<a class="anchor" aria-label="anchor" href="#amr-2119081"></a></h2>
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<h2 class="pkg-version" data-toc-text="2.1.1.9083" id="amr-2119083">AMR 2.1.1.9083<a class="anchor" aria-label="anchor" href="#amr-2119083"></a></h2>
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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 <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
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<div class="section level5">
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<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9081">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9081"></a></h5>
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<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9083">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9083"></a></h5>
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<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 <a href="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>
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</div>
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<div class="section level3">
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<h3 id="breaking-2-1-1-9081">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9081"></a></h3>
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<h3 id="breaking-2-1-1-9083">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9083"></a></h3>
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<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>
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</ul></div>
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<div class="section level3">
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<h3 id="new-2-1-1-9081">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9081"></a></h3>
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<h3 id="new-2-1-1-9083">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9083"></a></h3>
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<ul><li>
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<strong>One Health implementation</strong>
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<ul><li>Function <code><a href="../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>
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<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>
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<li>A remarkable addition of over 20,000 new fungal records</li>
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<li>New function <code><a href="../reference/mo_property.html">mo_mycobank()</a></code> to retrieve the MycoBank record number, analogous to existing functions such as <code><a href="../reference/mo_property.html">mo_lpsn()</a></code> and <code><a href="../reference/mo_property.html">mo_gbif()</a></code>.</li>
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<li>The <code><a href="../reference/as.mo.html">as.mo()</a></code> function and all <code>mo_*()</code> functions now includes 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>
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<li>The <code><a href="../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>
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<li>Also updated other kingdoms, welcoming a total of 2,149 new records from 2023 and 927 from 2024.</li>
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</ul></li>
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<li>
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</ul></li>
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</ul></div>
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<div class="section level3">
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<h3 id="changed-2-1-1-9081">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9081"></a></h3>
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<h3 id="changed-2-1-1-9083">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9083"></a></h3>
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<ul><li>SIR interpretation
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<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>
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<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
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<li>Added new argument <code>keep_operators</code> to <code><a href="../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><a href="../reference/as.mic.html">rescale_mic()</a></code> and <code>scale_*_mic()</code> functions.</li>
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<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>
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<li>Sorting of MIC values (using <code><a href="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>
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<li>Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range</li>
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</ul></li>
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<li>Updated <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to support HTML output</li>
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<li>
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<code><a href="../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>
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<li>
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<code><a href="../reference/mo_property.html">mo_info()</a></code> now contains an extra element <code>group_members</code>, with the contents of the new <code><a href="../reference/mo_property.html">mo_group_members()</a></code> function</li>
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<code><a href="../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><a href="../reference/mo_property.html">mo_group_members()</a></code> function)</li>
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<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><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/rowwise.html" class="external-link">rowwise()</a></code> and <code><a href="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>
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<li>Updated all ATC codes from WHOCC</li>
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<li>Updated all antibiotic DDDs from WHOCC</li>
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</li>
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<li>Fix for mapping ‘high level’ antibiotics in <code><a href="../reference/as.ab.html">as.ab()</a></code> (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)</li>
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<li>Improved overall algorithm of <code><a href="../reference/as.ab.html">as.ab()</a></code> for better performance and accuracy</li>
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<li>Improved overall algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code> for better performance and accuracy. Specifically, 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>
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<li>Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range</li>
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<li>Improved overall algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code> for better performance and accuracy. Specifically:
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<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>
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<li>Genera from the World Health Organization’s (WHO) Priority Pathogen List now have the highest prevalence</li>
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</ul></li>
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<li>Fixed a bug for when <code><a href="../reference/antibiogram.html">antibiogram()</a></code> returns an empty data set</li>
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<li>Updated the prevalence calculation to include genera from the World Health Organization’s (WHO) Priority Pathogen List</li>
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<li>Improved algorithm of <code><a href="../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>
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</ul></div>
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<div class="section level3">
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<h3 id="other-2-1-1-9081">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9081"></a></h3>
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<h3 id="other-2-1-1-9083">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9083"></a></h3>
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<ul><li>Greatly updated and expanded documentation</li>
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<li>Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
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<li>Added Larisse Bolton, Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
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<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>
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</ul></div>
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<div class="section level3">
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<h3 id="older-versions-2-1-1-9081">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9081"></a></h3>
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<h3 id="older-versions-2-1-1-9083">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9083"></a></h3>
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<p>This changelog only contains changes from AMR v3.0 (October 2024) and later.</p>
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<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
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<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>
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