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(v0.7.0.9014) unit tests
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Package: AMR
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Version: 0.7.0.9013
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Version: 0.7.0.9014
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Date: 2019-06-22
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 0.7.0.9013
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# AMR 0.7.0.9014
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#### New
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* Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9014</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9014</span>
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</span>
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</div>
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@ -241,10 +241,8 @@
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<li><a href="MDR.html">How to determine multi-drug resistance (MDR)</a></li>
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<li><a href="SPSS.html">How to import data from SPSS / SAS / Stata</a></li>
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<li><a href="WHONET.html">How to work with WHONET data</a></li>
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<li><a href="ab_property.html">How to get properties of an antibiotic</a></li>
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<li><a href="benchmarks.html">Benchmarks</a></li>
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<li><a href="freq.html">How to create frequency tables</a></li>
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<li><a href="mo_property.html">How to get properties of a microorganism</a></li>
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<li><a href="resistance_predict.html">How to predict antimicrobial resistance</a></li>
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</ul>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9014</span>
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</span>
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</div>
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@ -42,7 +42,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9014</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9012</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9014</span>
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</span>
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</div>
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@ -232,9 +232,9 @@
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</div>
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<div id="amr-0709012" class="section level1">
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<div id="amr-0709014" class="section level1">
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<h1 class="page-header">
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<a href="#amr-0709012" class="anchor"></a>AMR 0.7.0.9012<small> Unreleased </small>
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<a href="#amr-0709014" class="anchor"></a>AMR 0.7.0.9014<small> Unreleased </small>
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</h1>
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<div id="new" class="section level4">
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<h4 class="hasAnchor">
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@ -252,7 +252,7 @@
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<a class="sourceLine" id="cb1-8" title="8"><span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></a></code></pre></div>
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</li>
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<li>
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<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date. Supported are:</p>
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<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date (that we could find). Supported are:</p>
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<ul>
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<li>AIEC (Adherent-Invasive <em>E. coli</em>)</li>
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<li>ATEC (Atypical Entero-pathogenic <em>E. coli</em>)</li>
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@ -297,10 +297,12 @@
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<li>Removed <code>latest_annual_release</code> from the <code><a href="../reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> function</li>
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<li>Removed antibiotic code <code>PVM1</code> from the <code>antibiotics</code> data set as this was a duplicate of <code>PME</code>
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</li>
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<li>Fixed bug where not all old taxonomic named would not be printed when using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code>
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<li>Fixed bug where not all old taxonomic names would be printed, when using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code>
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</li>
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<li>Manually added <em>Trichomonas vaginalis</em> from the kingdom of Protozoa, which is missing from the Catalogue of Life</li>
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<li>Small improvements to <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> and <code><a href="https://www.rdocumentation.org/packages/graphics/topics/barplot">barplot()</a></code> for MIC and RSI classes</li>
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<li>Allow Catalogue of Life IDs to be coerced by <code><a href="../reference/as.mo.html">as.mo()</a></code>
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</li>
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</ul>
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</div>
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<div id="other" class="section level4">
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@ -1139,7 +1141,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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<div id="tocnav">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0709012">0.7.0.9012</a></li>
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<li><a href="#amr-0709014">0.7.0.9014</a></li>
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<li><a href="#amr-070">0.7.0</a></li>
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<li><a href="#amr-061">0.6.1</a></li>
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<li><a href="#amr-060">0.6.0</a></li>
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@ -7,10 +7,8 @@ articles:
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MDR: MDR.html
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SPSS: SPSS.html
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WHONET: WHONET.html
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ab_property: ab_property.html
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benchmarks: benchmarks.html
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freq: freq.html
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mo_property: mo_property.html
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resistance_predict: resistance_predict.html
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urls:
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reference: https://msberends.gitlab.io/AMR/reference
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9014</span>
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</span>
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</div>
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@ -153,18 +153,12 @@
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<url>
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<loc>https://msberends.gitlab.io/AMR/articles/WHONET.html</loc>
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</url>
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<url>
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<loc>https://msberends.gitlab.io/AMR/articles/ab_property.html</loc>
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</url>
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<url>
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<loc>https://msberends.gitlab.io/AMR/articles/benchmarks.html</loc>
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</url>
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<url>
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<loc>https://msberends.gitlab.io/AMR/articles/freq.html</loc>
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</url>
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<url>
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<loc>https://msberends.gitlab.io/AMR/articles/mo_property.html</loc>
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</url>
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<url>
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<loc>https://msberends.gitlab.io/AMR/articles/resistance_predict.html</loc>
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</url>
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@ -66,8 +66,7 @@ echo "• List of changed files •"
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echo "•••••••••••••••••••••••••"
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git status --short
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echo
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read -p "Pushing version ${new_version}. Continue (Y/n)? " choice
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read -p "Uploading version ${new_version}. Continue (Y/n)? " choice
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case "$choice" in
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n|N ) exit 1;;
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* ) ;;
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@ -82,6 +81,7 @@ git commit -a -m "(v$new_version) $1" --quiet
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git push --quiet
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echo "Comparison:"
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echo "https://gitlab.com/msberends/AMR/compare/master...premaster?view=inline"
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echo "Check for all CRAN tests:"
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echo "rhub::check_for_cran(devtools::build(args = c('--no-build-vignettes')))"
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echo
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echo "Done."
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@ -260,9 +260,9 @@ test_that("as.mo works", {
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expect_null(mo_failures())
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expect_true(septic_patients %>% pull(mo) %>% is.mo())
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expect_equal(get_mo_code("test", "mo"), "test")
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expect_equal(length(get_mo_code("Escherichia", "genus")),
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nrow(AMR::microorganisms[base::which(AMR::microorganisms[, "genus"] %in% "Escherichia"),]))
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# expect_equal(get_mo_code("test", "mo"), "test")
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# expect_equal(length(get_mo_code("Escherichia", "genus")),
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# nrow(AMR::microorganisms[base::which(AMR::microorganisms[, "genus"] %in% "Escherichia"),]))
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expect_error(translate_allow_uncertain(5))
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