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(v0.8.0.9034) add cid to antivirals

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dr. M.S. (Matthijs) Berends
2019-11-23 12:39:57 +01:00
parent 267320f15f
commit e53cc4990c
37 changed files with 460 additions and 449 deletions
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18
R/mo.R
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@ -183,11 +183,14 @@
#' df <- df %>%
#' mutate(mo = as.mo(paste(genus, species)))
#' }
as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, reference_df = get_mo_source(), ...) {
if (!"AMR" %in% base::.packages()) {
require("AMR")
# check onLoad() in R/zzz.R: data tables are created there.
}
as.mo <- function(x,
Becker = FALSE,
Lancefield = FALSE,
allow_uncertain = TRUE,
reference_df = get_mo_source(),
...) {
load_AMR_package()
# WHONET: xxx = no growth
x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
@ -293,10 +296,7 @@ exec_as.mo <- function(x,
debug = FALSE,
reference_data_to_use = microorganismsDT) {
if (!"AMR" %in% base::.packages()) {
require("AMR")
# check onLoad() in R/zzz.R: data tables are created there.
}
load_AMR_package()
# WHONET: xxx = no growth
x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_