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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
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commit a1411ddafc
15 changed files with 27 additions and 25 deletions
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DESCRIPTION
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Package: AMR Package: AMR
Version: 1.3.0.9024 Version: 1.3.0.9025
Date: 2020-09-19 Date: 2020-09-19
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

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NEWS.md
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# AMR 1.3.0.9024 # AMR 1.3.0.9025
## <small>Last updated: 19 September 2020</small> ## <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! 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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</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">1.3.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span> </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">1.3.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span> </span>
</div> </div>

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docs/articles/index.html
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</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">1.3.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span> </span>
</div> </div>

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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">1.3.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span> </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">1.3.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span> </span>
</div> </div>

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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">1.3.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span> </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-1309024" class="section level1"> <div id="amr-1309025" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9024"> <h1 class="page-header" data-toc-text="1.3.0.9025">
<a href="#amr-1309024" class="anchor"></a>AMR 1.3.0.9024<small> Unreleased </small> <a href="#amr-1309025" class="anchor"></a>AMR 1.3.0.9025<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-19-september-2020" class="section level2"> <div id="last-updated-19-september-2020" class="section level2">
<h2 class="hasAnchor"> <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: 1.5.1.9000
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: [] articles: []
last_built: 2020-09-19T10:17Z last_built: 2020-09-19T13:07Z
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">1.3.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span> </span>
</div> </div>

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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">1.3.0.9024</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9025</span>
</span> </span>
</div> </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", c("if_mo_property", "like.is.one_of", "this_value",
"and_these_antibiotics", "have_these_values", "and_these_antibiotics", "have_these_values",
"then_change_these_antibiotics", "to_value", "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(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))
expect_error(eucast_rules(x = "text")) 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")) expect_warning(as.mic("INVALID VALUE"))
# print plots pdf(NULL) # prevent Rplots.pdf being created
expect_success(x <- barplot(as.mic(c(1, 2, 4, 8)))) expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
expect_success(x <- plot(as.mic(c(1, 2, 4, 8)))) expect_silent(plot(as.mic(c(1, 2, 4, 8))))
expect_success(x <- print(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))), expect_equal(summary(as.mic(c(2, 8))),
structure(c("Class" = "mic", 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]) expect_true(AMX_R[3] < AMX_R[20])
x <- resistance_predict(example_isolates, col_ab = "AMX", year_min = 2010, model = "binomial") x <- resistance_predict(example_isolates, col_ab = "AMX", year_min = 2010, model = "binomial")
expect_success(y <- plot(x)) pdf(NULL) # prevent Rplots.pdf being created
expect_success(y <- ggplot_rsi_predict(x)) expect_silent(plot(x))
expect_silent(ggplot_rsi_predict(x))
expect_error(ggplot_rsi_predict(example_isolates)) expect_error(ggplot_rsi_predict(example_isolates))
library(dplyr) 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(as.rsi("I") < as.rsi("R"))
expect_true(is.rsi(as.rsi("S"))) expect_true(is.rsi(as.rsi("S")))
# print plots, should not raise errors pdf(NULL) # prevent Rplots.pdf being created
expect_success(x <- barplot(as.rsi(c("S", "I", "R")))) expect_silent(barplot(as.rsi(c("S", "I", "R"))))
expect_success(x <- plot(as.rsi(c("S", "I", "R")))) expect_silent(plot(as.rsi(c("S", "I", "R"))))
expect_success(x <- print(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")) expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))