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(v1.4.0.9049) unit tests
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Package: AMR
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Package: AMR
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Version: 1.4.0.9048
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Version: 1.4.0.9049
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Date: 2020-12-27
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Date: 2020-12-27
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Title: Antimicrobial Resistance Analysis
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 1.4.0.9048
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# AMR 1.4.0.9049
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## <small>Last updated: 27 December 2020</small>
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## <small>Last updated: 27 December 2020</small>
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### New
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### New
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@ -60,6 +60,7 @@ globalVariables(c(".rowid",
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"old_name",
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"old_name",
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"pattern",
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"pattern",
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"R",
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"R",
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"reference.rule",
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"reference.rule_group",
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"reference.rule_group",
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"reference.version",
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"reference.version",
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"rsi_translation",
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"rsi_translation",
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
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<a class="navbar-link" href="https://msberends.github.io/AMR//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">1.4.0.9048</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
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</span>
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</span>
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</div>
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</div>
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.4.0.9048</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
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</span>
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</span>
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</div>
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</div>
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@ -81,7 +81,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.4.0.9048</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
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</span>
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</span>
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</div>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.4.0.9048</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
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</span>
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</span>
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</div>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.4.0.9048</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
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</span>
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</span>
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</div>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.4.0.9048</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
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</span>
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</span>
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</div>
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</div>
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@ -236,9 +236,9 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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</div>
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<div id="amr-1409048" class="section level1">
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<div id="amr-1409049" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9048">
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<h1 class="page-header" data-toc-text="1.4.0.9049">
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<a href="#amr-1409048" class="anchor"></a>AMR 1.4.0.9048<small> Unreleased </small>
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<a href="#amr-1409049" class="anchor"></a>AMR 1.4.0.9049<small> Unreleased </small>
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</h1>
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</h1>
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<div id="last-updated-27-december-2020" class="section level2">
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<div id="last-updated-27-december-2020" class="section level2">
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<h2 class="hasAnchor">
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<h2 class="hasAnchor">
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@ -12,7 +12,7 @@ articles:
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datasets: datasets.html
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2020-12-27T13:22Z
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last_built: 2020-12-27T14:06Z
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urls:
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urls:
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reference: https://msberends.github.io/AMR//reference
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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article: https://msberends.github.io/AMR//articles
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.4.0.9048</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
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</span>
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</span>
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</div>
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</div>
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</button>
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</button>
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<span class="navbar-brand">
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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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<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">1.4.0.9048</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
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</span>
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</span>
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</div>
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</div>
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@ -122,19 +122,19 @@ test_that("EUCAST rules work", {
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expect_identical(
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expect_identical(
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eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
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eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
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cefotax = as.rsi(c("S", "S"))),
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cefotax = as.rsi(c("S", "S"))),
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ampc_derepressed_cephalosporins = "R",
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ampc_cephalosporin_resistance = "R",
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info = FALSE)$cefotax,
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info = FALSE)$cefotax,
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as.rsi(c("S", "R")))
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as.rsi(c("S", "R")))
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expect_identical(
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expect_identical(
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eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
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eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
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cefotax = as.rsi(c("S", "S"))),
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cefotax = as.rsi(c("S", "S"))),
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ampc_derepressed_cephalosporins = NA,
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ampc_cephalosporin_resistance = NA,
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info = FALSE)$cefotax,
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info = FALSE)$cefotax,
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as.rsi(c("S", NA)))
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as.rsi(c("S", NA)))
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expect_identical(
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expect_identical(
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eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
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eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
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cefotax = as.rsi(c("S", "S"))),
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cefotax = as.rsi(c("S", "S"))),
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ampc_derepressed_cephalosporins = NULL,
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ampc_cephalosporin_resistance = NULL,
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info = FALSE)$cefotax,
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info = FALSE)$cefotax,
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as.rsi(c("S", "S")))
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as.rsi(c("S", "S")))
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