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eucast rules fix, 1st isolate fix, website update

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dr. M.S. (Matthijs) Berends
2018-12-31 01:48:53 +01:00
parent 469b145d8c
commit 2e4d703338
51 changed files with 1473 additions and 1760 deletions
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45
R/eucast_rules.R
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@ -348,7 +348,7 @@ eucast_rules <- function(tbl,
# helper function for editing the table
edit_rsi <- function(to, rule, rows, cols) {
cols <- cols[!is.na(cols)]
cols <- unique(cols[!is.na(cols)])
if (length(rows) > 0 & length(cols) > 0) {
before <- as.character(unlist(as.list(tbl_original[rows, cols])))
tryCatch(
@ -367,6 +367,10 @@ eucast_rules <- function(tbl,
stop(e, call. = FALSE)
}
)
suppressMessages(
suppressWarnings(
tbl[rows, cols] <<- to
))
after <- as.character(unlist(as.list(tbl_original[rows, cols])))
amount_changed <<- amount_changed + sum(before != after, na.rm = TRUE)
amount_affected_rows <<- unique(c(amount_affected_rows, rows))
@ -404,27 +408,14 @@ eucast_rules <- function(tbl,
# join to microorganisms data set
tbl <- tbl %>%
mutate_at(vars(col_mo), as.mo) %>%
left_join_microorganisms(by = col_mo, suffix = c("_oldcols", ""))
# antibiotic classes
aminoglycosides <- c(tobr, gent, kana, neom, neti, siso)
tetracyclines <- c(doxy, mino, tetr) # since EUCAST v3.1 tige(cycline) is set apart
polymyxins <- c(poly, coli)
macrolides <- c(eryt, azit, roxi, clar) # since EUCAST v3.1 clinda is set apart
glycopeptides <- c(vanc, teic)
streptogramins <- c(qida, pris) # should officially also be quinupristin/dalfopristin
cephalosporins <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol)
carbapenems <- c(erta, imip, mero)
aminopenicillins <- c(ampi, amox)
ureidopenicillins <- c(pipe, pita, azlo, mezl)
fluoroquinolones <- c(oflo, cipr, norf, levo, moxi)
all_betalactam <- c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, amcl, oxac, clox, peni)
left_join_microorganisms(by = col_mo, suffix = c("_oldcols", "")) %>%
as.data.frame(stringsAsFactors = FALSE)
if (info == TRUE) {
cat("Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)\n")
cat("\nRules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)\n")
}
# since ampicillin ^= amoxicillin, get the first from the latter (not in original table)
# since ampicillin ^= amoxicillin, get the first from the latter (not in original EUCAST table)
if (!is.na(ampi) & !is.na(amox)) {
if (verbose == TRUE) {
cat(bgGreen("\n VERBOSE: transforming",
@ -440,8 +431,26 @@ eucast_rules <- function(tbl,
tbl[which(tbl[, amox] == "S" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "S"
tbl[which(tbl[, amox] == "I" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "I"
tbl[which(tbl[, amox] == "R" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "R"
} else if (is.na(ampi) & !is.na(amox)) {
# ampicillin column is missing, but amoxicillin is available
message(blue(paste0("NOTE: Using column `", bold(amox), "` as input for ampicillin (J01CA01) since many EUCAST rules depend on it.")))
ampi <- amox
}
# antibiotic classes
aminoglycosides <- c(tobr, gent, kana, neom, neti, siso)
tetracyclines <- c(doxy, mino, tetr) # since EUCAST v3.1 tige(cycline) is set apart
polymyxins <- c(poly, coli)
macrolides <- c(eryt, azit, roxi, clar) # since EUCAST v3.1 clinda is set apart
glycopeptides <- c(vanc, teic)
streptogramins <- c(qida, pris) # should officially also be quinupristin/dalfopristin
cephalosporins <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol)
carbapenems <- c(erta, imip, mero)
aminopenicillins <- c(ampi, amox)
ureidopenicillins <- c(pipe, pita, azlo, mezl)
fluoroquinolones <- c(oflo, cipr, norf, levo, moxi)
all_betalactam <- c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, amcl, oxac, clox, peni)
if (any(c("all", "breakpoints") %in% rules)) {
# BREAKPOINTS -------------------------------------------------------------