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(v1.4.0.9049) unit tests

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dr. M.S. (Matthijs) Berends 2020-12-27 15:07:01 +01:00
parent ed198916bf
commit 175e33abba
13 changed files with 18 additions and 17 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.4.0.9048 Version: 1.4.0.9049
Date: 2020-12-27 Date: 2020-12-27
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.4.0.9048 # AMR 1.4.0.9049
## <small>Last updated: 27 December 2020</small> ## <small>Last updated: 27 December 2020</small>
### New ### New

1
R/globals.R
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@ -60,6 +60,7 @@ globalVariables(c(".rowid",
"old_name", "old_name",
"pattern", "pattern",
"R", "R",
"reference.rule",
"reference.rule_group", "reference.rule_group",
"reference.version", "reference.version",
"rsi_translation", "rsi_translation",

2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
</span> </span>
</div> </div>

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docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
</span> </span>
</div> </div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1409048" class="section level1"> <div id="amr-1409049" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9048"> <h1 class="page-header" data-toc-text="1.4.0.9049">
<a href="#amr-1409048" class="anchor"></a>AMR 1.4.0.9048<small> Unreleased </small> <a href="#amr-1409049" class="anchor"></a>AMR 1.4.0.9049<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-27-december-2020" class="section level2"> <div id="last-updated-27-december-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">

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docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2020-12-27T13:22Z last_built: 2020-12-27T14:06Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

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docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
</span> </span>
</div> </div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9048</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9049</span>
</span> </span>
</div> </div>

6
tests/testthat/test-eucast_rules.R
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@ -122,19 +122,19 @@ test_that("EUCAST rules work", {
expect_identical( expect_identical(
eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"), eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.rsi(c("S", "S"))), cefotax = as.rsi(c("S", "S"))),
ampc_derepressed_cephalosporins = "R", ampc_cephalosporin_resistance = "R",
info = FALSE)$cefotax, info = FALSE)$cefotax,
as.rsi(c("S", "R"))) as.rsi(c("S", "R")))
expect_identical( expect_identical(
eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"), eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.rsi(c("S", "S"))), cefotax = as.rsi(c("S", "S"))),
ampc_derepressed_cephalosporins = NA, ampc_cephalosporin_resistance = NA,
info = FALSE)$cefotax, info = FALSE)$cefotax,
as.rsi(c("S", NA))) as.rsi(c("S", NA)))
expect_identical( expect_identical(
eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"), eucast_rules(data.frame(mo = c("Escherichia coli", "Enterobacter cloacae"),
cefotax = as.rsi(c("S", "S"))), cefotax = as.rsi(c("S", "S"))),
ampc_derepressed_cephalosporins = NULL, ampc_cephalosporin_resistance = NULL,
info = FALSE)$cefotax, info = FALSE)$cefotax,
as.rsi(c("S", "S"))) as.rsi(c("S", "S")))