diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 7b23dd58..1088df41 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -92,7 +92,7 @@ jobs: key: ${{ runner.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('.github/depends.Rds') }} restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-3- - - name: Install system dependencies + - name: Install Linux dependencies if: runner.os == 'Linux' env: RHUB_PLATFORM: linux-x86_64-ubuntu-gcc @@ -119,7 +119,15 @@ jobs: sessioninfo::session_info(pkgs, include_base = TRUE) shell: Rscript {0} - - name: Check + - name: Check on older R versions + if: matrix.config.r == '3.3' + env: + _R_CHECK_CRAN_INCOMING_: false + run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-build-vignettes" , "--ignore-vignettes"), error_on = "warning", check_dir = "check") + shell: Rscript {0} + + - name: Check on newer R versions + if: matrix.config.r != '3.3' env: _R_CHECK_CRAN_INCOMING_: false run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") diff --git a/DESCRIPTION b/DESCRIPTION index e85e5c97..f30c3e96 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.4.0.9022 -Date: 2020-11-16 +Version: 1.4.0.9023 +Date: 2020-11-17 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 1839e7fa..a80c8cb2 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 1.4.0.9022 -## Last updated: 16 November 2020 +# AMR 1.4.0.9023 +## Last updated: 17 November 2020 ### New * Functions `mo_is_gram_negative()` and `mo_is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria. If you have the `dplyr` package installed, they can even determine the column with microorganisms themselves when used inside `dplyr` verbs: diff --git a/docs/404.html b/docs/404.html index c0c00da4..366719f6 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9022 + 1.4.0.9023 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index bcc79324..05ebc80c 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9022 + 1.4.0.9023 diff --git a/docs/articles/index.html b/docs/articles/index.html index 89a76757..b815de3d 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9022 + 1.4.0.9023 diff --git a/docs/authors.html b/docs/authors.html index 804edbc7..c8229f1c 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9022 + 1.4.0.9023 diff --git a/docs/index.html b/docs/index.html index 8cf902e7..07cdd4a8 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.4.0.9022 + 1.4.0.9023 diff --git a/docs/news/index.html b/docs/news/index.html index 0c08f935..fc57574e 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9022 + 1.4.0.9023 @@ -236,13 +236,13 @@ Source: NEWS.md -
-

-AMR 1.4.0.9022 Unreleased +
+

+AMR 1.4.0.9023 Unreleased

-
+

-Last updated: 16 November 2020 +Last updated: 17 November 2020

@@ -252,14 +252,14 @@

Functions mo_is_gram_negative() and mo_is_gram_positive() as wrappers around mo_gramstain(). They always return TRUE or FALSE (except when the input is NA or the MO code is UNKNOWN), thus always return FALSE for species outside the taxonomic kingdom of Bacteria. If you have the dplyr package installed, they can even determine the column with microorganisms themselves when used inside dplyr verbs:

 example_isolates %>%
-  filter(mo_is_gram_positive())
+  filter(mo_is_gram_positive())
 #> NOTE: Using column `mo` as input for mo_is_gram_positive()

  • Function mo_is_intrinsic_resistant() to test for intrinsic resistance, based on EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2 from 2020. As with the new mo_is_gram_*() functions, if you have the dplyr package installed the column with microorganisms will be automatically determined when used inside dplyr verbs:

     example_isolates %>%
-  filter(mo_is_intrinsic_resistant(ab = "Vancomycin"))
+  filter(mo_is_intrinsic_resistant(ab = "Vancomycin"))
 #> NOTE: Using column `mo` as input for mo_is_intrinsic_resistant()

  • Functions %not_like% and %not_like_case% as wrappers around %like% and %like_case%. The RStudio addin to insert the text " %like% " as provided in this package now iterates over all like variants. So if you have defined the keyboard shortcut Ctrl/Cmd + L to this addin, it will first insert %like% and by pressing it again it will be replaced with %not_like%, etc.

    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 5cdea038..3618acfe 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: 2020-11-16T18:55Z +last_built: 2020-11-17T10:53Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/age_groups.html b/docs/reference/age_groups.html index e0e6de7f..cfadbe73 100644 --- a/docs/reference/age_groups.html +++ b/docs/reference/age_groups.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9021 + 1.4.0.9023

    diff --git a/docs/reference/as.disk.html b/docs/reference/as.disk.html index 650a7dcd..12c1c36c 100644 --- a/docs/reference/as.disk.html +++ b/docs/reference/as.disk.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9021 + 1.4.0.9023
    diff --git a/docs/reference/index.html b/docs/reference/index.html index d7435939..05da0206 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9022 + 1.4.0.9023
    diff --git a/docs/survey.html b/docs/survey.html index 16ad81da..2ec33762 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9022 + 1.4.0.9023