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AMR
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(v1.6.0.9055) support codecov again

This commit is contained in:
dr. M.S. (Matthijs) Berends 2021-05-21 20:20:51 +02:00
parent fecc5d183c
commit b210f1327c
72 changed files with 203 additions and 216 deletions
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13
.github/workflows/check.yaml vendored
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@ -61,6 +61,7 @@ jobs:
- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
@ -69,18 +70,6 @@ jobs:
- {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-16.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

9
.github/workflows/codecovr.yaml vendored
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@ -26,9 +26,11 @@
on:
push:
branches:
- premaster
- master
pull_request:
branches:
- premaster
- master
name: code-coverage
@ -67,5 +69,10 @@ jobs:
shell: Rscript {0}
- name: Test coverage
run: 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"), quiet = FALSE)
run: |
source_files <- list.files("R", pattern = ".R$", full.names = TRUE)
test_files <- list.files("inst/tinytest", full.names = TRUE)
cov <- covr::file_coverage(source_files = source_files, test_files = test_files, 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"))
attr(cov, which = "package") <- list(path = ".") # until https://github.com/r-lib/covr/issues/478 is solved
covr::codecov(cov, quiet = FALSE)
shell: Rscript {0}

4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.6.0.9054
Date: 2021-05-20
Version: 1.6.0.9055
Date: 2021-05-21
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(
person(role = c("aut", "cre"),

16
NEWS.md
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@ -1,5 +1,5 @@
# `AMR` 1.6.0.9054
## <small>Last updated: 20 May 2021</small>
# `AMR` 1.6.0.9055
## <small>Last updated: 21 May 2021</small>
### Breaking change
* 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.
@ -62,18 +62,6 @@
* Updated `skimr::skim()` usage for MIC values to also include 25th and 75th percentiles
* Fix for plotting missing MIC/disk diffusion values
* Updated join functions to always use `dplyr` join functions if the `dplyr` package is installed - now also preserving grouped variables
* Updates for filtering on antibiotic classes (e.g., using `filter_carbapenems()`):
* Support for dplyr groups
* Support for base R row filtering:
```r
dim(example_isolates)
#> [1] 2000 49
example_isolates[filter_carbapenems(), ]
#> ℹ Applying `filter_carbapenems()`: values in any of columns 'IPM' (imipenem)
#> or 'MEM' (meropenem) are either "R", "S" or "I"
#> [1] 962 49
```
* Antibiotic class selectors (such as `cephalosporins()`) now maintain the column order from the original data
* Fix for selecting columns using `fluoroquinolones()`

15
R/aa_helper_functions.R
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@ -290,6 +290,15 @@ stop_ifnot_installed <- function(package) {
return(invisible())
}
pkg_is_available <- function(pkg, also_load = TRUE) {
if (also_load == TRUE) {
out <- suppressWarnings(require(pkg, character.only = TRUE, warn.conflicts = FALSE, quietly = TRUE))
} else {
out <- requireNamespace(pkg, quietly = TRUE)
}
isTRUE(out)
}
import_fn <- function(name, pkg, error_on_fail = TRUE) {
if (isTRUE(error_on_fail)) {
stop_ifnot_installed(pkg)
@ -1189,7 +1198,7 @@ current_R_older_than <- function(version) {
}
# prevent dependency on package 'backports' ----
# these functions were not available in previous versions of R (last checked: R 4.0.5)
# these functions were not available in previous versions of R (last checked: R 4.1.0)
# see here for the full list: https://github.com/r-lib/backports
strrep <- function(x, times) {
x <- as.character(x)
@ -1243,3 +1252,7 @@ if (current_R_older_than(3.1)) {
sinpi <- function(...) 1
tanpi <- function(...) 1
}
dir.exists <- function (paths) {
x = base::file.info(paths)$isdir
!is.na(x) & x
}

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R/sysdata.rda
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data-raw/AMR_latest.tar.gz
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2
docs/404.html
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@ -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">1.6.0.9054</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -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">1.6.0.9054</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

6
docs/articles/datasets.html
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@ -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">1.6.0.9054</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>
@ -187,12 +187,12 @@
</header><script src="datasets_files/header-attrs-2.7/header-attrs.js"></script><div class="row">
</header><script src="datasets_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 class="date">20 May 2021</h4>
<h4 class="date">21 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>
<div class="hidden name"><code>datasets.Rmd</code></div>

12
docs/articles/datasets_files/header-attrs-2.8/header-attrs.js Normal file
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@ -0,0 +1,12 @@
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});

2
docs/articles/index.html
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@ -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">1.6.0.9054</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/authors.html
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@ -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">1.6.0.9054</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

11
docs/index.html
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@ -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">1.6.0.9054</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>
@ -196,7 +196,6 @@
<div class="page-header"><h1 class="hasAnchor">
<a href="#amr-for-r-" class="anchor"></a><code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px">
</h1></div>
<p><em>Note: the rules of ‘EUCAST Clinical Breakpoints v11.0 (2021)’ are now implemented.</em></p>
<div id="what-is-amr-for-r" class="section level3">
<h3 class="hasAnchor">
<a href="#what-is-amr-for-r" class="anchor"></a>What is <code>AMR</code> (for R)?</h3>
@ -221,13 +220,13 @@
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>bacteria <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</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_negative</a></span><span class="op">(</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">"cefotax"</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
<span class="co">#&gt; ℹ Using column 'mo' as input for mo_is_gram_negative()</span>
<span class="co">#&gt; ℹ Using column 'mo' as input for mo_is_intrinsic_resistant()</span>
<span class="co">#&gt; ℹ Using column 'mo' as input for `mo_is_gram_negative()`</span>
<span class="co">#&gt; ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`</span>
<span class="co">#&gt; ℹ Determining intrinsic resistance based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic</span>
<span class="co">#&gt; Resistance and Unusual Phenotypes' v3.2 (2020)</span>
<span class="co">#&gt; ℹ Applying `aminoglycosides()`: selecting columns 'AMK' (amikacin), 'GEN' (gentamicin), 'KAN'</span>
<span class="co">#&gt; ℹ For `aminoglycosides()` using columns: 'AMK' (amikacin), 'GEN' (gentamicin), 'KAN'</span>
<span class="co">#&gt; (kanamycin) and 'TOB' (tobramycin)</span>
<span class="co">#&gt; ℹ Applying `carbapenems()`: selecting columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></code></pre></div>
<span class="co">#&gt; ℹ For `carbapenems()` using columns: 'IPM' (imipenem) and 'MEM' (meropenem)</span></code></pre></div>
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
<table class="table">
<thead><tr class="header">

133
docs/news/index.html
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@ -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">1.6.0.9054</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</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-1609054" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9054">
<a href="#amr-1609054" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9054</h1>
<div id="last-updated-20-may-2021" class="section level2">
<div id="amr-1609055" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9055">
<a href="#amr-1609055" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9055</h1>
<div id="last-updated-21-may-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-20-may-2021" class="anchor"></a><small>Last updated: 20 May 2021</small>
<a href="#last-updated-21-may-2021" class="anchor"></a><small>Last updated: 21 May 2021</small>
</h2>
<div id="breaking-change" class="section level3">
<h3 class="hasAnchor">
@ -288,7 +288,7 @@
</ul>
</li>
<li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code><a href="../reference/AMR-deprecated.html">filter_betalactams()</a></code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
</li>
</ul>
</div>
@ -332,23 +332,6 @@
<li>Updated <code><a href="https://docs.ropensci.org/skimr/reference/skim.html">skimr::skim()</a></code> usage for MIC values to also include 25th and 75th percentiles</li>
<li>Fix for plotting missing MIC/disk diffusion values</li>
<li>Updated join functions to always use <code>dplyr</code> join functions if the <code>dplyr</code> package is installed - now also preserving grouped variables</li>
<li>Updates for filtering on antibiotic classes (e.g., using <code><a href="../reference/AMR-deprecated.html">filter_carbapenems()</a></code>):
<ul>
<li><p>Support for dplyr groups</p></li>
<li>
<p>Support for base R row filtering:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="https://rdrr.io/r/base/dim.html">dim</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
<span class="co">#&gt; [1] 2000 49</span>
<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="../reference/AMR-deprecated.html">filter_carbapenems</a></span><span class="op">(</span><span class="op">)</span>, <span class="op">]</span>
<span class="co">#&gt; ℹ Applying `filter_carbapenems()`: values in any of columns 'IPM' (imipenem)</span>
<span class="co">#&gt; or 'MEM' (meropenem) are either "R", "S" or "I"</span>
<span class="co">#&gt; [1] 962 49</span></code></pre></div>
</li>
</ul>
</li>
<li>Antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">cephalosporins()</a></code>) now maintain the column order from the original data</li>
<li>Fix for selecting columns using <code><a href="../reference/antibiotic_class_selectors.html">fluoroquinolones()</a></code>
</li>
@ -391,7 +374,7 @@
</li>
<li>
<p>Functions <code><a href="../reference/antibiotic_class_selectors.html">oxazolidinones()</a></code> (an antibiotic selector function) and <code><a href="../reference/AMR-deprecated.html">filter_oxazolidinones()</a></code> (an antibiotic filter function) to select/filter on e.g. linezolid and tedizolid</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
<span class="va">x</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">date</span>, <span class="va">hospital_id</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">oxazolidinones</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
@ -401,10 +384,10 @@
<span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
</li>
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li>
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/mo_property.html">mo_kingdom</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Aspergillus"</span>, <span class="st">"Candida"</span><span class="op">)</span><span class="op">)</span>
<span class="co">#&gt; [1] "Fungi" "Fungi"</span>
@ -416,7 +399,7 @@
<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html">which</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_is_yeast</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span> <span class="co"># base R</span>
<span class="va">example_isolates</span> <span class="op">%&gt;%</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_yeast</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="co"># dplyr</span></code></pre></div>
<p>The <code><a href="../reference/mo_property.html">mo_type()</a></code> function has also been updated to reflect this change:</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/mo_property.html">mo_type</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Aspergillus"</span>, <span class="st">"Candida"</span><span class="op">)</span><span class="op">)</span>
<span class="co"># [1] "Fungi" "Yeasts"</span>
@ -426,7 +409,7 @@
<li><p>Added Pretomanid (PMD, J04AK08) to the <code>antibiotics</code> data set</p></li>
<li>
<p>MIC values (see <code><a href="../reference/as.mic.html">as.mic()</a></code>) can now be used in any mathematical processing, such as usage inside functions <code><a href="https://rdrr.io/r/base/Extremes.html">min()</a></code>, <code><a href="https://rdrr.io/r/base/Extremes.html">max()</a></code>, <code><a href="https://rdrr.io/r/base/range.html">range()</a></code>, and with binary operators (<code><a href="https://rdrr.io/r/base/Arithmetic.html">+</a></code>, <code><a href="https://rdrr.io/r/base/Arithmetic.html">-</a></code>, etc.). This allows for easy distribution analysis and fast filtering on MIC values:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>
<span class="va">x</span>
@ -458,7 +441,7 @@
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
</ul>
</li>
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
@ -475,7 +458,7 @@
<code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now detects if the column name resembles an antibiotic name or code and now returns <code>TRUE</code> immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li>
<li>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</li>
<li>Argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only “S”)</li>
<li>Functions <code><a href="https://rdrr.io/r/base/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
<li>Functions <code><a href="https://docs.ropensci.org/skimr/reference/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
</li>
<li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
<li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>
@ -509,7 +492,7 @@
<ul>
<li>
<p>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> to determine (patient) episodes which are not necessarily based on microorganisms. The <code><a href="../reference/get_episode.html">get_episode()</a></code> function returns the index number of the episode per group, while the <code><a href="../reference/get_episode.html">is_new_episode()</a></code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode. They also support <code>dplyr</code>s grouping (i.e. using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code>):</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
<span class="va">example_isolates</span> <span class="op">%&gt;%</span>
@ -563,7 +546,7 @@
<code><a href="../reference/mdro.html">mdr_cmi2012()</a></code>,</li>
<li><code><a href="../reference/mdro.html">eucast_exceptional_phenotypes()</a></code></li>
</ul>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># to select first isolates that are Gram-negative </span>
<span class="co"># and view results of cephalosporins and aminoglycosides:</span>
@ -575,7 +558,7 @@
</li>
<li>
<p>For antibiotic selection functions (such as <code><a href="../reference/antibiotic_class_selectors.html">cephalosporins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>) to select columns based on a certain antibiotic group, the dependency on the <code>tidyselect</code> package was removed, meaning that they can now also be used without the need to have this package installed and now also work in base R function calls (they rely on R 3.2 or later):</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># above example in base R:</span>
<span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html">which</a></span><span class="op">(</span><span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="../reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,
@ -625,7 +608,7 @@
<li>
<p>Data set <code>intrinsic_resistant</code>. This data set contains all bug-drug combinations where the ‘bug’ is intrinsic resistant to the ‘drug’ according to the latest EUCAST insights. It contains just two columns: <code>microorganism</code> and <code>antibiotic</code>.</p>
<p>Curious about which enterococci are actually intrinsic resistant to vancomycin?</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
@ -648,7 +631,7 @@
<ul>
<li>
<p>Support for using <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/across.html">across()</a></code> to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.</p>
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># until dplyr 1.0.0</span>
<span class="va">your_data</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.rsi</span><span class="op">)</span>
@ -666,7 +649,7 @@
</li>
<li>
<p>Added intelligent data cleaning to <code><a href="../reference/as.disk.html">as.disk()</a></code>, so numbers can also be extracted from text and decimal numbers will always be rounded up:</p>
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/as.disk.html">as.disk</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"disk zone: 23.4 mm"</span>, <span class="fl">23.4</span><span class="op">)</span><span class="op">)</span>
<span class="co">#&gt; Class &lt;disk&gt;</span>
@ -726,7 +709,7 @@
<li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
<li>
<p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
@ -912,7 +895,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
<li>
<p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">yourdata</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span><span class="op">(</span><span class="va">antibiotic1</span><span class="op">:</span><span class="va">antibiotic25</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span><span class="op">)</span>
@ -940,7 +923,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Support for LOINC codes in the <code>antibiotics</code> data set. Use <code><a href="../reference/ab_property.html">ab_loinc()</a></code> to retrieve LOINC codes, or use a LOINC code for input in any <code>ab_*</code> function:</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/ab_property.html">ab_loinc</a></span><span class="op">(</span><span class="st">"ampicillin"</span><span class="op">)</span>
<span class="co">#&gt; [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
@ -951,7 +934,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>Support for SNOMED CT codes in the <code>microorganisms</code> data set. Use <code><a href="../reference/mo_property.html">mo_snomed()</a></code> to retrieve SNOMED codes, or use a SNOMED code for input in any <code>mo_*</code> function:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span><span class="op">(</span><span class="st">"S. aureus"</span><span class="op">)</span>
<span class="co">#&gt; [1] 115329001 3092008 113961008</span>
@ -1015,11 +998,11 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:</p>
<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_family</a></span><span class="op">(</span><span class="va">somebugs</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterobacteriaceae"</span><span class="op">)</span> <span class="va">...</span></code></pre></div>
<p>then please adjust this to:</p>
<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">somebugs</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterobacterales"</span><span class="op">)</span> <span class="va">...</span></code></pre></div>
</li>
@ -1033,7 +1016,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Functions <code><a href="../reference/proportion.html">susceptibility()</a></code> and <code><a href="../reference/proportion.html">resistance()</a></code> as aliases of <code><a href="../reference/proportion.html">proportion_SI()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code>, respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.</p>
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
<span class="va">example_isolates</span> <span class="op">%&gt;%</span>
@ -1062,7 +1045,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>More intelligent way of coping with some consonants like “l” and “r”</p></li>
<li>
<p>Added a score (a certainty percentage) to <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code>, that is calculated using the <a href="https://en.wikipedia.org/wiki/Levenshtein_distance">Levenshtein distance</a>:</p>
<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Stafylococcus aureus"</span>,
<span class="st">"staphylokok aureuz"</span><span class="op">)</span><span class="op">)</span>
@ -1120,14 +1103,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Determination of first isolates now <strong>excludes</strong> all ‘unknown’ microorganisms at default, i.e. microbial code <code>"UNKNOWN"</code>. They can be included with the new argument <code>include_unknown</code>:</p>
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">...</span>, include_unknown <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<p>For WHONET users, this means that all records/isolates with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default, since <code>as.mo("con") = "UNKNOWN"</code>. The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.</p>
</li>
<li>
<p>For code consistency, classes <code>ab</code> and <code>mo</code> will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result in <code>NA</code>:</p>
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># how it works in base R:</span>
<span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html">factor</a></span><span class="op">(</span><span class="st">"A"</span><span class="op">)</span>
@ -1152,7 +1135,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Function <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> to quickly get a <code>data.frame</code> with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed with <code><a href="../reference/mo_property.html">mo_shortname()</a></code> at default:</p>
<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
<span class="co">#&gt; NOTE: Using column `mo` as input for `col_mo`.</span>
@ -1175,13 +1158,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="co">#&gt; 4 Gram-negative AMX 227 0 405 632</span>
<span class="co">#&gt; NOTE: Use 'format()' on this result to get a publicable/printable format.</span></code></pre></div>
<p>You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R <code><a href="https://rdrr.io/r/base/format.html">format()</a></code> function:</p>
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="https://rdrr.io/r/base/format.html">format</a></span><span class="op">(</span><span class="va">x</span>, combine_IR <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
</li>
<li>
<p>Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for <code>portion_*</code> functions or <code>count_*</code> functions. This can be used to determine the empiric susceptibility of a combination therapy. A new argument <code>only_all_tested</code> (<strong>which defaults to <code>FALSE</code></strong>) replaces the old <code>also_single_tested</code> and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the <code>portion</code> and <code>count</code> help pages), where the %SI is being determined:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># --------------------------------------------------------------------</span>
<span class="co"># only_all_tested = FALSE only_all_tested = TRUE</span>
@ -1203,7 +1186,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p><code>tibble</code> printing support for classes <code>rsi</code>, <code>mic</code>, <code>disk</code>, <code>ab</code> <code>mo</code>. When using <code>tibble</code>s containing antimicrobial columns, values <code>S</code> will print in green, values <code>I</code> will print in yellow and values <code>R</code> will print in red. Microbial IDs (class <code>mo</code>) will emphasise on the genus and species, not on the kingdom.</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># (run this on your own console, as this page does not support colour printing)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
@ -1285,7 +1268,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Function <code><a href="../reference/proportion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code>portion_df()</code> to immediately show resistance percentages and number of available isolates:</p>
<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op">%&gt;%</span>
@ -1312,7 +1295,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li>UPEC (Uropathogenic <em>E. coli</em>)</li>
</ul>
<p>All these lead to the microbial ID of <em>E. coli</em>:</p>
<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"UPEC"</span><span class="op">)</span>
<span class="co"># B_ESCHR_COL</span>
@ -1416,7 +1399,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>when all values are unique it now shows a message instead of a warning</p></li>
<li>
<p>support for boxplots:</p>
<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%&gt;%</span>
@ -1509,7 +1492,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/AMR-deprecated.html">filter_aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>
<span class="fu"><a href="../reference/AMR-deprecated.html">filter_carbapenems</a></span><span class="op">(</span><span class="op">)</span>
@ -1523,7 +1506,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="fu"><a href="../reference/AMR-deprecated.html">filter_macrolides</a></span><span class="op">(</span><span class="op">)</span>
<span class="fu"><a href="../reference/AMR-deprecated.html">filter_tetracyclines</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/AMR-deprecated.html">filter_glycopeptides</a></span><span class="op">(</span>result <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span>
<span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span>
@ -1532,7 +1515,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">ab_property</span> <span class="op">-&gt;</span> <span class="fu">atc_property</span><span class="op">(</span><span class="op">)</span>
<span class="va">ab_name</span> <span class="op">-&gt;</span> <span class="fu">atc_name</span><span class="op">(</span><span class="op">)</span>
@ -1553,7 +1536,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic AMR data analysis per age group.</p></li>
<li>
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="../reference/plot.html">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span><span class="va">septic_patients</span>, col_ab <span class="op">=</span> <span class="st">"amox"</span><span class="op">)</span>
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
@ -1561,13 +1544,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/AMR-deprecated.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span>
<span class="co"># or</span>
<span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
<p>is equal to:</p>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>only_firsts <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>
@ -1600,7 +1583,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># mo_fullname() uses as.mo() internally</span>
@ -1612,7 +1595,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># equal:</span>
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">...</span>, allow_uncertain <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
@ -1627,7 +1610,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</p></li>
<li>
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"qwerty"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span>
<span class="co"># Warning: </span>
@ -1677,7 +1660,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
<span class="co"># OLD WAY</span>
@ -1760,7 +1743,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Fewer than 3 characters as input for <code>as.mo</code> will return NA</p></li>
<li>
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. species"</span><span class="op">)</span> <span class="co"># B_ESCHR</span>
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"E. spp."</span><span class="op">)</span> <span class="co"># "Escherichia species"</span>
@ -1777,7 +1760,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ul>
<li>
<p>Support for grouping variables, test with:</p>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span>
@ -1785,7 +1768,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
<li>
<p>Support for (un)selecting columns:</p>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%&gt;%</span>
@ -1864,7 +1847,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
<span class="co"># [1] "Gram negative"</span>
@ -1875,7 +1858,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="fu"><a href="../reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="st">"S. group A"</span>, language <span class="op">=</span> <span class="st">"pt"</span><span class="op">)</span> <span class="co"># Portuguese</span>
<span class="co"># [1] "Streptococcus grupo A"</span></code></pre></div>
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"Esc blattae"</span><span class="op">)</span>
<span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span>
@ -1890,7 +1873,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Function <code>is.rsi.eligible</code> to check for columns that have valid antimicrobial results, but do not have the <code>rsi</code> class yet. Transform the columns of your raw data with: <code>data %&gt;% mutate_if(is.rsi.eligible, as.rsi)</code></p></li>
<li>
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>
<span class="co"># [1] B_ESCHR_COL</span>
@ -1899,7 +1882,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S group A"</span><span class="op">)</span>
<span class="co"># [1] B_STRPTC_GRA</span></code></pre></div>
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">thousands_of_E_colis</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html">rep</a></span><span class="op">(</span><span class="st">"E. coli"</span>, <span class="fl">25000</span><span class="op">)</span>
<span class="fu">microbenchmark</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span><span class="op">(</span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">thousands_of_E_colis</span><span class="op">)</span>, unit <span class="op">=</span> <span class="st">"s"</span><span class="op">)</span>
@ -1933,7 +1916,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</p></li>
<li>
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
<div class="sourceCode" id="cb48"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu">ab_official</span><span class="op">(</span><span class="st">"Bactroban"</span><span class="op">)</span>
<span class="co"># [1] "Mupirocin"</span>
@ -1950,7 +1933,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added arguments <code>minimum</code> and <code>as_percent</code> to <code>portion_df</code></p></li>
<li>
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb48"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">septic_patients</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">amox</span>, <span class="va">cipr</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span><span class="op">(</span><span class="op">)</span>
<span class="co"># which is the same as:</span>
@ -1970,12 +1953,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Added longest en shortest character length in the frequency table (<code>freq</code>) header of class <code>character</code></p></li>
<li>
<p>Support for types (classes) list and matrix for <code>freq</code></p>
<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
<span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
<p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb51"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
<span class="va">my_list</span> <span class="op">%&gt;%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>

2
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View File

@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-05-20T13:05Z
last_built: 2021-05-21T18:20Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

2
docs/reference/AMR-deprecated.html
View File

@ -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">1.6.0.9048</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
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View File

@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
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@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/ab_property.html
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@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
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@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
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@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/antibiotic_class_selectors.html
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@ -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">1.6.0.9048</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/as.ab.html
View File

@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/as.disk.html
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@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/as.mic.html
View File

@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/as.mo.html
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@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/as.rsi.html
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@ -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">1.6.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/atc_online.html
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@ -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">1.6.0.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/bug_drug_combinations.html
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@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/count.html
View File

@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/eucast_rules.html
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@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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">1.6.0.9048</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/example_isolates.html
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@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/first_isolate.html
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@ -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">1.6.0.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/g.test.html
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@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/ggplot_pca.html
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@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/ggplot_rsi.html
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@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/guess_ab_col.html
View File

@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/index.html
View File

@ -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">1.6.0.9054</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/italicise_taxonomy.html
View File

@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/join.html
View File

@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/key_antimicrobials.html
View File

@ -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">1.6.0.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/kurtosis.html
View File

@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/like.html
View File

@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/mdro.html
View File

@ -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">1.6.0.9048</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/mo_property.html
View File

@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/pca.html
View File

@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

8
docs/reference/plot.html
View File

@ -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">1.6.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>
@ -258,7 +258,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for mic</span>
<span class='fu'>ggplot</span><span class='op'>(</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"MIC values of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
@ -289,7 +289,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for disk</span>
<span class='fu'>ggplot</span><span class='op'>(</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Disk zones of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,
@ -314,7 +314,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for rsi</span>
<span class='fu'>ggplot</span><span class='op'>(</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></span><span class='op'>(</span>
<span class='va'>data</span>,
mapping <span class='op'>=</span> <span class='cn'>NULL</span>,
title <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Resistance Overview of"</span>, <span class='fu'><a href='https://rdrr.io/r/base/deparse.html'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>substitute</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>,

2
docs/reference/proportion.html
View File

@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/random.html
View File

@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/resistance_predict.html
View File

@ -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">1.6.0.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/rsi_translation.html
View File

@ -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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/reference/skewness.html
View File

@ -83,7 +83,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
</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">1.6.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

2
docs/survey.html
View File

@ -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">1.6.0.9054</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9055</span>
</span>
</div>

10
index.md
View File

@ -1,7 +1,5 @@
# `AMR` (for R) <img src="./logo.png" align="right" height="120px" />
*Note: the rules of 'EUCAST Clinical Breakpoints v11.0 (2021)' are now implemented.*
### What is `AMR` (for R)?
*(To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html).)*
@ -30,13 +28,13 @@ example_isolates %>%
mutate(bacteria = mo_fullname(mo)) %>%
filter(mo_is_gram_negative(), mo_is_intrinsic_resistant(ab = "cefotax")) %>%
select(bacteria, aminoglycosides(), carbapenems())
#> ℹ Using column 'mo' as input for mo_is_gram_negative()
#> ℹ Using column 'mo' as input for mo_is_intrinsic_resistant()
#> ℹ Using column 'mo' as input for `mo_is_gram_negative()`
#> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`
#> ℹ Determining intrinsic resistance based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic
#> Resistance and Unusual Phenotypes' v3.2 (2020)
#> ℹ Applying `aminoglycosides()`: selecting columns 'AMK' (amikacin), 'GEN' (gentamicin), 'KAN'
#> ℹ For `aminoglycosides()` using columns: 'AMK' (amikacin), 'GEN' (gentamicin), 'KAN'
#> (kanamycin) and 'TOB' (tobramycin)
#> ℹ Applying `carbapenems()`: selecting columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For `carbapenems()` using columns: 'IPM' (imipenem) and 'MEM' (meropenem)
```
With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (`mo_is_gram_negative()` and `mo_is_intrinsic_resistant()`) and a column selection on two antibiotic groups (`aminoglycosides()` and `carbapenems()`), the reference data about [all microorganisms](./reference/microorganisms.html) and [all antibiotics](./reference/antibiotics.html) in the `AMR` package make sure you get what you meant:

4
inst/tinytest/test-_misc.R
View File

@ -41,14 +41,14 @@ expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX")))
expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
expect_warning(AMR:::get_column_abx(example_isolates, hard_dependencies = "FUS"))
expect_message(AMR:::get_column_abx(example_isolates, soft_dependencies = "FUS"))
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
}
# we rely on "grouped_tbl" being a class of grouped tibbles, so implement a test that checks for this:
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(hospital_id)))
}

6
inst/tinytest/test-atc_online.R
View File

@ -23,9 +23,9 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
if (pkg_is_available("curl", also_load = FALSE) &&
pkg_is_available("rvest", also_load = FALSE) &&
pkg_is_available("xml2", also_load = FALSE) &&
if (AMR:::pkg_is_available("curl", also_load = FALSE) &&
AMR:::pkg_is_available("rvest", also_load = FALSE) &&
AMR:::pkg_is_available("xml2", also_load = FALSE) &&
tryCatch(curl::has_internet(), error = function(e) FALSE)) {
expect_true(length(atc_online_groups(ab_atc("AMX"))) >= 1)
expect_equal(atc_online_ddd(ab_atc("AMX"), administration = "O"), 1.5)

2
inst/tinytest/test-count.R
View File

@ -53,7 +53,7 @@ expect_error(count_susceptible("test", as_percent = "test"))
expect_error(count_df(c("A", "B", "C")))
expect_error(count_df(example_isolates[, "date"]))
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687)
expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = FALSE), 1764)

4
inst/tinytest/test-disk.R
View File

@ -43,13 +43,13 @@ expect_silent(barplot(as.disk(c(10, 20, 40))))
expect_silent(plot(as.disk(c(10, 20, 40))))
expect_silent(plot(as.disk(c(10, 20, 40)), expand = FALSE))
expect_silent(plot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"))
if (pkg_is_available("ggplot2")) {
if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(ggplot(as.disk(c(10, 20, 40))), "gg")
expect_inherits(ggplot(as.disk(c(10, 20, 40)), expand = FALSE), "gg")
expect_inherits(ggplot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"), "gg")
}
expect_stdout(print(as.disk(12)))
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_stdout(print(tibble(d = as.disk(12))))
}

2
inst/tinytest/test-episode.R
View File

@ -36,7 +36,7 @@ test_df <- rbind(
expect_equal(get_episode(test_df$date, 365),
c(1, 1, 2, 2, 2, 3, 3, 4, 1, 2, 2, 2, 3))
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_identical(test_df %>% group_by(patient_id) %>% mutate(f = is_new_episode(date, 365)) %>% pull(f),
c(TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE))

6
inst/tinytest/test-eucast_rules.R
View File

@ -71,7 +71,7 @@ b <- data.frame(mo = c("Staphylococcus aureus",
expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
# piperacillin must be R in Enterobacteriaceae when tica is R
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_equal(suppressWarnings(
example_isolates %>%
filter(mo_family(mo) == "Enterobacteriaceae") %>%
@ -109,7 +109,7 @@ expect_equal(
"S")
# also test norf
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_stdout(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
}
@ -155,4 +155,4 @@ expect_equal(nrow(eucast_rules(example_isolates,
custom_rules = x,
info = FALSE,
verbose = TRUE)),
8)
8, tolerance = 0.5)

2
inst/tinytest/test-first_isolate.R
View File

@ -110,7 +110,7 @@ expect_error(first_isolate(example_isolates,
col_date = "non-existing col",
col_mo = "mo"))
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
# if mo is not an mo class, result should be the same
expect_identical(example_isolates %>%
mutate(mo = as.character(mo)) %>%

2
inst/tinytest/test-ggplot_rsi.R
View File

@ -23,7 +23,7 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
if (pkg_is_available("dplyr") & pkg_is_available("ggplot2")) {
if (AMR:::pkg_is_available("dplyr") & AMR:::pkg_is_available("ggplot2")) {
pdf(NULL) # prevent Rplots.pdf being created

2
inst/tinytest/test-mdro.R
View File

@ -232,7 +232,7 @@ expect_warning(mdro(example_isolates,
info = FALSE))
# print groups
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_stdout(x <- mdro(example_isolates %>% group_by(hospital_id), info = TRUE))
expect_stdout(x <- mdro(example_isolates %>% group_by(hospital_id), guideline = custom, info = TRUE))
}

14
inst/tinytest/test-mic.R
View File

@ -49,7 +49,7 @@ expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
expect_silent(plot(as.mic(c(1, 2, 4, 8))))
expect_silent(plot(as.mic(c(1, 2, 4, 8)), expand = FALSE))
expect_silent(plot(as.mic(c(1, 2, 4, 8)), mo = "esco", ab = "cipr"))
if (pkg_is_available("ggplot2")) {
if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(ggplot(as.mic(c(1, 2, 4, 8))), "gg")
expect_inherits(ggplot(as.mic(c(1, 2, 4, 8)), expand = FALSE), "gg")
expect_inherits(ggplot(as.mic(c(1, 2, 4, 8, 32)), mo = "esco", ab = "cipr"), "gg")
@ -58,7 +58,7 @@ expect_stdout(print(as.mic(c(1, 2, 4, 8))))
expect_inherits(summary(as.mic(c(2, 8))), c("summaryDefault", "table"))
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_stdout(print(tibble(m = as.mic(2:4))))
}
@ -85,9 +85,11 @@ suppressWarnings(expect_identical(log1p(x), log1p(x_double)))
suppressWarnings(expect_identical(cos(x), cos(x_double)))
suppressWarnings(expect_identical(sin(x), sin(x_double)))
suppressWarnings(expect_identical(tan(x), tan(x_double)))
suppressWarnings(expect_identical(cospi(x), cospi(x_double)))
suppressWarnings(expect_identical(sinpi(x), sinpi(x_double)))
suppressWarnings(expect_identical(tanpi(x), tanpi(x_double)))
if (!AMR:::current_R_older_than(3.1)) {
suppressWarnings(expect_identical(cospi(x), cospi(x_double)))
suppressWarnings(expect_identical(sinpi(x), sinpi(x_double)))
suppressWarnings(expect_identical(tanpi(x), tanpi(x_double)))
}
suppressWarnings(expect_identical(acos(x), acos(x_double)))
suppressWarnings(expect_identical(asin(x), asin(x_double)))
suppressWarnings(expect_identical(atan(x), atan(x_double)))
@ -105,7 +107,7 @@ suppressWarnings(expect_identical(cumsum(x), cumsum(x_double)))
suppressWarnings(expect_identical(cumprod(x), cumprod(x_double)))
suppressWarnings(expect_identical(cummax(x), cummax(x_double)))
suppressWarnings(expect_identical(cummin(x), cummin(x_double)))
suppressWarnings(expect_identical(!x, !(x_double)))
suppressWarnings(expect_identical(!x, !x_double))
suppressWarnings(expect_identical(all(x), all(x_double)))
suppressWarnings(expect_identical(any(x), any(x_double)))

6
inst/tinytest/test-mo.R
View File

@ -144,7 +144,7 @@ expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_S
expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SLVR")
expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRPK") # group K
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
# select with one column
expect_identical(
example_isolates[1:10, ] %>%
@ -273,7 +273,7 @@ expect_equal(as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),
expect_equal(suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))),
c("F_YEAST", "F_FUNGUS"))
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
# print tibble
expect_stdout(print(tibble(mo = as.mo("B_ESCHR_COLI"))))
}
@ -292,6 +292,6 @@ expect_equal(as.character(as.mo(c("E. coli", "E. coli ignorethis"), ignore_patte
c("B_ESCHR_COLI", NA))
# frequency tables
if (pkg_is_available("cleaner")) {
if (AMR:::pkg_is_available("cleaner")) {
expect_inherits(cleaner::freq(example_isolates$mo), "freq")
}

2
inst/tinytest/test-mo_property.R
View File

@ -119,7 +119,7 @@ expect_equal(mo_is_intrinsic_resistant(c("Escherichia coli", "Staphylococcus aur
# with reference data
expect_equal(mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")),
"Escherichia coli")
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),
730)
expect_equal(example_isolates %>% filter(mo_is_gram_positive()) %>% nrow(),

6
inst/tinytest/test-pca.R
View File

@ -42,12 +42,12 @@ expect_inherits(pca_model, "pca")
pdf(NULL) # prevent Rplots.pdf being created
if (pkg_is_available("ggplot2")) {
if (AMR:::pkg_is_available("ggplot2")) {
ggplot_pca(pca_model, ellipse = TRUE)
ggplot_pca(pca_model, arrows_textangled = FALSE)
}
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
resistance_data <- example_isolates %>%
group_by(order = mo_order(mo),
genus = mo_genus(mo)) %>%
@ -56,7 +56,7 @@ if (pkg_is_available("dplyr")) {
pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, "SXT")
expect_inherits(pca_result, "prcomp")
if (pkg_is_available("ggplot2")) {
if (AMR:::pkg_is_available("ggplot2")) {
ggplot_pca(pca_result, ellipse = TRUE)
ggplot_pca(pca_result, ellipse = FALSE, arrows_textangled = FALSE, scale = FALSE)
}

2
inst/tinytest/test-proportion.R
View File

@ -35,7 +35,7 @@ expect_equal(proportion_R(example_isolates$AMX) + proportion_I(example_isolates$
expect_equal(proportion_S(example_isolates$AMX) + proportion_I(example_isolates$AMX),
proportion_SI(example_isolates$AMX))
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_equal(example_isolates %>% proportion_SI(AMC),
0.7626397,
tolerance = 0.0001)

4
inst/tinytest/test-resistance_predict.R
View File

@ -23,7 +23,7 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_stdout(AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COLI") %>%
rsi_predict(col_ab = "AMX",
@ -43,7 +43,7 @@ expect_stdout(x <- suppressMessages(resistance_predict(example_isolates,
info = TRUE)))
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(plot(x))
if (pkg_is_available("ggplot2")) {
if (AMR:::pkg_is_available("ggplot2")) {
expect_silent(ggplot_rsi_predict(x))
expect_silent(ggplot(x))
expect_error(ggplot_rsi_predict(example_isolates))

14
inst/tinytest/test-rsi.R
View File

@ -34,7 +34,7 @@ expect_inherits(unique(x[1], x[9]), "rsi")
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.rsi(c("S", "I", "R"))))
expect_silent(plot(as.rsi(c("S", "I", "R"))))
if (pkg_is_available("ggplot2")) expect_inherits(ggplot(as.rsi(c("S", "I", "R"))), "gg")
if (AMR:::pkg_is_available("ggplot2")) expect_inherits(ggplot(as.rsi(c("S", "I", "R"))), "gg")
expect_stdout(print(as.rsi(c("S", "I", "R"))))
expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))
expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
@ -49,7 +49,7 @@ expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)),
expect_error(as.rsi.mic(as.mic(16)))
expect_error(as.rsi.disk(as.disk(16)))
expect_error(get_guideline("this one does not exist"))
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
# 40 rsi columns
expect_equal(example_isolates %>%
mutate_at(vars(PEN:RIF), as.character) %>%
@ -61,10 +61,10 @@ if (pkg_is_available("dplyr")) {
expect_stdout(print(tibble(ab = as.rsi("S"))))
}
if (pkg_is_available("skimr")) {
if (AMR:::pkg_is_available("skimr")) {
expect_inherits(skim(example_isolates),
"data.frame")
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_inherits(example_isolates %>%
mutate(m = as.mic(2),
d = as.disk(20)) %>%
@ -94,7 +94,7 @@ expect_equal(as.rsi(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020
as.rsi("S"))
expect_equal(as.rsi(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
as.rsi("R"))
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_true(suppressWarnings(example_isolates %>%
mutate(amox_mic = as.mic(2)) %>%
select(mo, amox_mic) %>%
@ -121,7 +121,7 @@ expect_equal(as.character(
ab = "ERY",
guideline = "CLSI")),
"R")
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_true(example_isolates %>%
mutate(amox_disk = as.disk(15)) %>%
select(mo, amox_disk) %>%
@ -130,7 +130,7 @@ if (pkg_is_available("dplyr")) {
is.rsi())
}
# frequency tables
if (pkg_is_available("cleaner")) {
if (AMR:::pkg_is_available("cleaner")) {
expect_inherits(cleaner::freq(example_isolates$AMX), "freq")
}

20
tests/tinytest.R
View File

@ -27,19 +27,15 @@
if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
# env var 'R_LIBS_USER' got overwritten during 'R CMD check' in GitHub Actions, so:
.libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths()))
# helper function
pkg_is_available <- function(pkg, also_load = TRUE) {
if (also_load == TRUE) {
out <- suppressWarnings(require(pkg, character.only = TRUE, warn.conflicts = FALSE, quietly = TRUE))
} else {
out <- requireNamespace(pkg, quietly = TRUE)
}
isTRUE(out)
}
if (pkg_is_available("tinytest")) {
print("here")
if (AMR:::pkg_is_available("tinytest")) {
print("here2")
library(AMR)
out <- test_package("AMR", verbose = FALSE)
out <- test_package("AMR",
testdir = ifelse(AMR:::dir.exists("inst/tinytest"),
"inst/tinytest",
"tinytest"),
verbose = FALSE)
cat(attributes(out)$duration, "\n")
print(summary(out))
}