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(v1.3.0.9035) mdro() for EUCAST 3.2, examples cleanup

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dr. M.S. (Matthijs) Berends
2020-09-29 23:35:46 +02:00
parent 68e6e1e329
commit 4e0374af29
94 changed files with 1143 additions and 1165 deletions
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29
R/join_microorganisms.R
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@ -39,19 +39,22 @@
#' left_join_microorganisms(as.mo("K. pneumoniae"))
#' left_join_microorganisms("B_KLBSL_PNE")
#'
#' \dontrun{
#' library(dplyr)
#' example_isolates %>% left_join_microorganisms()
#'
#' df <- data.frame(date = seq(from = as.Date("2018-01-01"),
#' to = as.Date("2018-01-07"),
#' by = 1),
#' bacteria = as.mo(c("S. aureus", "MRSA", "MSSA", "STAAUR",
#' "E. coli", "E. coli", "E. coli")),
#' stringsAsFactors = FALSE)
#' colnames(df)
#' df_joined <- left_join_microorganisms(df, "bacteria")
#' colnames(df_joined)
#' \donttest{
#' if (require("dplyr")) {
#' example_isolates %>%
#' left_join_microorganisms() %>%
#' colnames()
#'
#' df <- data.frame(date = seq(from = as.Date("2018-01-01"),
#' to = as.Date("2018-01-07"),
#' by = 1),
#' bacteria = as.mo(c("S. aureus", "MRSA", "MSSA", "STAAUR",
#' "E. coli", "E. coli", "E. coli")),
#' stringsAsFactors = FALSE)
#' colnames(df)
#' df_joined <- left_join_microorganisms(df, "bacteria")
#' colnames(df_joined)
#' }
#' }
inner_join_microorganisms <- function(x, by = NULL, suffix = c("2", ""), ...) {
check_dataset_integrity()