diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml index 02781777..119b6272 100644 --- a/.github/workflows/codecovr.yaml +++ b/.github/workflows/codecovr.yaml @@ -63,13 +63,16 @@ jobs: - name: Install dependencies run: | - install.packages(c("remotes")) + install.packages(c("remotes", "tinytest")) remotes::install_deps(dependencies = TRUE) remotes::install_cran("covr") + remotes::install_local("data-raw/AMR_latest.tar.gz") shell: Rscript {0} - name: Test coverage run: | + library(AMR) + library(tinytest) 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")) diff --git a/DESCRIPTION b/DESCRIPTION index a22abdee..65aee617 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.6.0.9055 +Version: 1.6.0.9056 Date: 2021-05-21 Title: Antimicrobial Resistance Data Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index a072bbb4..b196d575 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.6.0.9055 +# `AMR` 1.6.0.9056 ## Last updated: 21 May 2021 ### Breaking change diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index ad7e88f3..0ee14808 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/404.html b/docs/404.html index 38a8ac67..0aac421f 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9055 + 1.6.0.9056 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index f5b4cf1e..35cf50ed 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9055 + 1.6.0.9056 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 813b6b9f..3c958f1e 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 1.6.0.9055 + 1.6.0.9056 diff --git a/docs/articles/index.html b/docs/articles/index.html index d7bba97f..5ffc7c1c 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9055 + 1.6.0.9056 diff --git a/docs/authors.html b/docs/authors.html index 154822d2..71994244 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9055 + 1.6.0.9056 diff --git a/docs/index.html b/docs/index.html index f010f426..341f0b57 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.6.0.9055 + 1.6.0.9056 diff --git a/docs/news/index.html b/docs/news/index.html index 29c10024..ec7eb7ec 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9055 + 1.6.0.9056 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

- Unreleased AMR 1.6.0.9055

+
+

+ Unreleased AMR 1.6.0.9056

Last updated: 21 May 2021 @@ -288,7 +288,7 @@
  • Function betalactams() as additional antbiotic column selector and function filter_betalactams() as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
    • -
  • A ggplot() method for resistance_predict() +
  • A ggplot() method for resistance_predict()

    • @@ -384,7 +384,7 @@ #> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"

  • Support for custom MDRO guidelines, using the new custom_mdro_guideline() function, please see mdro() for additional info

    • -

  • ggplot() generics for classes <mic> and <disk>

    • +

  • ggplot() generics for classes <mic> and <disk>

  • Function mo_is_yeast(), which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:

    @@ -441,7 +441,7 @@
 
  • Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent
    • 
 
  • All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)
    • 
 
  • Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see translate)
    • 
-
  • Plotting is now possible with base R using plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion values
    • 
+
  • Plotting is now possible with base R using plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion values
    •
  • Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the microorganisms data set
    • @@ -458,7 +458,7 @@ is.rsi.eligible() now detects if the column name resembles an antibiotic name or code and now returns TRUE 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.
  • Functions get_episode() and is_new_episode() now support less than a day as value for argument episode_days (e.g., to include one patient/test per hour)
  • Argument ampc_cephalosporin_resistance in eucast_rules() now also applies to value “I” (not only “S”)
    • -
  • Functions print() and summary() on a Principal Components Analysis object (pca()) now print additional group info if the original data was grouped using dplyr::group_by() +
  • Functions print() and summary() on a Principal Components Analysis object (pca()) now print additional group info if the original data was grouped using dplyr::group_by()
  • Improved speed and reliability of guess_ab_col(). As this also internally improves the reliability of first_isolate() and mdro(), this might have a slight impact on the results of those functions.
  • Fix for mo_name() when used in other languages than English
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 7cc67ece..b5bf10ad 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: 2021-05-21T18:20Z +last_built: 2021-05-21T18:27Z 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 c3b072be..ab6fcd60 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9055 + 1.6.0.9056
    diff --git a/docs/survey.html b/docs/survey.html index 23b1b330..79119075 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9055 + 1.6.0.9056