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(v1.0.1.9006) added generic CLSI rules

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dr. M.S. (Matthijs) Berends
2020-04-14 14:12:31 +02:00
parent d1cb7d3b6f
commit 7a6f819232
23 changed files with 4318 additions and 496 deletions
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22
data-raw/read_EUCAST.R
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@ -26,7 +26,7 @@ library(AMR)
# USE THIS FUNCTION TO READ THE EUCAST EXCEL FILE THAT CONTAINS THE BREAKPOINT TABLES
read_EUCAST <- function(sheet, file = "data-raw/v_10.0_Breakpoint_Tables.xlsx") {
read_EUCAST <- function(sheet, file, guideline_name) {
message("Getting sheet ", sheet)
sheet.bak <- sheet
@ -172,7 +172,7 @@ read_EUCAST <- function(sheet, file = "data-raw/v_10.0_Breakpoint_Tables.xlsx")
mutate(method = ifelse(type %like% "MIC", "MIC", "DISK"),
type = gsub("^.*_", "breakpoint_", type)) %>%
pivot_wider(names_from = type, values_from = value) %>%
mutate(guideline = "EUCAST 2020",
mutate(guideline = guideline_name,
disk_dose = ifelse(method == "DISK", disk_dose, NA_character_),
mo = ifelse(mo == "", mo_sheet, mo)) %>%
filter(!(is.na(breakpoint_S) & is.na(breakpoint_R))) %>%
@ -219,8 +219,18 @@ sheets_to_analyse <- c("Enterobacterales",
"M.tuberculosis",
"PK PD breakpoints")
new_EUCAST <- read_EUCAST(sheets_to_analyse[1]) # takes the longest time
for (i in 2:length(sheets_to_analyse)) {
new_EUCAST <<- new_EUCAST %>% bind_rows(read_EUCAST(sheets_to_analyse[i]))
}
file <- "data-raw/v_10.0_Breakpoint_Tables.xlsx"
guideline_name <- "EUCAST 2020"
# takes the longest time:
new_EUCAST <- read_EUCAST(sheet = sheets_to_analyse[1],
file = file,
guideline_name = guideline_name)
for (i in 2:length(sheets_to_analyse)) {
tryCatch(
new_EUCAST <<- bind_rows(new_EUCAST,
read_EUCAST(sheet = sheets_to_analyse[i],
file = file,
guideline_name = guideline_name))
, error = function(e) message(e$message))
}