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(v1.6.0.9040) unit tests

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dr. M.S. (Matthijs) Berends 2021-05-16 09:25:36 +02:00
parent 6c3ab19e3a
commit 00496e45b7
18 changed files with 72 additions and 79 deletions
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33
.github/workflows/check.yaml vendored
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@ -89,18 +89,10 @@ jobs:
steps: steps:
- uses: actions/checkout@v2 - uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@master - uses: r-lib/actions/setup-r@v1
with: with:
r-version: ${{ matrix.config.r }} r-version: ${{ matrix.config.r }}
# - uses: r-lib/actions/setup-pandoc@master
# - name: Query dependencies
# if: matrix.config.r != '3.0'
# run: |
# saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
# shell: Rscript {0}
- name: Install Linux dependencies - name: Install Linux dependencies
if: runner.os == 'Linux' if: runner.os == 'Linux'
# update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu). # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
@ -108,7 +100,8 @@ jobs:
run: | run: |
sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev
- name: Cache R packages - name: Restore cached R packages
# this step will add the step 'Post Restore cached R packages' on a succesful run
if: runner.os != 'Windows' if: runner.os != 'Windows'
uses: actions/cache@v1 uses: actions/cache@v1
with: with:
@ -122,7 +115,7 @@ jobs:
source("data-raw/_install_deps.R") source("data-raw/_install_deps.R")
shell: Rscript {0} shell: Rscript {0}
- name: Session info - name: Show session info
run: | run: |
options(width = 100) options(width = 100)
utils::sessionInfo() utils::sessionInfo()
@ -137,8 +130,9 @@ jobs:
_R_CHECK_DEPENDS_ONLY_: true _R_CHECK_DEPENDS_ONLY_: true
_R_CHECK_LENGTH_1_CONDITION_: verbose _R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose _R_CHECK_LENGTH_1_LOGIC2_: verbose
R_LIBS_USER: ${{ env.R_LIBS_USER }} # during 'R CMD check', R_LIBS_USER will be overwritten, so:
R_TINYTEST: true R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
R_RUN_TINYTEST: true
run: | run: |
tar -xf data-raw/AMR_latest.tar.gz tar -xf data-raw/AMR_latest.tar.gz
rm -rf AMR/vignettes rm -rf AMR/vignettes
@ -153,8 +147,9 @@ jobs:
_R_CHECK_DEPENDS_ONLY_: true _R_CHECK_DEPENDS_ONLY_: true
_R_CHECK_LENGTH_1_CONDITION_: verbose _R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose _R_CHECK_LENGTH_1_LOGIC2_: verbose
R_LIBS_USER: ${{ env.R_LIBS_USER }} # during 'R CMD check', R_LIBS_USER will be overwritten, so:
R_TINYTEST: true R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
R_RUN_TINYTEST: true
run: | run: |
tar -xf data-raw/AMR_latest.tar.gz tar -xf data-raw/AMR_latest.tar.gz
rm -rf AMR/vignettes rm -rf AMR/vignettes
@ -167,9 +162,9 @@ jobs:
find . -name 'tinytest.Rout*' -exec cat '{}' \; || true find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
shell: bash shell: bash
- name: Upload check results - name: Upload artifacts
if: failure() if: always()
uses: actions/upload-artifact@master uses: actions/upload-artifact@v2
with: with:
name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
path: AMR.Rcheck path: AMR.Rcheck

6
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.6.0.9038 Version: 1.6.0.9040
Date: 2021-05-15 Date: 2021-05-16
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),
@ -57,7 +57,7 @@ Suggests:
skimr, skimr,
tidyr, tidyr,
tinytest, tinytest,
xml2, xml2
VignetteBuilder: knitr,rmarkdown VignetteBuilder: knitr,rmarkdown
URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
BugReports: https://github.com/msberends/AMR/issues BugReports: https://github.com/msberends/AMR/issues

4
NEWS.md
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@ -1,5 +1,5 @@
# `AMR` 1.6.0.9035 # `AMR` 1.6.0.9040
## <small>Last updated: 15 May 2021</small> ## <small>Last updated: 16 May 2021</small>
### New ### New
* Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()` * Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`

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data-raw/AMR_latest.tar.gz
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2
data-raw/_install_deps.R
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@ -43,5 +43,3 @@ for (i in seq_len(length(to_update))) {
warning = function(w) message(w$message), warning = function(w) message(w$message),
error = function(e) message(e$message)) error = function(e) message(e$message))
} }
# saveRDS(to_update, ".github/depends.Rds", version = 2)

2
docs/404.html
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@ -81,7 +81,7 @@
</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">1.6.0.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
</span> </span>
</div> </div>

2
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">1.6.0.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
</span> </span>
</div> </div>

57
docs/articles/datasets.html
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@ -39,7 +39,7 @@
</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">1.6.0.9011</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
</span> </span>
</div> </div>
@ -47,14 +47,14 @@
<ul class="nav navbar-nav"> <ul class="nav navbar-nav">
<li> <li>
<a href="../index.html"> <a href="../index.html">
<span class="fa fa-home"></span> <span class="fas fa-home"></span>
Home Home
</a> </a>
</li> </li>
<li class="dropdown"> <li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-question-circle"></span> <span class="fas fa-question-circle"></span>
How to How to
@ -63,77 +63,77 @@
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="../articles/AMR.html"> <a href="../articles/AMR.html">
<span class="fa fa-directions"></span> <span class="fas fa-directions"></span>
Conduct AMR analysis Conduct AMR analysis
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/resistance_predict.html"> <a href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span> <span class="fas fa-dice"></span>
Predict antimicrobial resistance Predict antimicrobial resistance
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/datasets.html"> <a href="../articles/datasets.html">
<span class="fa fa-database"></span> <span class="fas fa-database"></span>
Data sets for download / own use Data sets for download / own use
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/PCA.html"> <a href="../articles/PCA.html">
<span class="fa fa-compress"></span> <span class="fas fa-compress"></span>
Conduct principal component analysis for AMR Conduct principal component analysis for AMR
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/MDR.html"> <a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span> <span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR) Determine multi-drug resistance (MDR)
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/WHONET.html"> <a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span> <span class="fas fa-globe-americas"></span>
Work with WHONET data Work with WHONET data
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/SPSS.html"> <a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span> <span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata Import data from SPSS/SAS/Stata
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/EUCAST.html"> <a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span> <span class="fas fa-exchange-alt"></span>
Apply EUCAST rules Apply EUCAST rules
</a> </a>
</li> </li>
<li> <li>
<a href="../reference/mo_property.html"> <a href="../reference/mo_property.html">
<span class="fa fa-bug"></span> <span class="fas fa-bug"></span>
Get properties of a microorganism Get properties of a microorganism
</a> </a>
</li> </li>
<li> <li>
<a href="../reference/ab_property.html"> <a href="../reference/ab_property.html">
<span class="fa fa-capsules"></span> <span class="fas fa-capsules"></span>
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/benchmarks.html"> <a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span> <span class="fas fa-shipping-fast"></span>
Other: benchmarks Other: benchmarks
</a> </a>
@ -142,21 +142,21 @@
</li> </li>
<li> <li>
<a href="../reference/index.html"> <a href="../reference/index.html">
<span class="fa fa-book-open"></span> <span class="fas fa-book-open"></span>
Manual Manual
</a> </a>
</li> </li>
<li> <li>
<a href="../authors.html"> <a href="../authors.html">
<span class="fa fa-users"></span> <span class="fas fa-users"></span>
Authors Authors
</a> </a>
</li> </li>
<li> <li>
<a href="../news/index.html"> <a href="../news/index.html">
<span class="far fa far fa-newspaper"></span> <span class="far fa-newspaper"></span>
Changelog Changelog
</a> </a>
@ -165,14 +165,14 @@
<ul class="nav navbar-nav navbar-right"> <ul class="nav navbar-nav navbar-right">
<li> <li>
<a href="https://github.com/msberends/AMR"> <a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span> <span class="fab fa-github"></span>
Source Code Source Code
</a> </a>
</li> </li>
<li> <li>
<a href="../survey.html"> <a href="../survey.html">
<span class="fa fa-clipboard-list"></span> <span class="fas fa-clipboard-list"></span>
Survey Survey
</a> </a>
@ -187,13 +187,12 @@
</header><link href="datasets_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet"> </header><script src="datasets_files/header-attrs-2.7/header-attrs.js"></script><div class="row">
<script src="datasets_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
<div class="col-md-9 contents"> <div class="col-md-9 contents">
<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 class="date">27 April 2021</h4> <h4 class="date">16 May 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> <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> <div class="hidden name"><code>datasets.Rmd</code></div>
@ -212,7 +211,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2> <a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
<p>A data set with 70,026 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p> <p>A data set with 70,026 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p> <p>It was last updated on 11 March 2021 20:59:32 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.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/microorganisms.rds">R file</a> (2.2 MB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">R file</a> (2.2 MB)<br>
@ -433,7 +432,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<p>A data set with 14,100 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p> <p>A data set with 14,100 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p> <p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p> <p>It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.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/microorganisms.old.rds">R file</a> (0.2 MB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds">R file</a> (0.2 MB)<br>
@ -498,7 +497,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2> <a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>atc</em>, <em>cid</em>, <em>name</em>, <em>group</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>atc</em>, <em>cid</em>, <em>name</em>, <em>group</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 27 April 2021 08:12:46 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 4 May 2021 13:38:27 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">R file</a> (32 kB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">R file</a> (32 kB)<br>
@ -666,7 +665,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#antiviral-agents" class="anchor"></a>Antiviral agents</h2> <a href="#antiviral-agents" class="anchor"></a>Antiviral agents</h2>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p> <p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 April 2021 08:12:46 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 29 August 2020 19:53:07 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/antivirals.rds">R file</a> (5 kB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds">R file</a> (5 kB)<br>
@ -793,7 +792,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#intrinsic-bacterial-resistance" class="anchor"></a>Intrinsic bacterial resistance</h2> <a href="#intrinsic-bacterial-resistance" class="anchor"></a>Intrinsic bacterial resistance</h2>
<p>A data set with 93,892 rows and 2 columns, containing the following column names:<br><em>microorganism</em> and <em>antibiotic</em>.</p> <p>A data set with 93,892 rows and 2 columns, containing the following column names:<br><em>microorganism</em> and <em>antibiotic</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p> <p>It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.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/intrinsic_resistant.rds">R file</a> (69 kB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds">R file</a> (69 kB)<br>
@ -1008,7 +1007,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2> <a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
<p>A data set with 20,486 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p> <p>A data set with 20,486 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p> <p>It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.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/rsi_translation.rds">R file</a> (34 kB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (34 kB)<br>
@ -1138,7 +1137,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<a href="#dosage-guidelines-from-eucast" class="anchor"></a>Dosage guidelines from EUCAST</h2> <a href="#dosage-guidelines-from-eucast" class="anchor"></a>Dosage guidelines from EUCAST</h2>
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p> <p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p> <p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p> <p>It was last updated on 25 January 2021 20:58:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.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/dosage.rds">R file</a> (3 kB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/dosage.rds">R file</a> (3 kB)<br>

2
docs/articles/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">1.6.0.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
</span> </span>
</div> </div>

2
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">1.6.0.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -42,7 +42,7 @@
</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">1.6.0.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
</span> </span>
</div> </div>

12
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">1.6.0.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
</span> </span>
</div> </div>
@ -236,12 +236,12 @@
<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-1609031" class="section level1"> <div id="amr-1609040" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9031"> <h1 class="page-header" data-toc-text="1.6.0.9040">
<a href="#amr-1609031" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9031</h1> <a href="#amr-1609040" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9040</h1>
<div id="last-updated-15-may-2021" class="section level2"> <div id="last-updated-16-may-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-15-may-2021" class="anchor"></a><small>Last updated: 15 May 2021</small> <a href="#last-updated-16-may-2021" class="anchor"></a><small>Last updated: 16 May 2021</small>
</h2> </h2>
<div id="new" class="section level3"> <div id="new" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-05-15T19:35Z last_built: 2021-05-16T07:24Z
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

2
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">1.6.0.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
</span> </span>
</div> </div>

2
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">1.6.0.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
</span> </span>
</div> </div>

2
git_premaster.sh
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@ -134,6 +134,8 @@ echo "•••••••••••••••••"
echo "• Building site •" echo "• Building site •"
echo "•••••••••••••••••" echo "•••••••••••••••••"
Rscript -e "suppressMessages(pkgdown::build_site(lazy = $lazy, examples = FALSE))" Rscript -e "suppressMessages(pkgdown::build_site(lazy = $lazy, examples = FALSE))"
# always rebuild datasets vignette
Rscript -e "pkgdown::build_article('datasets', lazy = FALSE, quiet = TRUE)"
# add the survey page # add the survey page
Rscript -e "source('data-raw/create_survey_page.R')" Rscript -e "source('data-raw/create_survey_page.R')"
echo echo

12
inst/tinytest/test-join_microorganisms.R
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@ -24,12 +24,12 @@
# ==================================================================== # # ==================================================================== #
unjoined <- example_isolates unjoined <- example_isolates
inner <- example_isolates %>% inner_join_microorganisms() inner <- inner_join_microorganisms(example_isolates)
left <- example_isolates %>% left_join_microorganisms() left <- left_join_microorganisms(example_isolates)
semi <- example_isolates %>% semi_join_microorganisms() semi <- semi_join_microorganisms(example_isolates)
anti <- example_isolates %>% anti_join_microorganisms() anti <- anti_join_microorganisms(example_isolates)
suppressWarnings(right <- example_isolates %>% right_join_microorganisms()) suppressWarnings(right <- right_join_microorganisms(example_isolates))
suppressWarnings(full <- example_isolates %>% full_join_microorganisms()) suppressWarnings(full <- full_join_microorganisms(example_isolates))
expect_true(ncol(unjoined) < ncol(inner)) expect_true(ncol(unjoined) < ncol(inner))
expect_true(nrow(unjoined) == nrow(inner)) expect_true(nrow(unjoined) == nrow(inner))

7
tests/tinytest.R
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@ -24,11 +24,10 @@
# ==================================================================== # # ==================================================================== #
# test only on GitHub Actions and at home - not on CRAN as tests are lengthy # test only on GitHub Actions and at home - not on CRAN as tests are lengthy
if (identical(Sys.getenv("R_TINYTEST"), "true")) { if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
print(Sys.getenv("R_LIBS_USER")) # env var 'R_LIBS_USER' got overwritten during 'R CMD check' in GitHub Actions, so:
.libPaths(c("/Users/runner/work/_temp/Library", .libPaths())) .libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths()))
print(.libPaths()) print(.libPaths())
print(as.data.frame(utils::installed.packages())[, "Version", drop = FALSE])
library(tinytest) library(tinytest)
library(AMR) library(AMR)
test_package("AMR") test_package("AMR")