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(v1.3.0.9038) prefinal 1.4.0

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dr. M.S. (Matthijs) Berends
2020-10-04 19:26:43 +02:00
parent 3136bc54aa
commit baf510183c
89 changed files with 570 additions and 548 deletions
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62
R/eucast_rules.R
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@ -39,7 +39,7 @@ EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1",
#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details.
#' @inheritSection lifecycle Stable lifecycle
#' @param x data with antibiotic columns, such as `amox`, `AMX` and `AMC`
#' @param info print progress
#' @param info a logical to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions
#' @param rules a character vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value, e.g. using `options(AMR_eucastrules = "all")`.
#' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.
#' @param version_breakpoints the version number to use for the EUCAST Clinical Breakpoints guideline. Currently supported: `r paste0(names(EUCAST_VERSION_BREAKPOINTS), collapse = ", ")`.
@ -132,7 +132,7 @@ eucast_rules <- function(x,
...) {
x_deparsed <- deparse(substitute(x))
if (length(x_deparsed) > 0 || !all(x_deparsed %like% "[a-z]")) {
if (length(x_deparsed) > 1 || !all(x_deparsed %like% "[a-z]+")) {
x_deparsed <- "your_data"
}
@ -188,7 +188,7 @@ eucast_rules <- function(x,
}
warned <- FALSE
warn_lacking_rsi_class <- FALSE
warn_lacking_rsi_class <- character(0)
txt_ok <- function(n_added, n_changed, warned = FALSE) {
if (warned == FALSE) {
if (n_added + n_changed == 0) {
@ -447,7 +447,7 @@ eucast_rules <- function(x,
if (info == TRUE & NROW(x) > 10000) {
message(font_blue("NOTE: Preparing data..."), appendLF = FALSE)
}
# nolint start
# antibiotic classes ----
aminoglycosides <- c(AMK, DKB, GEN, ISE, KAN, NEO, NET, RST, SIS, STR, STR1, TOB)
@ -612,9 +612,7 @@ eucast_rules <- function(x,
# Set base to R where base + enzyme inhibitor is R
rule_current <- paste0("Set ", ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = R where ",
ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = R")
if (info == TRUE) {
cat(rule_current)
}
cat(rule_current)
run_changes <- edit_rsi(x = x,
col_mo = col_mo,
to = "R",
@ -629,7 +627,7 @@ eucast_rules <- function(x,
n_changed <- n_changed + run_changes$changed
verbose_info <- run_changes$verbose_info
x <- run_changes$output
warn_lacking_rsi_class <- warn_lacking_rsi_class | run_changes$rsi_warn
warn_lacking_rsi_class <- c(warn_lacking_rsi_class, run_changes$rsi_warn)
# Print number of new changes
if (info == TRUE) {
# print only on last one of rules in this group
@ -659,7 +657,7 @@ eucast_rules <- function(x,
n_changed <- n_changed + run_changes$changed
verbose_info <- run_changes$verbose_info
x <- run_changes$output
warn_lacking_rsi_class <- warn_lacking_rsi_class | run_changes$rsi_warn
warn_lacking_rsi_class <- c(warn_lacking_rsi_class, run_changes$rsi_warn)
# Print number of new changes
if (info == TRUE) {
# print only on last one of rules in this group
@ -691,7 +689,7 @@ eucast_rules <- function(x,
if (any(c("all", "breakpoints") %in% rules)) {
eucast_rules_df <- subset(eucast_rules_df,
!reference.rule_group %like% "breakpoint" |
(reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints))
(reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints))
}
if (any(c("all", "expert") %in% rules)) {
eucast_rules_df <- subset(eucast_rules_df,
@ -846,7 +844,7 @@ eucast_rules <- function(x,
}
cols <- get_antibiotic_columns(target_antibiotics, x)
# Apply rule on data ------------------------------------------------------
# this will return the unique number of changes
run_changes <- edit_rsi(x = x,
@ -866,7 +864,7 @@ eucast_rules <- function(x,
n_changed <- n_changed + run_changes$changed
verbose_info <- run_changes$verbose_info
x <- run_changes$output
warn_lacking_rsi_class <- warn_lacking_rsi_class | run_changes$rsi_warn
warn_lacking_rsi_class <- c(warn_lacking_rsi_class, run_changes$rsi_warn)
# Print number of new changes ---------------------------------------------
if (info == TRUE & rule_next != rule_current) {
# print only on last one of rules in this group
@ -878,8 +876,7 @@ eucast_rules <- function(x,
}
# Print overview ----------------------------------------------------------
if (info == TRUE) {
if (info == TRUE | verbose == TRUE) {
verbose_info <- x.bak %pm>%
pm_mutate(row = pm_row_number()) %pm>%
pm_select(`.rowid`, row) %pm>%
@ -890,6 +887,9 @@ eucast_rules <- function(x,
pm_filter(!is.na(new)) %pm>%
pm_arrange(row, rule_group, rule_name, col)
rownames(verbose_info) <- NULL
}
if (info == TRUE) {
if (verbose == TRUE) {
wouldve <- "would have "
@ -899,16 +899,16 @@ eucast_rules <- function(x,
cat(paste0("\n", font_grey(strrep("-", 0.95 * options()$width)), "\n"))
cat(paste0("The rules ", paste0(wouldve, "affected "),
font_bold(formatnr(pm_n_distinct(verbose_info$row)),
"out of", formatnr(nrow(x.bak)),
"rows"),
", making a total of ",
font_bold(formatnr(nrow(verbose_info)), "edits\n")))
total_n_added <- verbose_info %pm>% pm_filter(is.na(old)) %pm>% nrow()
total_n_changed <- verbose_info %pm>% pm_filter(!is.na(old)) %pm>% nrow()
# print added values
font_bold(formatnr(pm_n_distinct(verbose_info$row)),
"out of", formatnr(nrow(x.bak)),
"rows"),
", making a total of ",
font_bold(formatnr(nrow(verbose_info)), "edits\n")))
total_n_added <- verbose_info %pm>% pm_filter(is.na(old)) %pm>% nrow()
total_n_changed <- verbose_info %pm>% pm_filter(!is.na(old)) %pm>% nrow()
# print added values
if (total_n_added == 0) {
colour <- cat # is function
} else {
@ -961,12 +961,14 @@ total_n_changed <- verbose_info %pm>% pm_filter(!is.na(old)) %pm>% nrow()
}
}
if (isTRUE(warn_lacking_rsi_class)) {
unique_cols <- colnames(x.bak)[colnames(x.bak) %in% verbose_info$col]
if (length(warn_lacking_rsi_class) > 0) {
warn_lacking_rsi_class <- unique(warn_lacking_rsi_class)
warning("Not all columns with antimicrobial results are of class <rsi>. Transform them on beforehand, with e.g.:\n",
" ", x_deparsed, " %>% mutate_if(is.rsi.eligible, as.rsi)\n",
" ", x_deparsed, " %>% as.rsi(", unique_cols[1], ":", unique_cols[length(unique_cols)], ")",
" ", x_deparsed, " %>% as.rsi(", ifelse(length(warn_lacking_rsi_class) == 1,
warn_lacking_rsi_class,
paste0(warn_lacking_rsi_class[1], ":", warn_lacking_rsi_class[length(warn_lacking_rsi_class)])),
")",
call. = FALSE)
}
@ -1004,7 +1006,7 @@ edit_rsi <- function(x,
changed = 0,
output = x,
verbose_info = last_verbose_info,
rsi_warn = FALSE)
rsi_warn = character(0))
txt_error <- function() {
if (info == TRUE) cat("", font_red_bg(font_white(" ERROR ")), "\n\n")
@ -1019,7 +1021,7 @@ edit_rsi <- function(x,
if (length(rows) > 0 & length(cols) > 0) {
new_edits <- x
if (any(!sapply(x[, cols, drop = FALSE], is.rsi), na.rm = TRUE)) {
track_changes$rsi_warn <- TRUE
track_changes$rsi_warn <- cols[!sapply(x[, cols, drop = FALSE], is.rsi)]
}
tryCatch(
# insert into original table