diff --git a/DESCRIPTION b/DESCRIPTION index f6d90a95..3cd96180 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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"), diff --git a/NEWS.md b/NEWS.md index 55b4c5a3..e5f5d7f4 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# `AMR` 1.7.1.9017 -## Last updated: 8 July 2021 +# `AMR` 1.7.1.9018 +## Last updated: 11 July 2021 ### Changed * Antibiotic class selectors (see `ab_class()`) @@ -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 diff --git a/R/sysdata.rda b/R/sysdata.rda index 841000a5..e10d4816 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index 639ed4ef..e6a7acbc 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/data-raw/translations.tsv b/data-raw/translations.tsv index 440dd639..803901ec 100644 --- a/data-raw/translations.tsv +++ b/data-raw/translations.tsv @@ -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 diff --git a/docs/404.html b/docs/404.html index 4faddf8a..6eed235a 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9017 + 1.7.1.9018 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 0d494d67..b6205e4a 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9017 + 1.7.1.9018 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index c3fe53b9..6d57e4fb 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 1.7.1.9017 + 1.7.1.9018 @@ -192,7 +192,7 @@

Data sets for download / own use

-

08 July 2021

+

11 July 2021

Source: vignettes/datasets.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index c84e597b..ffb7c393 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9017 + 1.7.1.9018
diff --git a/docs/authors.html b/docs/authors.html index 9733f61b..cc556c79 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9017 + 1.7.1.9018 diff --git a/docs/index.html b/docs/index.html index e787f33d..bf834b2c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.7.1.9017 + 1.7.1.9018 @@ -382,17 +382,17 @@

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 CodeFactor Codecov

The latest and unpublished development version can be installed from GitHub in two ways:

  1. -

    Directly, using:

    +

    Manually, using:

     install.packages("remotes") # if you haven't already
 remotes::install_github("msberends/AMR")
  2. -

    From the rOpenSci R-universe platform, by adding our R-universe address to your list of repositories (‘repos’):

    +

    Automatically, using the rOpenSci R-universe platform, by adding our R-universe address to your list of repositories (‘repos’):

     options(repos = c(getOption("repos"),
                   msberends = "https://msberends.r-universe.dev"))
    @@ -405,7 +405,7 @@

    Get started

    -

    To find out how to conduct AMR data analysis, please continue reading here to get started 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 or click a link in the ‘How to’ menu.

    diff --git a/docs/news/index.html b/docs/news/index.html index 9eb9a769..71053124 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9017 + 1.7.1.9018

    @@ -236,12 +236,12 @@ Source: NEWS.md
-
-

- Unreleased AMR 1.7.1.9017

-
+
+

+ Unreleased AMR 1.7.1.9018

+

-Last updated: 8 July 2021 +Last updated: 11 July 2021

@@ -273,7 +273,8 @@
  • 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

    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index c86399ae..b56f517d 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -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 diff --git a/docs/reference/index.html b/docs/reference/index.html index 012705f2..1694d4c3 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9017 + 1.7.1.9018
    diff --git a/docs/survey.html b/docs/survey.html index 98220aa2..7fc9ddf6 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9017 + 1.7.1.9018
    diff --git a/index.md b/index.md index 3cd7eb10..425e7b33 100644 --- a/index.md +++ b/index.md @@ -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: ### 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 diff --git a/inst/tinytest/test-get_locale.R b/inst/tinytest/test-get_locale.R index b4ce26f1..102c28cf 100644 --- a/inst/tinytest/test-get_locale.R +++ b/inst/tinytest/test-get_locale.R @@ -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)")