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(v1.7.1.9018) translation fix

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dr. M.S. (Matthijs) Berends 1 year ago
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17 changed files with 46 additions and 43 deletions
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  1. 4
      DESCRIPTION
  2. 7
      NEWS.md
  3. BIN
      R/sysdata.rda
  4. BIN
      data-raw/AMR_latest.tar.gz
  5. 4
      data-raw/translations.tsv
  6. 2
      docs/404.html
  7. 2
      docs/LICENSE-text.html
  8. 4
      docs/articles/datasets.html
  9. 2
      docs/articles/index.html
  10. 2
      docs/authors.html
  11. 10
      docs/index.html
  12. 15
      docs/news/index.html
  13. 2
      docs/pkgdown.yml
  14. 2
      docs/reference/index.html
  15. 2
      docs/survey.html
  16. 15
      index.md
  17. 16
      inst/tinytest/test-get_locale.R

4
DESCRIPTION
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@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
Package: AMR
Version: 1.7.1.9017
Date: 2021-07-08
Version: 1.7.1.9018
Date: 2021-07-11
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(
person(role = c("aut", "cre"),

7
NEWS.md
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# `AMR` 1.7.1.9017
## <small>Last updated: 8 July 2021</small>
# `AMR` 1.7.1.9018
## <small>Last updated: 11 July 2021</small>
### Changed
* Antibiotic class selectors (see `ab_class()`)
@ -18,7 +18,8 @@ @@ -18,7 +18,8 @@
* When warnings are throws because of too few isolates in any `count_*()`, `proportion_*()` function (or `resistant()` or `susceptible()`), the `dplyr` group will be shown, if available
* Taxonomic names now print in italic in tibbles, if created with `mo_name()`, `mo_fullname()`, `mo_shortname()`, `mo_genus()` or `mo_family()`
* `ab_name()` gained argument `snake_case`, which is useful for column renaming
* Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is `ggplot2` bug #4511, soon to be fixed)
* Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is bug ggplot2#4511, soon to be fixed)
* Fix for minor translation errors
# `AMR` 1.7.1

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data-raw/translations.tsv
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@ -17,8 +17,8 @@ unknown species TRUE TRUE FALSE TRUE unbekannte Art onbekende soort especie desc @@ -17,8 +17,8 @@ unknown species TRUE TRUE FALSE TRUE unbekannte Art onbekende soort especie desc
unknown subspecies TRUE TRUE FALSE TRUE unbekannte Unterart onbekende ondersoort subespecie desconocida sottospecie sconosciute sous-espèce inconnue subespécies desconhecida
unknown rank TRUE TRUE FALSE TRUE unbekannter Rang onbekende rang rango desconocido grado sconosciuto rang inconnu classificação desconhecido
group TRUE TRUE FALSE TRUE Gruppe groep grupo gruppo groupe grupo
CoNS FALSE TRUE FALSE FALSE KNS CNS SCN
CoPS FALSE TRUE FALSE FALSE KPS CPS SCP
CoNS FALSE TRUE FALSE TRUE KNS CNS SCN
CoPS FALSE TRUE FALSE TRUE KPS CPS SCP
Gram-negative TRUE TRUE FALSE FALSE Gramnegativ Gram-negatief Gram negativo Gram negativo Gram négatif Gram negativo
Gram-positive TRUE TRUE FALSE FALSE Grampositiv Gram-positief Gram positivo Gram positivo Gram positif Gram positivo
^Bacteria$ TRUE TRUE FALSE FALSE Bakterien Bacteriën Bacterias Batteri Bactéries Bactérias

1 pattern regular_expr case_sensitive affect_ab_name affect_mo_name de nl es it fr pt
17 unknown subspecies TRUE TRUE FALSE TRUE unbekannte Unterart onbekende ondersoort subespecie desconocida sottospecie sconosciute sous-espèce inconnue subespécies desconhecida
18 unknown rank TRUE TRUE FALSE TRUE unbekannter Rang onbekende rang rango desconocido grado sconosciuto rang inconnu classificação desconhecido
19 group TRUE TRUE FALSE TRUE Gruppe groep grupo gruppo groupe grupo
20 CoNS FALSE TRUE FALSE FALSE TRUE KNS CNS SCN
21 CoPS FALSE TRUE FALSE FALSE TRUE KPS CPS SCP
22 Gram-negative TRUE TRUE FALSE FALSE Gramnegativ Gram-negatief Gram negativo Gram negativo Gram négatif Gram negativo
23 Gram-positive TRUE TRUE FALSE FALSE Grampositiv Gram-positief Gram positivo Gram positivo Gram positif Gram positivo
24 ^Bacteria$ TRUE TRUE FALSE FALSE Bakterien Bacteriën Bacterias Batteri Bactéries Bactérias

2
docs/404.html
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@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
</span>
</div>

4
docs/articles/datasets.html
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@ -39,7 +39,7 @@ @@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
</span>
</div>
@ -192,7 +192,7 @@ @@ -192,7 +192,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 class="date">08 July 2021</h4>
<h4 class="date">11 July 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>

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docs/articles/index.html
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@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
</span>
</div>

2
docs/authors.html
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@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
</span>
</div>

10
docs/index.html
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@ -42,7 +42,7 @@ @@ -42,7 +42,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
</span>
</div>
@ -382,17 +382,17 @@ @@ -382,17 +382,17 @@
<div id="latest-development-version" class="section level4">
<h4 class="hasAnchor">
<a href="#latest-development-version" class="anchor"></a>Latest development version</h4>
<p>[R-code-check][<a href="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" class="uri">https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master</a>](<a href="https://github.com/msberends/AMR/actions" class="uri">https://github.com/msberends/AMR/actions</a>) [CodeFactor][<a href="https://www.codefactor.io/repository/github/msberends/amr/badge" class="uri">https://www.codefactor.io/repository/github/msberends/amr/badge</a>](<a href="https://www.codefactor.io/repository/github/msberends/amr" class="uri">https://www.codefactor.io/repository/github/msberends/amr</a>) [Codecov][<a href="https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg" class="uri">https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg</a>](<a href="https://codecov.io/gh/msberends/AMR?branch=master" class="uri">https://codecov.io/gh/msberends/AMR?branch=master</a>)</p>
<p><a href="https://codecov.io/gh/msberends/AMR?branch=master"><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" alt="R-code-check"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=master"><img src="https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg" alt="Codecov"></a></p>
<p>The latest and unpublished development version can be installed from GitHub in two ways:</p>
<ol>
<li>
<p>Directly, using:</p>
<p>Manually, using:</p>
<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>
<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>
</li>
<li>
<p>From the <a href="https://ropensci.org/r-universe/">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev">our R-universe address</a> to your list of repositories (‘repos’):</p>
<p>Automatically, using the <a href="https://ropensci.org/r-universe/">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev">our R-universe address</a> to your list of repositories (‘repos’):</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/options.html">options</a></span><span class="op">(</span>repos <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="fu"><a href="https://rdrr.io/r/base/options.html">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,
msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
@ -405,7 +405,7 @@ @@ -405,7 +405,7 @@
<div id="get-started" class="section level3">
<h3 class="hasAnchor">
<a href="#get-started" class="anchor"></a>Get started</h3>
<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click the links in the ‘How to’ menu.</p>
<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
</div>
<div id="short-introduction" class="section level3">
<h3 class="hasAnchor">

15
docs/news/index.html
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@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
</span>
</div>
@ -236,12 +236,12 @@ @@ -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-1719017" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9017">
<a href="#amr-1719017" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9017</h1>
<div id="last-updated-8-july-2021" class="section level2">
<div id="amr-1719018" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9018">
<a href="#amr-1719018" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9018</h1>
<div id="last-updated-11-july-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-8-july-2021" class="anchor"></a><small>Last updated: 8 July 2021</small>
<a href="#last-updated-11-july-2021" class="anchor"></a><small>Last updated: 11 July 2021</small>
</h2>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
@ -273,7 +273,8 @@ @@ -273,7 +273,8 @@
</li>
<li>
<code><a href="../reference/ab_property.html">ab_name()</a></code> gained argument <code>snake_case</code>, which is useful for column renaming</li>
<li>Fix for legends created with <code><a href="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code> when using <code>ggplot2</code> v3.3.4 or higher (this is <code>ggplot2</code> bug <a href='https://github.com/msberends/AMR/issues/4511'>#4511</a>, soon to be fixed)</li>
<li>Fix for legends created with <code><a href="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code> when using <code>ggplot2</code> v3.3.4 or higher (this is bug ggplot2<a href='https://github.com/msberends/AMR/issues/4511'>#4511</a>, soon to be fixed)</li>
<li>Fix for minor translation errors</li>
</ul>
</div>
</div>

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles: @@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-07-08T21:03Z
last_built: 2021-07-11T11:19Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

2
docs/reference/index.html
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@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
</span>
</div>

2
docs/survey.html
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@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9018</span>
</span>
</div>

15
index.md
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@ -110,30 +110,33 @@ It will be downloaded and installed automatically. For RStudio, click on the men @@ -110,30 +110,33 @@ It will be downloaded and installed automatically. For RStudio, click on the men
#### Latest development version
![R-code-check][https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master](https://github.com/msberends/AMR/actions)
![CodeFactor][https://www.codefactor.io/repository/github/msberends/amr/badge](https://www.codefactor.io/repository/github/msberends/amr)
![Codecov][https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg](https://codecov.io/gh/msberends/AMR?branch=master)
[![R-code-check](https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master)](https://codecov.io/gh/msberends/AMR?branch=master)
[![CodeFactor](https://www.codefactor.io/repository/github/msberends/amr/badge)](https://www.codefactor.io/repository/github/msberends/amr)
[![Codecov](https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gh/msberends/AMR?branch=master)
The latest and unpublished development version can be installed from GitHub in two ways:
1. Directly, using:
1. Manually, using:
```r
install.packages("remotes") # if you haven't already
remotes::install_github("msberends/AMR")
```
2. From the [rOpenSci R-universe platform](https://ropensci.org/r-universe/), by adding [our R-universe address](https://msberends.r-universe.dev) to your list of repositories ('repos'):
2. Automatically, using the [rOpenSci R-universe platform](https://ropensci.org/r-universe/), by adding [our R-universe address](https://msberends.r-universe.dev) to your list of repositories ('repos'):
```r
options(repos = c(getOption("repos"),
msberends = "https://msberends.r-universe.dev"))
```
After this, you can install and update this `AMR` package like any official release (e.g., using `install.packages("AMR")` or in RStudio via *Tools* > *Check for Package Updates...*).
You can also download the latest build from our repository: <https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz>
### Get started
To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click the links in the 'How to' menu.
To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click a link in the ['How to' menu](https://msberends.github.io/AMR/articles/).
### Short introduction

16
inst/tinytest/test-get_locale.R
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@ -23,12 +23,10 @@ @@ -23,12 +23,10 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_identical(as.character(mo_genus("B_GRAMP", language = "pt")),
"(Gram positivos desconhecidos)")
expect_identical(as.character(mo_fullname("CoNS", "en")), "Coagulase-negative Staphylococcus (CoNS)")
expect_identical(as.character(mo_fullname("CoNS", "de")), "Koagulase-negative Staphylococcus (KNS)")
expect_identical(as.character(mo_fullname("CoNS", "nl")), "Coagulase-negatieve Staphylococcus (CNS)")
expect_identical(as.character(mo_fullname("CoNS", "es")), "Staphylococcus coagulasa negativo (SCN)")
expect_identical(as.character(mo_fullname("CoNS", "it")), "Staphylococcus negativo coagulasi (CoNS)")
expect_identical(as.character(mo_fullname("CoNS", "pt")), "Staphylococcus coagulase negativo (CoNS)")
expect_identical(mo_genus("B_GRAMP", language = "pt"), "(Gram positivos desconhecidos)")
expect_identical(mo_fullname("CoNS", "en"), "Coagulase-negative Staphylococcus (CoNS)")
expect_identical(mo_fullname("CoNS", "de"), "Koagulase-negative Staphylococcus (KNS)")
expect_identical(mo_fullname("CoNS", "nl"), "Coagulase-negatieve Staphylococcus (CNS)")
expect_identical(mo_fullname("CoNS", "es"), "Staphylococcus coagulasa negativo (SCN)")
expect_identical(mo_fullname("CoNS", "it"), "Staphylococcus negativo coagulasi (CoNS)")
expect_identical(mo_fullname("CoNS", "pt"), "Staphylococcus coagulase negativo (CoNS)")

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