P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 19:01:51 +02:00
Code Releases Activity

(v0.7.1.9100) bug_drug speed, MIC levels

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-10-08 22:21:33 +02:00
parent 683d226fd3
commit c8f6b97847
22 changed files with 117 additions and 70 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
R/ab_property.R
View File

@ -181,12 +181,12 @@ ab_validate <- function(x, property, ...) {
library("AMR")
# check onLoad() in R/zzz.R: data tables are created there.
}
# try to catch an error when inputting an invalid parameter
# so the 'call.' can be set to FALSE
tryCatch(x[1L] %in% AMR::antibiotics[1, property],
error = function(e) stop(e$message, call. = FALSE))
x_bak <- x
if (!all(x %in% AMR::antibiotics[, property])) {
x <- data.frame(ab = AMR::as.ab(x, ...), stringsAsFactors = FALSE) %>%
left_join(AMR::antibiotics, by = "ab") %>%
@ -199,6 +199,8 @@ ab_validate <- function(x, property, ...) {
} else if (property %like% "ddd") {
return(as.double(x))
} else {
# return "(input)" for NAs
x[is.na(x) & !is.na(x_bak)] <- paste0("(", x_bak[is.na(x) & !is.na(x_bak)], ")")
return(x)
}
}