1
0
mirror of https://github.com/msberends/AMR.git synced 2024-12-25 17:26:12 +01:00

(v1.7.1.9039) reinitiate all units tests

This commit is contained in:
dr. M.S. (Matthijs) Berends 2021-09-03 13:08:36 +02:00
parent 81a1a432bd
commit 5f433d6e5c
8 changed files with 14 additions and 27 deletions

View File

@ -128,18 +128,6 @@ jobs:
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
shell: Rscript {0} shell: Rscript {0}
# - name: Only keep vignettes on release version
- name: Remove vignettes
# if: matrix.config.r != 'release'
if: always()
# writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite
run: |
rm -rf AMR/vignettes
Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION2')"
rm AMR/DESCRIPTION
mv AMR/DESCRIPTION2 AMR/DESCRIPTION
shell: bash
- name: Run R CMD check - name: Run R CMD check
if: always() if: always()
env: env:

View File

@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.7.1.9038 Version: 1.7.1.9039
Date: 2021-09-01 Date: 2021-09-03
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

View File

@ -1,5 +1,5 @@
# `AMR` 1.7.1.9038 # `AMR` 1.7.1.9039
## <small>Last updated: 1 September 2021</small> ## <small>Last updated: 3 September 2021</small>
### Breaking changes ### Breaking changes
* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version * Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version

Binary file not shown.

View File

@ -44,7 +44,7 @@
</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">1.7.1.9038</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9039</span>
</span> </span>
</div> </div>
@ -190,7 +190,7 @@
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1> <h1 data-toc-skip>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">01 September 2021</h4> <h4 data-toc-skip class="date">03 September 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div> <div class="hidden name"><code>datasets.Rmd</code></div>
@ -495,7 +495,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#antibiotic-agents" class="anchor" aria-hidden="true"></a>Antibiotic agents</h2> <a href="#antibiotic-agents" class="anchor" aria-hidden="true"></a>Antibiotic agents</h2>
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p> <p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 19 August 2021 21:21:57 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p> <p>It was last updated on 2 September 2021 11:50:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
<p><strong>Direct download links:</strong></p> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (32 kB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds" class="external-link">R file</a> (32 kB)<br>

View File

@ -92,7 +92,7 @@
</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">1.7.1.9038</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9039</span>
</span> </span>
</div> </div>
@ -240,12 +240,12 @@
<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-1719038" class="section level1"> <div id="amr-1719039" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9038"> <h1 class="page-header" data-toc-text="1.7.1.9039">
<a href="#amr-1719038" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9038</h1> <a href="#amr-1719039" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9039</h1>
<div id="last-updated-1-september-2021" class="section level2"> <div id="last-updated-3-september-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-1-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 1 September 2021</small> <a href="#last-updated-3-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 3 September 2021</small>
</h2> </h2>
<div id="breaking-changes" class="section level3"> <div id="breaking-changes" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">

View File

@ -56,6 +56,7 @@ expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance
expect_equal(ncol(example_isolates[, c(administrable_per_os() & penicillins())]), 5, tolerance = 0.5) expect_equal(ncol(example_isolates[, c(administrable_per_os() & penicillins())]), 5, tolerance = 0.5)
expect_equal(ncol(example_isolates[, c(administrable_iv() & penicillins())]), 7, tolerance = 0.5) expect_equal(ncol(example_isolates[, c(administrable_iv() & penicillins())]), 7, tolerance = 0.5)
expect_equal(ncol(example_isolates[, c(administrable_iv() | penicillins())]), 37, tolerance = 0.5)
# filter using any() or all() # filter using any() or all()
expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5) expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)

View File

@ -34,13 +34,11 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
"inst/tinytest", "inst/tinytest",
"tinytest"), "tinytest"),
verbose = 99, verbose = 99,
pattern = "first.*\\.[rR]$",
color = FALSE) color = FALSE)
cat("SUMMARY:\n") cat("SUMMARY:\n")
print(summary(out)) print(summary(out))
cat("WARNINGS:\n") cat("WARNINGS:\n")
print(warnings()) print(warnings())
cat(attributes(out)$duration, "\n") cat(attributes(out)$duration, "\n")
} }
} }