diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 88dc2760..f32a98e4 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -23,6 +23,8 @@ # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # ==================================================================== # +# This GitHub Actions file runs without ANY dependency, so works on all versions of R since R-3.0. + on: push: branches: @@ -96,12 +98,18 @@ jobs: run: | sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev + - name: Query dependencies + # this will change once a week, so it will cache dependency updates + run: | + writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version") + shell: Rscript {0} + - name: Restore cached R packages # this step will add the step 'Post Restore cached R packages' on a succesful run uses: actions/cache@v2 with: path: ${{ env.R_LIBS_USER }} - key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4 + key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4 - name: Unpack AMR and install R dependencies if: always() diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml index ce3dcfdf..6dd0afaa 100644 --- a/.github/workflows/codecovr.yaml +++ b/.github/workflows/codecovr.yaml @@ -48,12 +48,18 @@ jobs: - uses: r-lib/actions/setup-pandoc@master + - name: Query dependencies + # this will change once a week, so it will cache dependency updates + run: | + writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version") + shell: Rscript {0} + - name: Restore cached R packages # this step will add the step 'Post Restore cached R packages' on a succesful run uses: actions/cache@v2 with: path: ${{ env.R_LIBS_USER }} - key: macOS-latest-r-release-v5-codecovr + key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4 - name: Unpack AMR and install R dependencies run: | @@ -73,6 +79,7 @@ jobs: CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} R_RUN_TINYTEST: true run: | + install.packages("covr", repos = "https://cran.rstudio.com/") library(AMR) library(tinytest) x <- 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")) diff --git a/DESCRIPTION b/DESCRIPTION index ebe46a15..b2b74f41 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.7.1.9000 -Date: 2021-06-04 +Version: 1.7.1.9001 +Date: 2021-06-05 Title: Antimicrobial Resistance Data Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 5e421489..3196c43e 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# `AMR` 1.7.1.9000 -## Last updated: 4 June 2021 +# `AMR` 1.7.1.9001 +## Last updated: 5 June 2021 ### Changed * Added more antibiotic class selectors, such as `lincosamides()` and `lipoglycopeptides()` @@ -8,7 +8,6 @@ # `AMR` 1.7.1 ### Breaking change -* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`) * 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. Examples of how the selectors can be used for filtering: ```r # select columns with results for carbapenems @@ -28,6 +27,7 @@ ``` ### New +* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`) * Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()` * Function `italicise_taxonomy()` to make taxonomic names within a string italic, with support for markdown and ANSI * Support for all four methods to determine first isolates as summarised by Hindler *et al.* (doi: [10.1086/511864](https://doi.org/10.1086/511864)): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default. diff --git a/R/amr.R b/R/amr.R index e86029ce..20345278 100644 --- a/R/amr.R +++ b/R/amr.R @@ -61,7 +61,7 @@ #' Matthijs S. Berends \cr #' m.s.berends \[at\] umcg \[dot\] nl \cr #' University of Groningen -#' Department of Medical Microbiology and Infection Prevention +#' Department of Medical Microbiology and Infection Prevention \cr #' University Medical Center Groningen \cr #' Post Office Box 30001 \cr #' 9700 RB Groningen \cr diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index 84bc2487..b9c5b823 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/data-raw/_install_deps.R b/data-raw/_install_deps.R index 2335d8b5..42aac100 100644 --- a/data-raw/_install_deps.R +++ b/data-raw/_install_deps.R @@ -26,7 +26,6 @@ # some old R instances have trouble installing tinytest, so we ship it too install.packages("data-raw/tinytest_1.2.4.10.tar.gz") install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE) -install.packages("covr", repos = "https://cran.rstudio.com/") pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", unlist(strsplit(packageDescription("AMR", fields = "Suggests"), ", ?"))) cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n") diff --git a/docs/404.html b/docs/404.html index f4b7f40a..b1ca057c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9000 + 1.7.1.9001 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index dc371719..73d7ad02 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9000 + 1.7.1.9001 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index ee42f971..61c3b6a9 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 1.7.1.9000 + 1.7.1.9001 @@ -192,7 +192,7 @@

Data sets for download / own use

-

04 June 2021

+

05 June 2021

Source: vignettes/datasets.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 88db3d47..bfe5c0c4 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9000 + 1.7.1.9001
diff --git a/docs/authors.html b/docs/authors.html index 594ed8e9..32037449 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9000 + 1.7.1.9001 diff --git a/docs/index.html b/docs/index.html index a43dbfde..9df87552 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.7.1.9000 + 1.7.1.9001 diff --git a/docs/news/index.html b/docs/news/index.html index b0ef4737..379fdd32 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9000 + 1.7.1.9001 @@ -236,12 +236,12 @@ Source: NEWS.md -
-

- Unreleased AMR 1.7.1.9000

-
+
+

+ Unreleased AMR 1.7.1.9001

+

-Last updated: 4 June 2021 +Last updated: 5 June 2021

@@ -260,7 +260,6 @@

Breaking change

    -

  • Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using as.rsi())

  • 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. Examples of how the selectors can be used for filtering:

    @@ -286,6 +285,7 @@
 
    
 New
    
 
      
+
    • Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using as.rsi())
      • 
 
    • Function custom_eucast_rules() that brings support for custom AMR rules in eucast_rules()
 
      • 
 
    • Function italicise_taxonomy() to make taxonomic names within a string italic, with support for markdown and ANSI
      • 
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 98b5057d..4fc4fc0d 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: 2021-06-04T19:07Z
+last_built: 2021-06-05T13:10Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles
diff --git a/docs/reference/AMR.html b/docs/reference/AMR.html
index d6e21836..1734524e 100644
--- a/docs/reference/AMR.html
+++ b/docs/reference/AMR.html
@@ -82,7 +82,7 @@
       
       
         AMR (for R)
-        1.7.1
+        1.7.1.9001
    @@ -286,7 +286,7 @@

    Matthijs S. Berends
    m.s.berends [at] umcg [dot] nl
    University of Groningen -Department of Medical Microbiology and Infection Prevention +Department of Medical Microbiology and Infection Prevention
    University Medical Center Groningen
    Post Office Box 30001
    9700 RB Groningen
    diff --git a/docs/reference/antibiotic_class_selectors.html b/docs/reference/antibiotic_class_selectors.html index 2d6925b1..8264b3ac 100644 --- a/docs/reference/antibiotic_class_selectors.html +++ b/docs/reference/antibiotic_class_selectors.html @@ -83,7 +83,7 @@ AMR (for R) - 1.7.1.9000 + 1.7.1.9001

diff --git a/docs/reference/custom_eucast_rules.html b/docs/reference/custom_eucast_rules.html index c9133282..5226a7ba 100644 --- a/docs/reference/custom_eucast_rules.html +++ b/docs/reference/custom_eucast_rules.html @@ -82,7 +82,7 @@ AMR (for R) - 1.7.1.9000 + 1.7.1.9001
diff --git a/docs/reference/index.html b/docs/reference/index.html index 6685715c..9de75c81 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9000 + 1.7.1.9001
diff --git a/docs/survey.html b/docs/survey.html index 7dbfb806..645ca556 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9000 + 1.7.1.9001
diff --git a/man/AMR.Rd b/man/AMR.Rd index 7fcbe362..8fb7ae70 100644 --- a/man/AMR.Rd +++ b/man/AMR.Rd @@ -50,7 +50,7 @@ For suggestions, comments or questions, please contact us at: Matthijs S. Berends \cr m.s.berends [at] umcg [dot] nl \cr University of Groningen -Department of Medical Microbiology and Infection Prevention +Department of Medical Microbiology and Infection Prevention \cr University Medical Center Groningen \cr Post Office Box 30001 \cr 9700 RB Groningen \cr