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(v1.6.0.9043) translation update

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dr. M.S. (Matthijs) Berends 2021-05-17 19:43:01 +02:00
parent 83fec69a03
commit be49131ed7
22 changed files with 132 additions and 123 deletions
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3
.github/workflows/check.yaml vendored
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@ -109,9 +109,10 @@ jobs:
key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4 key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
- name: Install AMR and tinytest and update dependencies - name: Install AMR and tinytest and update dependencies
# some old R instances have trouble installing tinytest, so we ship it too
run: | run: |
install.packages("data-raw/AMR_latest.tar.gz") install.packages("data-raw/AMR_latest.tar.gz")
install.packages("data-raw/tinytest_1.2.4.tar.gz") trimws <- AMR:::trimws; install.packages("data-raw/tinytest_1.2.4.tar.gz")
source("data-raw/_install_deps.R") source("data-raw/_install_deps.R")
shell: Rscript {0} shell: Rscript {0}

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.6.0.9042 Version: 1.6.0.9043
Date: 2021-05-17 Date: 2021-05-17
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# `AMR` 1.6.0.9042 # `AMR` 1.6.0.9043
## <small>Last updated: 17 May 2021</small> ## <small>Last updated: 17 May 2021</small>
### New ### New

2
R/first_isolate.R
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@ -50,7 +50,7 @@
#' @details #' @details
#' To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below. #' To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below.
#' #'
#' These functions are context-aware. This means that then the `x` argument can be left blank, see *Examples*. #' These functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
#' #'
#' The [first_isolate()] function is a wrapper around the [is_new_episode()] function, but more efficient for data sets containing microorganism codes or names. #' The [first_isolate()] function is a wrapper around the [is_new_episode()] function, but more efficient for data sets containing microorganism codes or names.
#' #'

2
R/key_antimicrobials.R
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@ -37,7 +37,7 @@
#' @param only_rsi_columns a [logical] to indicate whether only columns must be included that were transformed to class `<rsi>` (see [as.rsi()]) on beforehand (defaults to `FALSE`) #' @param only_rsi_columns a [logical] to indicate whether only columns must be included that were transformed to class `<rsi>` (see [as.rsi()]) on beforehand (defaults to `FALSE`)
#' @param ... ignored, only in place to allow future extensions #' @param ... ignored, only in place to allow future extensions
#' @details #' @details
#' The [key_antimicrobials()] and [all_antimicrobials()] functions are context-aware. This means that then the `x` argument can be left blank, see *Examples*. #' The [key_antimicrobials()] and [all_antimicrobials()] functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
#' #'
#' The function [key_antimicrobials()] returns a [character] vector with 12 antimicrobial results for every isolate. The function [all_antimicrobials()] returns a [character] vector with all antimicrobial results for every isolate. These vectors can then be compared using [antimicrobials_equal()], to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (`"."`) by [key_antimicrobials()] and ignored by [antimicrobials_equal()]. #' The function [key_antimicrobials()] returns a [character] vector with 12 antimicrobial results for every isolate. The function [all_antimicrobials()] returns a [character] vector with all antimicrobial results for every isolate. These vectors can then be compared using [antimicrobials_equal()], to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (`"."`) by [key_antimicrobials()] and ignored by [antimicrobials_equal()].
#' #'

2
R/mdro.R
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@ -37,7 +37,7 @@
#' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not. #' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
#' @inheritSection eucast_rules Antibiotics #' @inheritSection eucast_rules Antibiotics
#' @details #' @details
#' These functions are context-aware. This means that then the `x` argument can be left blank, see *Examples*. #' These functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
#' #'
#' For the `pct_required_classes` argument, values above 1 will be divided by 100. This is to support both fractions (`0.75` or `3/4`) and percentages (`75`). #' For the `pct_required_classes` argument, values above 1 will be divided by 100. This is to support both fractions (`0.75` or `3/4`) and percentages (`75`).
#' #'

2
R/mo.R
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@ -469,7 +469,7 @@ exec_as.mo <- function(x,
x <- strip_whitespace(x, dyslexia_mode) x <- strip_whitespace(x, dyslexia_mode)
# translate 'unknown' names back to English # translate 'unknown' names back to English
if (any(x %like% "unbekannt|onbekend|desconocid|sconosciut|iconnu|desconhecid", na.rm = TRUE)) { if (any(x %like% "unbekannt|onbekend|desconocid|sconosciut|iconnu|desconhecid", na.rm = TRUE)) {
trns <- subset(translations_file, pattern %like% "unknown" | only_affect_mo_names == TRUE) trns <- subset(translations_file, pattern %like% "unknown" | affect_mo_name == TRUE)
langs <- LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"] langs <- LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]
for (l in langs) { for (l in langs) {
for (i in seq_len(nrow(trns))) { for (i in seq_len(nrow(trns))) {

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data-raw/AMR_latest.tar.gz
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docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9042</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9043</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9042</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9043</span>
</span> </span>
</div> </div>

2
docs/articles/datasets.html
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@ -39,7 +39,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9042</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9043</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9042</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9043</span>
</span> </span>
</div> </div>

9
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9042</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9043</span>
</span> </span>
</div> </div>
@ -236,13 +236,14 @@
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/inst/CITATION'><code>inst/CITATION</code></a></small> <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/inst/CITATION'><code>inst/CITATION</code></a></small>
</div> </div>
<p>Berends MS, Luz CF et al. (2021). AMR - An R Package for Working with Antimicrobial Resistance Data. bioRxiv, https://doi.org/10.1101/810622</p> <p>Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2021). AMR - An R Package for Working with
Antimicrobial Resistance Data. Journal of Statistical Software (accepted for publication), https://www.biorxiv.org/content/10.1101/810622v4</p>
<pre>@Article{, <pre>@Article{,
title = {AMR - An R Package for Working with Antimicrobial Resistance Data}, title = {AMR - An R Package for Working with Antimicrobial Resistance Data},
author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner}, author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner},
doi = {1.24720276528394e-05}, doi = {1.24720276528394e-05},
journal = {bioRxiv}, journal = {Journal of Statistical Software},
publisher = {Cold Spring Harbor Laboratory}, pages = {Accepted for publication},
year = {2021}, year = {2021},
url = {https://www.biorxiv.org/content/10.1101/810622v4}, url = {https://www.biorxiv.org/content/10.1101/810622v4},
}</pre> }</pre>

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docs/index.html
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@ -1,37 +1,76 @@
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data analysis and to work with microbial and antimicrobial properties by
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@ -42,13 +81,13 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9042</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9043</span>
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@ -64,7 +103,7 @@
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<a href="articles/AMR.html"> <a href="articles/AMR.html">
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@ -165,8 +204,8 @@
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@ -181,21 +220,23 @@
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<h1>AMR (for R) </h1>
</div>
<div id="amr-for-r-" class="section level1"> <div id="amr-for-r-" class="section level1">
<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> <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"> <div id="what-is-amr-for-r" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -218,9 +259,9 @@
<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="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> <span class="va">example_isolates</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>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://rdrr.io/pkg/dplyr/man/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://rdrr.io/pkg/dplyr/man/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="fu"><a href="https://rdrr.io/pkg/dplyr/man/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; NOTE: Using column 'mo' as input for mo_is_gram_negative()</span> <span class="co">#&gt; NOTE: Using column 'mo' as input for mo_is_gram_negative()</span>
<span class="co">#&gt; NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant()</span> <span class="co">#&gt; NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant()</span>
<span class="co">#&gt; NOTE: Determining intrinsic resistance based on 'EUCAST Expert Rules' and</span> <span class="co">#&gt; NOTE: Determining intrinsic resistance based on 'EUCAST Expert Rules' and</span>
@ -229,7 +270,7 @@
<span class="co">#&gt; 'KAN' (kanamycin) and 'TOB' (tobramycin)</span> <span class="co">#&gt; 'KAN' (kanamycin) and 'TOB' (tobramycin)</span>
<span class="co">#&gt; Selecting carbapenems: columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></code></pre></div> <span class="co">#&gt; Selecting carbapenems: 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> <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"> <table>
<thead><tr class="header"> <thead><tr class="header">
<th align="left">bacteria</th> <th align="left">bacteria</th>
<th align="center">AMK</th> <th align="center">AMK</th>
@ -391,7 +432,7 @@
<p>The latest and unpublished development version can be installed from GitHub using:</p> <p>The latest and unpublished development version can be installed from GitHub using:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span>
<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div> <span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/remotes/man/install_github.html">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
<p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz" class="uri">https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz</a></p> <p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz" class="uri">https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz</a></p>
</div> </div>
</div> </div>
@ -453,7 +494,7 @@
<li> <li>
<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p> <p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
<ul> <ul>
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>, <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>, <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>)</li> <li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>, <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>, <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code><a href="https://rdrr.io/pkg/dplyr/man/summarise.html">summarise()</a></code>)</li>
<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li> <li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code> function</li> <li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code> function</li>
</ul> </ul>
@ -500,59 +541,22 @@
</ul> </ul>
</div> </div>
</div> </div>
</div> </div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<div class="links"> <nav id="toc" data-toggle="toc" class="sticky-top">
<h2>Links</h2> <h2 data-toc-skip>Contents</h2>
<ul class="list-unstyled"> </nav>
<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=AMR">https://​cloud.r-project.org/​package=AMR</a>
</li>
<li>Browse source code at <br><a href="https://github.com/msberends/AMR/">https://​github.com/​msberends/​AMR/​</a>
</li>
<li>Report a bug at <br><a href="https://github.com/msberends/AMR/issues">https://​github.com/​msberends/​AMR/​issues</a>
</li>
</ul>
</div>
<div class="license">
<h2>License</h2>
<ul class="list-unstyled">
<li>
<a href="https://www.r-project.org/Licenses/GPL-2">GPL-2</a> | file <a href="LICENSE-text.html">LICENSE</a>
</li>
</ul>
</div>
<div class="citation">
<h2>Citation</h2>
<ul class="list-unstyled">
<li><a href="authors.html">Citing AMR</a></li>
</ul>
</div>
<div class="developers">
<h2>Developers</h2>
<ul class="list-unstyled">
<li>
<a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a> <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>
<a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a> <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>
<a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-4881-038X" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>
<a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>
<a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0002-9213-6743" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>
<a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li><a href="authors.html">All authors...</a></li>
</ul>
</div>
</div> </div>
</div> </div>
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p> <footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div> </div>
<div class="pkgdown"> <div class="pkgdown">
@ -560,10 +564,12 @@
</div> </div>
</footer> </footer>
</div> </div>
</body> </body>
</html> </html>

8
docs/news/index.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9042</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9043</span>
</span> </span>
</div> </div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1609042" class="section level1"> <div id="amr-1609043" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9042"> <h1 class="page-header" data-toc-text="1.6.0.9043">
<a href="#amr-1609042" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9042</h1> <a href="#amr-1609043" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9043</h1>
<div id="last-updated-17-may-2021" class="section level2"> <div id="last-updated-17-may-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-17-may-2021" class="anchor"></a><small>Last updated: 17 May 2021</small> <a href="#last-updated-17-may-2021" class="anchor"></a><small>Last updated: 17 May 2021</small>

2
docs/pkgdown.yml
View File

@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-05-17T09:24Z last_built: 2021-05-17T17:42Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

2
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9042</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9043</span>
</span> </span>
</div> </div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9042</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9043</span>
</span> </span>
</div> </div>

7
inst/CITATION
View File

@ -5,11 +5,12 @@ citEntry(
title = "AMR - An R Package for Working with Antimicrobial Resistance Data", title = "AMR - An R Package for Working with Antimicrobial Resistance Data",
author = "M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner", author = "M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner",
doi = {10.1101/810622}, doi = {10.1101/810622},
journal = "bioRxiv", journal = "Journal of Statistical Software",
publisher = "Cold Spring Harbor Laboratory", pages = "Accepted for publication",
year = 2021, year = 2021,
url = "https://www.biorxiv.org/content/10.1101/810622v4", url = "https://www.biorxiv.org/content/10.1101/810622v4",
textVersion = "Berends MS, Luz CF et al. (2021). AMR - An R Package for Working with Antimicrobial Resistance Data. bioRxiv, https://doi.org/10.1101/810622" textVersion = "Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2021). AMR - An R Package for Working with
Antimicrobial Resistance Data. Journal of Statistical Software (accepted for publication), https://www.biorxiv.org/content/10.1101/810622v4"
) )
citFooter("This preprint was accepted for publication in the Journal of Statistical Software, but we are awaiting the actual publication. Many thanks for using our open-source method to work with microbial and antimicrobial data!") citFooter("This preprint was accepted for publication in the Journal of Statistical Software, but we are awaiting the actual publication. Many thanks for using our open-source method to work with microbial and antimicrobial data!")

2
man/first_isolate.Rd
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@ -95,7 +95,7 @@ Determine first (weighted) isolates of all microorganisms of every patient per e
\details{ \details{
To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below. To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below.
These functions are context-aware. This means that then the \code{x} argument can be left blank, see \emph{Examples}. These functions are context-aware. This means that the \code{x} argument can be left blank if used inside a \link{data.frame} call, see \emph{Examples}.
The \code{\link[=first_isolate]{first_isolate()}} function is a wrapper around the \code{\link[=is_new_episode]{is_new_episode()}} function, but more efficient for data sets containing microorganism codes or names. The \code{\link[=first_isolate]{first_isolate()}} function is a wrapper around the \code{\link[=is_new_episode]{is_new_episode()}} function, but more efficient for data sets containing microorganism codes or names.

2
man/key_antimicrobials.Rd
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@ -61,7 +61,7 @@ antimicrobials_equal(
These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see \code{\link[=first_isolate]{first_isolate()}}). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes. These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see \code{\link[=first_isolate]{first_isolate()}}). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes.
} }
\details{ \details{
The \code{\link[=key_antimicrobials]{key_antimicrobials()}} and \code{\link[=all_antimicrobials]{all_antimicrobials()}} functions are context-aware. This means that then the \code{x} argument can be left blank, see \emph{Examples}. The \code{\link[=key_antimicrobials]{key_antimicrobials()}} and \code{\link[=all_antimicrobials]{all_antimicrobials()}} functions are context-aware. This means that the \code{x} argument can be left blank if used inside a \link{data.frame} call, see \emph{Examples}.
The function \code{\link[=key_antimicrobials]{key_antimicrobials()}} returns a \link{character} vector with 12 antimicrobial results for every isolate. The function \code{\link[=all_antimicrobials]{all_antimicrobials()}} returns a \link{character} vector with all antimicrobial results for every isolate. These vectors can then be compared using \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}) by \code{\link[=key_antimicrobials]{key_antimicrobials()}} and ignored by \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}. The function \code{\link[=key_antimicrobials]{key_antimicrobials()}} returns a \link{character} vector with 12 antimicrobial results for every isolate. The function \code{\link[=all_antimicrobials]{all_antimicrobials()}} returns a \link{character} vector with all antimicrobial results for every isolate. These vectors can then be compared using \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}) by \code{\link[=key_antimicrobials]{key_antimicrobials()}} and ignored by \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}.

2
man/mdro.Rd
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@ -80,7 +80,7 @@ Ordered \link{factor} with levels \code{Negative} < \verb{Positive, unconfirmed}
Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines. Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines.
} }
\details{ \details{
These functions are context-aware. This means that then the \code{x} argument can be left blank, see \emph{Examples}. These functions are context-aware. This means that the \code{x} argument can be left blank if used inside a \link{data.frame} call, see \emph{Examples}.
For the \code{pct_required_classes} argument, values above 1 will be divided by 100. This is to support both fractions (\code{0.75} or \code{3/4}) and percentages (\code{75}). For the \code{pct_required_classes} argument, values above 1 will be divided by 100. This is to support both fractions (\code{0.75} or \code{3/4}) and percentages (\code{75}).