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(v1.7.1.9039) reinitiate all units tests
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12
.github/workflows/check.yaml
vendored
12
.github/workflows/check.yaml
vendored
@ -128,18 +128,6 @@ jobs:
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as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
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shell: Rscript {0}
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# - name: Only keep vignettes on release version
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- name: Remove vignettes
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# if: matrix.config.r != 'release'
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if: always()
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# writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite
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run: |
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rm -rf AMR/vignettes
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Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION2')"
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rm AMR/DESCRIPTION
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mv AMR/DESCRIPTION2 AMR/DESCRIPTION
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shell: bash
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- name: Run R CMD check
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if: always()
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env:
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.7.1.9038
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Date: 2021-09-01
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Version: 1.7.1.9039
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Date: 2021-09-03
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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4
NEWS.md
4
NEWS.md
@ -1,5 +1,5 @@
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# `AMR` 1.7.1.9038
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## <small>Last updated: 1 September 2021</small>
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# `AMR` 1.7.1.9039
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## <small>Last updated: 3 September 2021</small>
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### Breaking changes
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* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
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Binary file not shown.
@ -44,7 +44,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9038</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9039</span>
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</span>
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</div>
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@ -190,7 +190,7 @@
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>Data sets for download / own use</h1>
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<h4 data-toc-skip class="date">01 September 2021</h4>
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<h4 data-toc-skip class="date">03 September 2021</h4>
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<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>
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<div class="hidden name"><code>datasets.Rmd</code></div>
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@ -495,7 +495,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
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<a href="#antibiotic-agents" class="anchor" aria-hidden="true"></a>Antibiotic agents</h2>
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<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>
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<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
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<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>
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<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>
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<p><strong>Direct download links:</strong></p>
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<ul>
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<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>
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@ -92,7 +92,7 @@
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</button>
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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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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9038</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9039</span>
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</span>
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</div>
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@ -240,12 +240,12 @@
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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 id="amr-1719038" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9038">
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<a href="#amr-1719038" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9038</h1>
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<div id="last-updated-1-september-2021" class="section level2">
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<div id="amr-1719039" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9039">
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<a href="#amr-1719039" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9039</h1>
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<div id="last-updated-3-september-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-1-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 1 September 2021</small>
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<a href="#last-updated-3-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 3 September 2021</small>
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</h2>
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<div id="breaking-changes" class="section level3">
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<h3 class="hasAnchor">
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@ -56,6 +56,7 @@ expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance
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expect_equal(ncol(example_isolates[, c(administrable_per_os() & penicillins())]), 5, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, c(administrable_iv() & penicillins())]), 7, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, c(administrable_iv() | penicillins())]), 37, tolerance = 0.5)
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# filter using any() or all()
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expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)
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@ -34,13 +34,11 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
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"inst/tinytest",
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"tinytest"),
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verbose = 99,
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pattern = "first.*\\.[rR]$",
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color = FALSE)
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cat("SUMMARY:\n")
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print(summary(out))
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cat("WARNINGS:\n")
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print(warnings())
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cat(attributes(out)$duration, "\n")
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}
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}
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