(v1.7.1.9001) unit tests

v1.8.2
parent 1908e7cc7a
commit 683a0e748a
  1. 10
      .github/workflows/check.yaml
  2. 9
      .github/workflows/codecovr.yaml
  3. 4
      DESCRIPTION
  4. 6
      NEWS.md
  5. 2
      R/amr.R
  6. BIN
      data-raw/AMR_latest.tar.gz
  7. 1
      data-raw/_install_deps.R
  8. 2
      docs/404.html
  9. 2
      docs/LICENSE-text.html
  10. 4
      docs/articles/datasets.html
  11. 2
      docs/articles/index.html
  12. 2
      docs/authors.html
  13. 2
      docs/index.html
  14. 14
      docs/news/index.html
  15. 2
      docs/pkgdown.yml
  16. 4
      docs/reference/AMR.html
  17. 2
      docs/reference/antibiotic_class_selectors.html
  18. 2
      docs/reference/custom_eucast_rules.html
  19. 2
      docs/reference/index.html
  20. 2
      docs/survey.html
  21. 2
      man/AMR.Rd

@ -23,6 +23,8 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# This GitHub Actions file runs without ANY dependency, so works on all versions of R since R-3.0.
on:
push:
branches:
@ -96,12 +98,18 @@ jobs:
run: |
sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
- name: Query dependencies
# this will change once a week, so it will cache dependency updates
run: |
writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
shell: Rscript {0}
- name: Restore cached R packages
# this step will add the step 'Post Restore cached R packages' on a succesful run
uses: actions/cache@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
- name: Unpack AMR and install R dependencies
if: always()

@ -48,12 +48,18 @@ jobs:
- uses: r-lib/actions/setup-pandoc@master
- name: Query dependencies
# this will change once a week, so it will cache dependency updates
run: |
writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
shell: Rscript {0}
- name: Restore cached R packages
# this step will add the step 'Post Restore cached R packages' on a succesful run
uses: actions/cache@v2
with:
path: ${{ env.R_LIBS_USER }}
key: macOS-latest-r-release-v5-codecovr
key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
- name: Unpack AMR and install R dependencies
run: |
@ -73,6 +79,7 @@ jobs:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
R_RUN_TINYTEST: true
run: |
install.packages("covr", repos = "https://cran.rstudio.com/")
library(AMR)
library(tinytest)
x <- covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))

@ -1,6 +1,6 @@
Package: AMR
Version: 1.7.1.9000
Date: 2021-06-04
Version: 1.7.1.9001
Date: 2021-06-05
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(
person(role = c("aut", "cre"),

@ -1,5 +1,5 @@
# `AMR` 1.7.1.9000
## <small>Last updated: 4 June 2021</small>
# `AMR` 1.7.1.9001
## <small>Last updated: 5 June 2021</small>
### Changed
* Added more antibiotic class selectors, such as `lincosamides()` and `lipoglycopeptides()`
@ -8,7 +8,6 @@
# `AMR` 1.7.1
### Breaking change
* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`)
* All antibiotic class selectors (such as `carbapenems()`, `aminoglycosides()`) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as `filter_carbapenems()`, `filter_aminoglycosides()`). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:
```r
# select columns with results for carbapenems
@ -28,6 +27,7 @@
```
### New
* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`)
* Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
* Function `italicise_taxonomy()` to make taxonomic names within a string italic, with support for markdown and ANSI
* Support for all four methods to determine first isolates as summarised by Hindler *et al.* (doi: [10.1086/511864](https://doi.org/10.1086/511864)): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.

@ -61,7 +61,7 @@
#' Matthijs S. Berends \cr
#' m.s.berends \[at\] umcg \[dot\] nl \cr
#' University of Groningen
#' Department of Medical Microbiology and Infection Prevention
#' Department of Medical Microbiology and Infection Prevention \cr
#' University Medical Center Groningen \cr
#' Post Office Box 30001 \cr
#' 9700 RB Groningen \cr

Binary file not shown.

@ -26,7 +26,6 @@
# some old R instances have trouble installing tinytest, so we ship it too
install.packages("data-raw/tinytest_1.2.4.10.tar.gz")
install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
install.packages("covr", repos = "https://cran.rstudio.com/")
pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", unlist(strsplit(packageDescription("AMR", fields = "Suggests"), ", ?")))
cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n")

@ -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">1.7.1.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
</span>
</div>

@ -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">1.7.1.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
</span>
</div>

@ -39,7 +39,7 @@
</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">1.7.1.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
</span>
</div>
@ -192,7 +192,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 class="date">04 June 2021</h4>
<h4 class="date">05 June 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>

@ -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">1.7.1.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
</span>
</div>

@ -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">1.7.1.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
</span>
</div>

@ -42,7 +42,7 @@
</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">1.7.1.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
</span>
</div>

@ -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">1.7.1.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
</span>
</div>
@ -236,12 +236,12 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1719000" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9000">
<a href="#amr-1719000" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9000</h1>
<div id="last-updated-4-june-2021" class="section level2">
<div id="amr-1719001" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9001">
<a href="#amr-1719001" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9001</h1>
<div id="last-updated-5-june-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-4-june-2021" class="anchor"></a><small>Last updated: 4 June 2021</small>
<a href="#last-updated-5-june-2021" class="anchor"></a><small>Last updated: 5 June 2021</small>
</h2>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
@ -260,7 +260,6 @@
<h3 class="hasAnchor">
<a href="#breaking-change" class="anchor"></a>Breaking change</h3>
<ul>
<li><p>Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>)</p></li>
<li>
<p>All antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>) can now be used for filtering as well, making all their accompanying <code>filter_*()</code> functions redundant (such as <code><a href="../reference/AMR-deprecated.html">filter_carbapenems()</a></code>, <code><a href="../reference/AMR-deprecated.html">filter_aminoglycosides()</a></code>). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
@ -286,6 +285,7 @@
<h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3>
<ul>
<li>Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>)</li>
<li>Function <code><a href="../reference/custom_eucast_rules.html">custom_eucast_rules()</a></code> that brings support for custom AMR rules in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>
</li>
<li>Function <code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> to make taxonomic names within a string italic, with support for markdown and ANSI</li>

@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-06-04T19:07Z
last_built: 2021-06-05T13:10Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

@ -82,7 +82,7 @@
</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">1.7.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
</span>
</div>
@ -286,7 +286,7 @@
<p>Matthijs S. Berends <br />
m.s.berends [at] umcg [dot] nl <br />
University of Groningen
Department of Medical Microbiology and Infection Prevention
Department of Medical Microbiology and Infection Prevention <br />
University Medical Center Groningen <br />
Post Office Box 30001 <br />
9700 RB Groningen <br />

@ -83,7 +83,7 @@
</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">1.7.1.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
</span>
</div>

@ -82,7 +82,7 @@
</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">1.7.1.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
</span>
</div>

@ -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">1.7.1.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
</span>
</div>

@ -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">1.7.1.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9001</span>
</span>
</div>

@ -50,7 +50,7 @@ For suggestions, comments or questions, please contact us at:
Matthijs S. Berends \cr
m.s.berends [at] umcg [dot] nl \cr
University of Groningen
Department of Medical Microbiology and Infection Prevention
Department of Medical Microbiology and Infection Prevention \cr
University Medical Center Groningen \cr
Post Office Box 30001 \cr
9700 RB Groningen \cr

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