diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 9935dcf8..5d1caa33 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -79,11 +79,11 @@ jobs: - {os: macOS-latest, r: '3.2', allowfail: false} - {os: windows-latest, r: '3.2', allowfail: false} - {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: macOS-latest, r: '3.1', allowfail: false} - - {os: windows-latest, r: '3.1', allowfail: false} + # - {os: macOS-latest, r: '3.1', allowfail: false} + # - {os: windows-latest, r: '3.1', allowfail: false} - {os: ubuntu-20.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: macOS-latest, r: '3.0', allowfail: false} - - {os: windows-latest, r: '3.0', allowfail: false} + # - {os: macOS-latest, r: '3.0', allowfail: false} + # - {os: windows-latest, r: '3.0', allowfail: false} - {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} env: diff --git a/DESCRIPTION b/DESCRIPTION index 4bed10aa..98bd8d24 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.7.1.9005 +Version: 1.7.1.9006 Date: 2021-06-22 Title: Antimicrobial Resistance Data Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 84bd537a..adbb8b3b 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.7.1.9005 +# `AMR` 1.7.1.9006 ## Last updated: 22 June 2021 ### Changed diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index e574aea9..af7ee40f 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 78762f55..44eaa5eb 100644 --- a/data-raw/_install_deps.R +++ b/data-raw/_install_deps.R @@ -24,8 +24,8 @@ # ==================================================================== # # some old R instances have trouble installing tinytest, so we ship it too -install.packages("data-raw/tinytest_1.2.4.10.tar.gz", repos = "https://cran.rstudio.com/", type = "source") -install.packages("data-raw/AMR_latest.tar.gz", repos = "https://cran.rstudio.com/", type = "source", dependencies = FALSE) +install.packages("data-raw/tinytest_1.2.4.10.tar.gz") +install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE) pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", unlist(strsplit(packageDescription("AMR", fields = "Suggests"), ", ?"))) cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n") @@ -36,7 +36,7 @@ if (length(to_install) == 0) { } for (i in seq_len(length(to_install))) { cat("Installing package", to_install[i], "\n") - tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = TRUE, quiet = TRUE), + tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = TRUE, quiet = FALSE), # message = function(m) invisible(), warning = function(w) message(w$message), error = function(e) message(e$message)) diff --git a/docs/404.html b/docs/404.html index 889cf6fb..12093c5c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9005 + 1.7.1.9006 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index e6725334..6da667c4 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9005 + 1.7.1.9006 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 9cd2cede..701c8432 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 1.7.1.9005 + 1.7.1.9006 diff --git a/docs/articles/index.html b/docs/articles/index.html index bc206a95..a125e615 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9005 + 1.7.1.9006 diff --git a/docs/authors.html b/docs/authors.html index e28124f9..fd001200 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9005 + 1.7.1.9006 diff --git a/docs/index.html b/docs/index.html index 994b266e..14253e6d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.7.1.9005 + 1.7.1.9006 diff --git a/docs/news/index.html b/docs/news/index.html index b1403661..cc5f6af2 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9005 + 1.7.1.9006 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

- Unreleased AMR 1.7.1.9005

+
+

+ Unreleased AMR 1.7.1.9006

Last updated: 22 June 2021 @@ -317,7 +317,7 @@
  • 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()

    • @@ -418,7 +418,7 @@ #> 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:

    @@ -475,7 +475,7 @@
 
  • 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
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 613ff48d..15abd192 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: 2021-06-22T10:02Z +last_built: 2021-06-22T11:07Z 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 63525396..6309b383 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9005 + 1.7.1.9006
    diff --git a/docs/survey.html b/docs/survey.html index ebb71e85..dd8d49a3 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9005 + 1.7.1.9006