diff --git a/.Rbuildignore b/.Rbuildignore index 254a4265..1bcf3840 100755 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -23,14 +23,15 @@ ^data-raw$ ^\.lintr$ ^tests/testthat/_snaps$ -^vignettes/AMR.Rmd$ -^vignettes/benchmarks.Rmd$ -^vignettes/datasets.Rmd$ -^vignettes/EUCAST.Rmd$ -^vignettes/MDR.Rmd$ -^vignettes/PCA.Rmd$ -^vignettes/resistance_predict.Rmd$ -^vignettes/SPSS.Rmd$ -^vignettes/WHONET.Rmd$ +^vignettes/AMR\.Rmd$ +^vignettes/benchmarks\.Rmd$ +^vignettes/*\.not$ +^vignettes/datasets\.Rmd$ +^vignettes/EUCAST\.Rmd$ +^vignettes/MDR\.Rmd$ +^vignettes/PCA\.Rmd$ +^vignettes/resistance_predict\.Rmd$ +^vignettes/SPSS\.Rmd$ +^vignettes/WHONET\.Rmd$ ^logo.svg$ ^CRAN-SUBMISSION$ diff --git a/DESCRIPTION b/DESCRIPTION index 71fc1350..846d10f5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.1.9019 +Version: 1.8.1.9020 Date: 2022-08-21 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 68dbd54b..a7a12d6b 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.1.9019 +# AMR 1.8.1.9020 ### New * EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations. diff --git a/R/disk.R b/R/disk.R index 7a6a2c81..cdb359fc 100644 --- a/R/disk.R +++ b/R/disk.R @@ -44,7 +44,7 @@ #' df[, 2:5] <- lapply(df[, 2:5], as.disk) #' str(df) #' -#' #' \donttest{ +#' \donttest{ #' # transforming is easier with dplyr: #' if (require("dplyr")) { #' df %>% mutate(across(AMP:TOB, as.disk)) diff --git a/man/as.disk.Rd b/man/as.disk.Rd index a0b8852a..b2ec2339 100644 --- a/man/as.disk.Rd +++ b/man/as.disk.Rd @@ -43,7 +43,7 @@ df <- data.frame(microorganism = "Escherichia coli", df[, 2:5] <- lapply(df[, 2:5], as.disk) str(df) -#' \donttest{ +\donttest{ # transforming is easier with dplyr: if (require("dplyr")) { df \%>\% mutate(across(AMP:TOB, as.disk)) diff --git a/vignettes/AMR.Rmd b/vignettes/AMR.Rmd index 4dda8291..03cd1d9b 100755 --- a/vignettes/AMR.Rmd +++ b/vignettes/AMR.Rmd @@ -1,6 +1,6 @@ --- title: "How to conduct AMR data analysis" -author: "Dr Matthijs Berends" +author: "Dr. Matthijs Berends" date: '`r format(Sys.Date(), "%d %B %Y")`' output: rmarkdown::html_vignette: diff --git a/vignettes/benchmarks.Rmd b/vignettes/benchmarks.Rmd.not similarity index 100% rename from vignettes/benchmarks.Rmd rename to vignettes/benchmarks.Rmd.not