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better verbose in EUCAST

This commit is contained in:
dr. M.S. (Matthijs) Berends 2018-10-19 00:57:10 +02:00
parent b464dd524a
commit 032c0d51ef
1 changed files with 28 additions and 17 deletions
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45
R/eucast.R
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@ -407,22 +407,22 @@ EUCAST_rules <- function(tbl,
cat("Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)\n") cat("Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)\n")
} }
# since ampicillin ^= amoxicillin, get the first from the latter # since ampicillin ^= amoxicillin, get the first from the latter (not in original table)
if (!is.na(ampi) & !is.na(amox)) { if (!is.na(ampi) & !is.na(amox)) {
rule_group <- "Ampicillin susceptibility" if (verbose == TRUE) {
rule <- "Get ampicillin results from amoxicillin where ampicillin is missing" cat("\n VERBOSE: transforming",
edit_rsi(to = 'S', length(which(tbl[, amox] == "S" & !tbl[, ampi] %in% c("S", "I", "R"))),
rule = c(rule_group, rule), "empty ampicillin fields to 'S' based on amoxicillin.")
rows = which(tbl[, amox] == 'S' & !tbl[, ampi] %in% c("S", "I", "R")), cat("\n VERBOSE: transforming",
cols = ampi) length(which(tbl[, amox] == "I" & !tbl[, ampi] %in% c("S", "I", "R"))),
edit_rsi(to = 'I', "empty ampicillin fields to 'I' based on amoxicillin.")
rule = c(rule_group, rule), cat("\n VERBOSE: transforming",
rows = which(tbl[, amox] == 'I' & !tbl[, ampi] %in% c("S", "I", "R")), length(which(tbl[, amox] == "R" & !tbl[, ampi] %in% c("S", "I", "R"))),
cols = ampi) "empty ampicillin fields to 'R' based on amoxicillin.\n")
edit_rsi(to = 'R', }
rule = c(rule_group, rule), tbl[which(tbl[, amox] == "S" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "S"
rows = which(tbl[, amox] == 'R' & !tbl[, ampi] %in% c("S", "I", "R")), tbl[which(tbl[, amox] == "I" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "I"
cols = ampi) tbl[which(tbl[, amox] == "R" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "R"
} }
if (any(c("all", "breakpoints") %in% rules)) { if (any(c("all", "breakpoints") %in% rules)) {
@ -1651,11 +1651,22 @@ EUCAST_rules <- function(tbl,
# } # }
if (info == TRUE) { if (info == TRUE) {
if (verbose == TRUE) {
wouldve <- "would have "
} else {
wouldve <- ""
}
if (amount_changed == 0) {
colour <- green
} else {
colour <- blue
}
cat(bold('\n=> EUCAST rules affected', cat(bold('\n=> EUCAST rules affected',
amount_affected_rows %>% length() %>% format(big.mark = ","), amount_affected_rows %>% length() %>% format(big.mark = ","),
'out of', nrow(tbl_original) %>% format(big.mark = ","), 'out of', nrow(tbl_original) %>% format(big.mark = ","),
'rows -- changed', 'rows ->',
amount_changed %>% format(big.mark = ","), 'test results.\n\n')) colour(paste0(wouldve, 'changed'),
amount_changed %>% format(big.mark = ","), 'test results.\n\n')))
} }
if (verbose == TRUE) { if (verbose == TRUE) {