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(v1.4.0.9023) unit tests

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dr. M.S. (Matthijs) Berends 2020-11-17 11:53:56 +01:00
parent 93428415d0
commit 0800d33228
14 changed files with 32 additions and 24 deletions
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12
.github/workflows/check.yaml vendored
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@ -92,7 +92,7 @@ jobs:
key: ${{ runner.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('.github/depends.Rds') }} key: ${{ runner.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-3- restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-3-
- name: Install system dependencies - name: Install Linux dependencies
if: runner.os == 'Linux' if: runner.os == 'Linux'
env: env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
@ -119,7 +119,15 @@ jobs:
sessioninfo::session_info(pkgs, include_base = TRUE) sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0} shell: Rscript {0}
- name: Check - name: Check on older R versions
if: matrix.config.r == '3.3'
env:
_R_CHECK_CRAN_INCOMING_: false
run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-build-vignettes" , "--ignore-vignettes"), error_on = "warning", check_dir = "check")
shell: Rscript {0}
- name: Check on newer R versions
if: matrix.config.r != '3.3'
env: env:
_R_CHECK_CRAN_INCOMING_: false _R_CHECK_CRAN_INCOMING_: false
run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")

4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.4.0.9022 Version: 1.4.0.9023
Date: 2020-11-16 Date: 2020-11-17
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

4
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.4.0.9022 # AMR 1.4.0.9023
## <small>Last updated: 16 November 2020</small> ## <small>Last updated: 17 November 2020</small>
### New ### New
* Functions `mo_is_gram_negative()` and `mo_is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria. If you have the `dplyr` package installed, they can even determine the column with microorganisms themselves when used inside `dplyr` verbs: * Functions `mo_is_gram_negative()` and `mo_is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria. If you have the `dplyr` package installed, they can even determine the column with microorganisms themselves when used inside `dplyr` verbs:

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">1.4.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9023</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">1.4.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9023</span>
</span> </span>
</div> </div>

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">1.4.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9023</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">1.4.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9023</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">1.4.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9023</span>
</span> </span>
</div> </div>

16
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">1.4.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9023</span>
</span> </span>
</div> </div>
@ -236,13 +236,13 @@
<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-1409022" class="section level1"> <div id="amr-1409023" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9022"> <h1 class="page-header" data-toc-text="1.4.0.9023">
<a href="#amr-1409022" class="anchor"></a>AMR 1.4.0.9022<small> Unreleased </small> <a href="#amr-1409023" class="anchor"></a>AMR 1.4.0.9023<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-16-november-2020" class="section level2"> <div id="last-updated-17-november-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-16-november-2020" class="anchor"></a><small>Last updated: 16 November 2020</small> <a href="#last-updated-17-november-2020" class="anchor"></a><small>Last updated: 17 November 2020</small>
</h2> </h2>
<div id="new" class="section level3"> <div id="new" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -252,14 +252,14 @@
<p>Functions <code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code> as wrappers around <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>. They always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria. If you have the <code>dplyr</code> package installed, they can even determine the column with microorganisms themselves when used inside <code>dplyr</code> verbs:</p> <p>Functions <code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code> as wrappers around <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>. They always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria. If you have the <code>dplyr</code> package installed, they can even determine the column with microorganisms themselves when used inside <code>dplyr</code> verbs:</p>
<div class="sourceCode" id="cb1"><pre class="downlit"> <div class="sourceCode" id="cb1"><pre class="downlit">
<span class="va">example_isolates</span> <span class="op">%&gt;%</span> <span class="va">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/stats/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_is_gram_positive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_is_gram_positive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
<span class="co">#&gt; NOTE: Using column `mo` as input for mo_is_gram_positive()</span></pre></div> <span class="co">#&gt; NOTE: Using column `mo` as input for mo_is_gram_positive()</span></pre></div>
</li> </li>
<li> <li>
<p>Function <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to test for intrinsic resistance, based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2</a> from 2020. As with the new <code>mo_is_gram_*()</code> functions, if you have the <code>dplyr</code> package installed the column with microorganisms will be automatically determined when used inside <code>dplyr</code> verbs:</p> <p>Function <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to test for intrinsic resistance, based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2</a> from 2020. As with the new <code>mo_is_gram_*()</code> functions, if you have the <code>dplyr</code> package installed the column with microorganisms will be automatically determined when used inside <code>dplyr</code> verbs:</p>
<div class="sourceCode" id="cb2"><pre class="downlit"> <div class="sourceCode" id="cb2"><pre class="downlit">
<span class="va">example_isolates</span> <span class="op">%&gt;%</span> <span class="va">example_isolates</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://rdrr.io/r/stats/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"Vancomycin"</span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"Vancomycin"</span><span class="op">)</span><span class="op">)</span>
<span class="co">#&gt; NOTE: Using column `mo` as input for mo_is_intrinsic_resistant()</span></pre></div> <span class="co">#&gt; NOTE: Using column `mo` as input for mo_is_intrinsic_resistant()</span></pre></div>
</li> </li>
<li><p>Functions <code><a href="../reference/like.html">%not_like%</a></code> and <code><a href="../reference/like.html">%not_like_case%</a></code> as wrappers around <code><a href="../reference/like.html">%like%</a></code> and <code><a href="../reference/like.html">%like_case%</a></code>. The RStudio addin to insert the text " %like% " as provided in this package now iterates over all like variants. So if you have defined the keyboard shortcut Ctrl/Cmd + L to this addin, it will first insert <code><a href="../reference/like.html">%like%</a></code> and by pressing it again it will be replaced with <code><a href="../reference/like.html">%not_like%</a></code>, etc.</p></li> <li><p>Functions <code><a href="../reference/like.html">%not_like%</a></code> and <code><a href="../reference/like.html">%not_like_case%</a></code> as wrappers around <code><a href="../reference/like.html">%like%</a></code> and <code><a href="../reference/like.html">%like_case%</a></code>. The RStudio addin to insert the text " %like% " as provided in this package now iterates over all like variants. So if you have defined the keyboard shortcut Ctrl/Cmd + L to this addin, it will first insert <code><a href="../reference/like.html">%like%</a></code> and by pressing it again it will be replaced with <code><a href="../reference/like.html">%not_like%</a></code>, etc.</p></li>

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: 2020-11-16T18:55Z last_built: 2020-11-17T10:53Z
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/age_groups.html
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@ -82,7 +82,7 @@
</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">1.4.0.9021</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9023</span>
</span> </span>
</div> </div>

2
docs/reference/as.disk.html
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@ -82,7 +82,7 @@
</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">1.4.0.9021</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9023</span>
</span> </span>
</div> </div>

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">1.4.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9023</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">1.4.0.9022</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9023</span>
</span> </span>
</div> </div>