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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="">1.8.2.9039</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9040</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="1.8.2.9039" id="amr-1829039">AMR 1.8.2.9039<a class="anchor" aria-label="anchor" href="#amr-1829039"></a></h2>
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<h2 class="pkg-version" data-toc-text="1.8.2.9040" id="amr-1829040">AMR 1.8.2.9040<a class="anchor" aria-label="anchor" href="#amr-1829040"></a></h2>
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<p>This version will eventually become v2.0! We’re happy to reach a new major milestone soon!</p>
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<div class="section level4">
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<h4 id="breaking-1-8-2-9039">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9039"></a></h4>
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<h4 id="breaking-1-8-2-9040">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9040"></a></h4>
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<ul><li>Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons:
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<ul><li>CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them</li>
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<li>Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package</li>
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<li>Removal of interpretation guidelines older than 10 years, the oldest now included guidelines of EUCAST and CLSI are from 2013</li>
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</ul></div>
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<div class="section level4">
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<h4 id="new-1-8-2-9039">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9039"></a></h4>
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<h4 id="new-1-8-2-9040">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9040"></a></h4>
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<ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
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<li>Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages. The automatic language determination will give a note at start-up on systems in supported languages.</li>
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<li>All new algorithm for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and thus all <code>mo_*()</code> functions) while still following our original set-up as described in our paper (DOI 10.18637/jss.v104.i03).
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<ul><li>A new argument <code>keep_synonyms</code> allows to <em>not</em> correct for updated taxonomy, in favour of the now deleted argument <code>allow_uncertain</code>
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</li>
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<li>It has increased tremendously in speed and returns generally more consequent results</li>
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<li>Sequential coercion is now extremely fast as results are stored to the package environment, although coercion of unknown values must be run once per session. Previous results can be reset/removed with the new <code><a href="../reference/as.mo.html">mo_reset_session()</a></code> function.</li>
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</ul></li>
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<li>Support for microorganism codes of the ASIan Antimicrobial Resistance Surveillance Network (ASIARS-Net)</li>
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<li>Function <code><a href="../reference/proportion.html">rsi_confidence_interval()</a></code> to add confidence intervals in AMR calculation. This is also included in <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/proportion.html">proportion_df()</a></code>
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</ul></li>
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<li>New functions!
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<ul><li>Function <code><a href="../reference/proportion.html">rsi_confidence_interval()</a></code> to add confidence intervals in AMR calculation. This is also included in <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/proportion.html">proportion_df()</a></code>
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</li>
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<li>Function <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code> to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.</li>
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<li>Function <code><a href="../reference/as.rsi.html">rsi_interpretation_history()</a></code> to view the history of previous runs of <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which <code><a href="../reference/as.rsi.html">as.rsi()</a></code> was run.</li>
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<li>Function <code><a href="../reference/mo_property.html">mo_current()</a></code> to get the currently valid taxonomic name of a microorganism</li>
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<li>Function <code><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> to add custom antimicrobial codes and names to the <code>AMR</code> package</li>
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<li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code><a href="https://Rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table::data.table</a></code>, <code><a href="https://rdrr.io/pkg/janitor/man/tabyl.html" class="external-link">janitor::tabyl</a></code>, <code><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a></code>, and <code><a href="https://tsibble.tidyverts.org/reference/tsibble.html" class="external-link">tsibble::tsibble</a></code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input.</li>
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<li>All data sets in this package are now exported as <code>tibble</code>, instead of base R <code>data.frame</code>s. Older R versions are still supported.</li>
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<li>Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages. The automatic language determination will give a note at start-up on systems in supported languages.</li>
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<li>Our data sets are now also continually exported to Apache Feather and Apache Parquet formats. You can find more info <a href="https://msberends.github.io/AMR/articles/datasets.html">in this article on our website</a>.</li>
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<li>Support for using antibiotic selectors in scoped <code>dplyr</code> verbs (with or without <code><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars()</a></code>), such as in: <code>... %>% summarise_at(aminoglycosides(), resistance)</code>, see <code><a href="../reference/proportion.html">resistance()</a></code>
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</li>
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<li>Support for antimicrobial interpretation of anaerobic bacteria, by adding a ‘placeholder’ code <code>B_ANAER</code> to the <code>microorganisms</code> data set and add the breakpoints of anaerobics to the <code>rsi_interpretation</code> data set, which is used by <code><a href="../reference/as.rsi.html">as.rsi()</a></code> when interpreting MIC and disk diffusion values</li>
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</ul></li>
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<li>New and updated entries for the <code>antibiotics</code> data set
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<ul><li>The following 20 antibiotics have been added (also includes the <a href="https://www.whocc.no/atc_ddd_index/?code=J01RA&showdescription=no" class="external-link">new J01RA ATC group</a>): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT)</li>
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<li>Added some missing ATC codes</li>
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<li>Updated DDDs and PubChem Compound IDs</li>
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<li>Updated some antibiotic name spelling, now used by WHOCC (such as cephalexin -> cefalexin, and phenethicillin -> pheneticillin)</li>
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<li>Antibiotic code “CEI” for ceftolozane/tazobactam has been replaced with “CZT” to comply with EARS-Net and WHONET 2022. The old code will still work in all cases when using <code><a href="../reference/as.ab.html">as.ab()</a></code> or any of the <code>ab_*()</code> functions.</li>
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<li>Support for antimicrobial interpretation of anaerobic bacteria, by adding a ‘placeholder’ code <code>B_ANAER</code> to the <code>microorganisms</code> data set and add the breakpoints of anaerobics to the <code>rsi_interpretation</code> data set, which is used by <code><a href="../reference/as.rsi.html">as.rsi()</a></code> when interpreting MIC and disk diffusion values</li>
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</ul></li>
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<li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code><a href="https://Rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table::data.table</a></code>, <code><a href="https://rdrr.io/pkg/janitor/man/tabyl.html" class="external-link">janitor::tabyl</a></code>, <code><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a></code>, and <code><a href="https://tsibble.tidyverts.org/reference/tsibble.html" class="external-link">tsibble::tsibble</a></code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input.</li>
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<li>All data sets in this package are now exported as <code>tibble</code>, instead of base R <code>data.frame</code>s. Older R versions are still supported.</li>
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<li>Our data sets are now also continually exported to Apache Feather and Apache Parquet formats. You can find more info <a href="https://msberends.github.io/AMR/articles/datasets.html">in this article on our website</a>.</li>
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<li>Support for using antibiotic selectors in scoped <code>dplyr</code> verbs (with or without <code><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars()</a></code>), such as in: <code>... %>% summarise_at(aminoglycosides(), resistance)</code>, see <code><a href="../reference/proportion.html">resistance()</a></code>
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</li>
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</ul></div>
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<div class="section level4">
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<h4 id="changed-1-8-2-9039">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9039"></a></h4>
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<h4 id="changed-1-8-2-9040">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9040"></a></h4>
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<ul><li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
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<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
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<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on drug-drug combinations with multiple breakpoints for different body sites</li>
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<li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on bug-drug combinations with multiple breakpoints for different body sites</li>
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<li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
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<li>
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<code><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels()</a></code> on MIC will now return a common <code>factor</code> at default and will lose the <code>mic</code> class. Use <code>droplevels(..., as.mic = TRUE)</code> to keep the <code>mic</code> class.</li>
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<li>Added <em>Toxoplasma gondii</em> (<code>P_TXPL_GOND</code>) to the <code>microorganisms</code> data set, together with its genus, family, and order</li>
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<li>Changed value in column <code>prevalence</code> of the <code>microorganisms</code> data set from 3 to 2 for these genera: <em>Acholeplasma</em>, <em>Alistipes</em>, <em>Alloprevotella</em>, <em>Bergeyella</em>, <em>Borrelia</em>, <em>Brachyspira</em>, <em>Butyricimonas</em>, <em>Cetobacterium</em>, <em>Chlamydia</em>, <em>Chlamydophila</em>, <em>Deinococcus</em>, <em>Dysgonomonas</em>, <em>Elizabethkingia</em>, <em>Empedobacter</em>, <em>Haloarcula</em>, <em>Halobacterium</em>, <em>Halococcus</em>, <em>Myroides</em>, <em>Odoribacter</em>, <em>Ornithobacterium</em>, <em>Parabacteroides</em>, <em>Pedobacter</em>, <em>Phocaeicola</em>, <em>Porphyromonas</em>, <em>Riemerella</em>, <em>Sphingobacterium</em>, <em>Streptobacillus</em>, <em>Tenacibaculum</em>, <em>Terrimonas</em>, <em>Victivallis</em>, <em>Wautersiella</em>, <em>Weeksella</em>
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</li>
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<li>Fix for using the form <code>df[carbapenems() == "R", ]</code> when using the latest <code>vctrs</code> package</li>
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<li>Extended support for the <code>vctrs</code> package, used internally by the tidyverse. This allows to change values of class <code>mic</code>, <code>disk</code>, <code>rsi</code>, <code>mo</code> and <code>ab</code> in tibbles, and to use antibiotic selectors for selecting/filtering, e.g. <code>df[carbapenems() == "R", ]</code>
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</li>
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<li>Fix for using <code>info = FALSE</code> in <code><a href="../reference/mdro.html">mdro()</a></code>
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</li>
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<li>For all interpretation guidelines using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on amoxicillin, the rules for ampicillin will be used if amoxicillin rules are not available</li>
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<li>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> in case of higher taxonomic ranks (order, class, phylum)</li>
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</ul></div>
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<div class="section level4">
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<h4 id="other-1-8-2-9039">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9039"></a></h4>
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<h4 id="other-1-8-2-9040">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9040"></a></h4>
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<ul><li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
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<li>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input</li>
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<li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>
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