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(v1.3.0.9025) optimalisation

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dr. M.S. (Matthijs) Berends 2020-09-19 15:15:57 +02:00
parent 2f0186ace2
commit a1411ddafc
15 changed files with 27 additions and 25 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.3.0.9024
Version: 1.3.0.9025
Date: 2020-09-19
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.3.0.9024
# AMR 1.3.0.9025
## <small>Last updated: 19 September 2020</small>
Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!

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docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.3.0.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span>
</div>

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docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.3.0.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span>
</div>

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docs/articles/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.3.0.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span>
</div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.3.0.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span>
</div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<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">1.3.0.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span>
</div>

8
docs/news/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.3.0.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1309024" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9024">
<a href="#amr-1309024" class="anchor"></a>AMR 1.3.0.9024<small> Unreleased </small>
<div id="amr-1309025" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9025">
<a href="#amr-1309025" class="anchor"></a>AMR 1.3.0.9025<small> Unreleased </small>
</h1>
<div id="last-updated-19-september-2020" class="section level2">
<h2 class="hasAnchor">

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docs/pkgdown.yml
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@ -2,7 +2,7 @@ pandoc: 2.7.3
pkgdown: 1.5.1.9000
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: []
last_built: 2020-09-19T10:17Z
last_built: 2020-09-19T13:07Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

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docs/reference/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.3.0.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span>
</div>

2
docs/survey.html
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</button>
<span class="navbar-brand">
<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">1.3.0.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span>
</div>

3
tests/testthat/test-eucast_rules.R
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@ -30,7 +30,8 @@ test_that("EUCAST rules work", {
c("if_mo_property", "like.is.one_of", "this_value",
"and_these_antibiotics", "have_these_values",
"then_change_these_antibiotics", "to_value",
"reference.rule", "reference.rule_group"))
"reference.rule", "reference.rule_group",
"reference.version"))
expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))
expect_error(eucast_rules(x = "text"))

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tests/testthat/test-mic.R
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@ -38,10 +38,10 @@ test_that("mic works", {
expect_warning(as.mic("INVALID VALUE"))
# print plots
expect_success(x <- barplot(as.mic(c(1, 2, 4, 8))))
expect_success(x <- plot(as.mic(c(1, 2, 4, 8))))
expect_success(x <- print(as.mic(c(1, 2, 4, 8))))
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
expect_silent(plot(as.mic(c(1, 2, 4, 8))))
expect_output(print(as.mic(c(1, 2, 4, 8))))
expect_equal(summary(as.mic(c(2, 8))),
structure(c("Class" = "mic",

5
tests/testthat/test-resistance_predict.R
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@ -35,8 +35,9 @@ test_that("prediction of rsi works", {
expect_true(AMX_R[3] < AMX_R[20])
x <- resistance_predict(example_isolates, col_ab = "AMX", year_min = 2010, model = "binomial")
expect_success(y <- plot(x))
expect_success(y <- ggplot_rsi_predict(x))
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(plot(x))
expect_silent(ggplot_rsi_predict(x))
expect_error(ggplot_rsi_predict(example_isolates))
library(dplyr)

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tests/testthat/test-rsi.R
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@ -28,10 +28,10 @@ test_that("rsi works", {
expect_true(as.rsi("I") < as.rsi("R"))
expect_true(is.rsi(as.rsi("S")))
# print plots, should not raise errors
expect_success(x <- barplot(as.rsi(c("S", "I", "R"))))
expect_success(x <- plot(as.rsi(c("S", "I", "R"))))
expect_success(x <- print(as.rsi(c("S", "I", "R"))))
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.rsi(c("S", "I", "R"))))
expect_silent(plot(as.rsi(c("S", "I", "R"))))
expect_output(print(as.rsi(c("S", "I", "R"))))
expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))