diff --git a/DESCRIPTION b/DESCRIPTION index 7bce8c0d..9452f0a7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 0.8.0.9008 +Version: 0.8.0.9009 Date: 2019-11-03 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 8153b720..c7175adb 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.8.0.9008 +# AMR 0.8.0.9009 Last updated: 03-Nov-2019 ### New diff --git a/R/age.R b/R/age.R index 4ebcb70e..55b00135 100755 --- a/R/age.R +++ b/R/age.R @@ -133,6 +133,7 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE) { #' # same: #' age_groups(ages, c(1, 2, 4, 6, 13, 17)) #' +#' \dontrun{ #' # resistance of ciprofloxacine per age group #' library(dplyr) #' example_isolates %>% @@ -141,6 +142,7 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE) { #' group_by(age_group = age_groups(age)) %>% #' select(age_group, CIP) %>% #' ggplot_rsi(x = "age_group") +#' } age_groups <- function(x, split_at = c(12, 25, 55, 75), na.rm = FALSE) { if (!is.numeric(x)) { stop("`x` and must be numeric, not a ", paste0(class(x), collapse = "/"), ".") diff --git a/R/ggplot_rsi.R b/R/ggplot_rsi.R index 2a7a953e..9e64bfa1 100755 --- a/R/ggplot_rsi.R +++ b/R/ggplot_rsi.R @@ -99,7 +99,9 @@ #' example_isolates %>% #' select(AMX) %>% #' ggplot_rsi(colours = c(SI = "yellow")) -#' +#' +#' \dontrun{ +#' #' # resistance of ciprofloxacine per age group #' example_isolates %>% #' mutate(first_isolate = first_isolate(.)) %>% @@ -110,8 +112,7 @@ #' select(age_group, #' CIP) %>% #' ggplot_rsi(x = "age_group") -#' \donttest{ -#' +#' #' # for colourblind mode, use divergent colours from the viridis package: #' example_isolates %>% #' select(AMX, NIT, FOS, TMP, CIP) %>% diff --git a/R/mdro.R b/R/mdro.R index ec990963..e488d8de 100755 --- a/R/mdro.R +++ b/R/mdro.R @@ -25,7 +25,6 @@ #' @param guideline a specific guideline to follow. When left empty, the publication by Magiorakos \emph{et al.} (2012, Clinical Microbiology and Infection) will be followed, see Details. #' @param info print progress #' @inheritParams eucast_rules -#' @param verbose print additional info: missing antibiotic columns per parameter #' @param pct_required_classes minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for \emph{S. aureus}. Setting this \code{pct_required_classes} argument to \code{0.5} (default) means that for every \emph{S. aureus} isolate at least 8 different classes must be available. Any lower number of available classes will return \code{NA} for that isolate. #' @param verbose a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not. #' @inheritSection eucast_rules Antibiotics diff --git a/docs/404.html b/docs/404.html index a23546f3..0b15d515 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index d9a871a9..06fef11a 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -84,7 +84,7 @@ diff --git a/docs/articles/index.html b/docs/articles/index.html index 463a45d8..9cdfcec1 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@ diff --git a/docs/authors.html b/docs/authors.html index 965cb58c..2f37b2a9 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -84,7 +84,7 @@ diff --git a/docs/index.html b/docs/index.html index 2c98ae4d..fee36aad 100644 --- a/docs/index.html +++ b/docs/index.html @@ -45,7 +45,7 @@ diff --git a/docs/news/index.html b/docs/news/index.html index 0b35e58b..3d832dc1 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -84,7 +84,7 @@ @@ -231,9 +231,9 @@ -Last updated: 03-Nov-2019
as.mo(..., allow_uncertain = 3)
Contents
print additional info: missing antibiotic columns per parameter
a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
column name of an antibiotic, see section Antibiotics
a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.