From 0800d332286464b00414d22f38cbe4f9aabb60ec Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Tue, 17 Nov 2020 11:53:56 +0100 Subject: [PATCH] (v1.4.0.9023) unit tests --- .github/workflows/check.yaml | 12 ++++++++++-- DESCRIPTION | 4 ++-- NEWS.md | 4 ++-- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 16 ++++++++-------- docs/pkgdown.yml | 2 +- docs/reference/age_groups.html | 2 +- docs/reference/as.disk.html | 2 +- docs/reference/index.html | 2 +- docs/survey.html | 2 +- 14 files changed, 32 insertions(+), 24 deletions(-) diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 7b23dd58e..1088df41e 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 e85e5c976..f30c3e96f 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 1839e7fae..a80c8cb24 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 c0c00da43..366719f6a 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 bcc79324c..05ebc80cb 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 89a767579..b815de3d1 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 804edbc78..c8229f1c3 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 8cf902e70..07cdd4a81 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 0c08f9356..fc57574e6 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 5cdea0381..3618acfe1 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 e0e6de7f8..cfadbe738 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 650a7dcdf..12c1c36cb 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 d74359390..05da0206c 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 16ad81daf..2ec337622 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9022 + 1.4.0.9023