disk documentation fix

.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$

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)

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.

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))

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))

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: