mirror of
https://github.com/msberends/AMR.git
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(v2.1.1.9225) fix geom_hline()/_vline() in MIC plotting, add EUCAT 1.2 in full, add London contribs, fix mo codes, add Kleb pneu complex
This commit is contained in:
204
R/eucast_rules.R
204
R/eucast_rules.R
@ -61,11 +61,11 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see *Details*.
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#' @param x a data set with antimicrobials columns, such as `amox`, `AMX` and `AMC`
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#' @param info a [logical] to indicate whether progress should be printed to the console - the default is only print while in interactive sessions
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#' @param rules a [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value using the package option [`AMR_eucastrules`][AMR-options]: `options(AMR_eucastrules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()].
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#' @param rules a [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expected_phenotypes"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expected_phenotypes")`. The default value can be set to another value using the package option [`AMR_eucastrules`][AMR-options]: `options(AMR_eucastrules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()].
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#' @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.
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#' @param version_breakpoints the version number to use for the EUCAST Clinical Breakpoints guideline. Can be `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), reverse = TRUE)`.
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#' @param version_expected_phenotypes the version number to use for the EUCAST Expected Phenotypes. Can be `r vector_or(names(EUCAST_VERSION_EXPECTED_PHENOTYPES), reverse = TRUE)`.
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#' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`.
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# @param version_resistant_phenotypes the version number to use for the EUCAST Expected Resistant Phenotypes. Can be `r vector_or(names(EUCAST_VERSION_RESISTANTPHENOTYPES), reverse = TRUE)`.
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#' @param ampc_cephalosporin_resistance a [character] value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is `NA`. Currently only works when `version_expertrules` is `3.2` and higher; these version of '*EUCAST Expert Rules on Enterobacterales*' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of `NA` (the default) for this argument will remove results for these three drugs, while e.g. a value of `"R"` will make the results for these drugs resistant. Use `NULL` or `FALSE` to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using `TRUE` is equal to using `"R"`. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: `r vector_and(gsub("[^a-zA-Z ]+", "", unlist(strsplit(EUCAST_RULES_DF[which(EUCAST_RULES_DF$reference.version %in% c(3.2, 3.3) & EUCAST_RULES_DF$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`.
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#' @param ... column name of an antimicrobial, see section *Antimicrobials* below
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#' @param ab any (vector of) text that can be coerced to a valid antimicrobial drug code with [as.ab()]
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@ -146,14 +146,14 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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#'
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#'
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#' # apply EUCAST rules: some results wil be changed
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#' b <- eucast_rules(a)
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#' b <- eucast_rules(a, overwrite = TRUE)
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#'
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#' head(b)
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#'
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#'
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#' # do not apply EUCAST rules, but rather get a data.frame
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#' # containing all details about the transformations:
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#' c <- eucast_rules(a, verbose = TRUE)
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#' c <- eucast_rules(a, overwrite = TRUE, verbose = TRUE)
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#' head(c)
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#' }
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#'
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@ -165,11 +165,11 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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eucast_rules <- function(x,
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col_mo = NULL,
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info = interactive(),
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rules = getOption("AMR_eucastrules", default = c("breakpoints", "expert")),
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rules = getOption("AMR_eucastrules", default = c("breakpoints", "expected_phenotypes")),
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verbose = FALSE,
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version_breakpoints = 14.0,
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version_expected_phenotypes = 1.2,
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version_expertrules = 3.3,
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# TODO version_resistant_phenotypes = 1.2,
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ampc_cephalosporin_resistance = NA,
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only_sir_columns = FALSE,
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custom_rules = NULL,
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@ -178,11 +178,11 @@ eucast_rules <- function(x,
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meet_criteria(x, allow_class = "data.frame")
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meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
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meet_criteria(info, allow_class = "logical", has_length = 1)
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meet_criteria(rules, allow_class = "character", has_length = c(1, 2, 3, 4, 5), is_in = c("breakpoints", "expert", "other", "all", "custom"))
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meet_criteria(rules, allow_class = "character", has_length = c(1, 2, 3, 4, 5, 6), is_in = c("breakpoints", "expected_phenotypes", "expert", "other", "all", "custom"))
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meet_criteria(verbose, allow_class = "logical", has_length = 1)
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meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS)))
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meet_criteria(version_expected_phenotypes, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_EXPECTED_PHENOTYPES)))
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meet_criteria(version_expertrules, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_EXPERT_RULES)))
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# meet_criteria(version_resistant_phenotypes, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_RESISTANTPHENOTYPES)))
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meet_criteria(ampc_cephalosporin_resistance, allow_class = c("logical", "character", "sir"), has_length = 1, allow_NA = TRUE, allow_NULL = TRUE)
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
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@ -209,13 +209,8 @@ eucast_rules <- function(x,
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}
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breakpoints_info <- EUCAST_VERSION_BREAKPOINTS[[which(as.double(names(EUCAST_VERSION_BREAKPOINTS)) == version_breakpoints)]]
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expected_phenotypes_info <- EUCAST_VERSION_EXPECTED_PHENOTYPES[[which(as.double(names(EUCAST_VERSION_EXPECTED_PHENOTYPES)) == version_expected_phenotypes)]]
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expertrules_info <- EUCAST_VERSION_EXPERT_RULES[[which(as.double(names(EUCAST_VERSION_EXPERT_RULES)) == version_expertrules)]]
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# resistantphenotypes_info <- EUCAST_VERSION_RESISTANTPHENOTYPES[[which(as.double(names(EUCAST_VERSION_RESISTANTPHENOTYPES)) == version_resistant_phenotypes)]]
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# support old setting (until AMR v1.3.0)
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if (missing(rules) && !is.null(getOption("AMR.eucast_rules"))) {
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rules <- getOption("AMR.eucast_rules")
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}
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if (interactive() && isTRUE(verbose) && isTRUE(info)) {
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txt <- paste0(
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@ -390,6 +385,24 @@ eucast_rules <- function(x,
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}
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suppressWarnings(as.sir(x))
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}
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expand_groups <- function(entry) {
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parts <- trimws(strsplit(entry, ",")[[1]])
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group_names <- tolower(AMR::microorganisms.groups$mo_group_name)
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mo_names <- AMR::microorganisms.groups$mo_name
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group_names_lc <- tolower(group_names)
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result <- unlist(lapply(parts, function(part) {
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match_idx <- which(group_names_lc == tolower(part))
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if (length(match_idx) > 0) {
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mo_names[match_idx]
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} else {
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part
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}
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}))
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# only the ones with genus or genus/species, not subspecies (as genus_species will be matched)
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spaces <- vapply(FUN.VALUE = integer(1), strsplit(result, " "), length)
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result <- result[spaces < 3]
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return(paste0(unique(result), collapse = ", "))
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}
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# Preparing the data ------------------------------------------------------
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@ -442,15 +455,6 @@ eucast_rules <- function(x,
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message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
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}
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if (any(x$genus == "Staphylococcus", na.rm = TRUE)) {
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all_staph <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$genus == "Staphylococcus"), , drop = FALSE]
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all_staph$CNS_CPS <- suppressWarnings(mo_name(all_staph$mo, Becker = "all", language = NULL, info = FALSE))
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}
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if (any(x$genus == "Streptococcus", na.rm = TRUE)) {
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all_strep <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$genus == "Streptococcus"), , drop = FALSE]
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all_strep$Lancefield <- suppressWarnings(mo_name(all_strep$mo, Lancefield = TRUE, language = NULL, info = FALSE))
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}
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n_added <- 0
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n_changed <- 0
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@ -577,7 +581,17 @@ eucast_rules <- function(x,
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} else {
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if (isTRUE(info)) {
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cat("\n")
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message_("Skipping inheritance rules defined by this AMR package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R. Add \"other\" or \"all\" to the `rules` argument to apply those rules.")
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message_(paste0(
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font_red("Skipping inhibitor-inheritance rules defined by this AMR package: setting "),
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font_green_bg(" S "),
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font_red(" to drug+inhibitor where drug is "),
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font_green_bg(" S "),
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font_red(", and setting "),
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font_rose_bg(" R "),
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font_red(" to drug where drug+inhibitor is "),
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font_rose_bg(" R "),
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font_red(". Add \"other\" or \"all\" to the `rules` argument to apply those rules.")
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))
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}
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}
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@ -592,26 +606,43 @@ eucast_rules <- function(x,
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eucast_notification_shown <- FALSE
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if (!is.null(list(...)$eucast_rules_df)) {
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# this allows: eucast_rules(x, eucast_rules_df = AMR:::EUCAST_RULES_DF %>% filter(is.na(have_these_values)))
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eucast_rules_df <- list(...)$eucast_rules_df
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eucast_rules_df_total <- list(...)$eucast_rules_df
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} else {
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# otherwise internal data file, created in data-raw/_pre_commit_checks.R
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eucast_rules_df <- EUCAST_RULES_DF
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eucast_rules_df_total <- EUCAST_RULES_DF
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}
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## filter on user-set guideline versions ----
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eucast_rules_df <- data.frame()
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if (any(c("all", "breakpoints") %in% rules)) {
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eucast_rules_df <- subset(
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eucast_rules_df,
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reference.rule_group %unlike% "breakpoint" |
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(reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints)
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)
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eucast_rules_df <- eucast_rules_df %pm>%
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rbind_AMR(eucast_rules_df_total %pm>%
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subset(reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints))
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# eucast_rules_df <- subset(
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# eucast_rules_df,
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# reference.rule_group %unlike% "breakpoint" |
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# (reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints)
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# )
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}
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if (any(c("all", "expected_phenotypes") %in% rules)) {
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eucast_rules_df <- eucast_rules_df %pm>%
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rbind_AMR(eucast_rules_df_total %pm>%
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subset(reference.rule_group %like% "expected" & reference.version == version_expected_phenotypes))
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# eucast_rules_df <- subset(
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# eucast_rules_df,
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# reference.rule_group %unlike% "expected" |
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# (reference.rule_group %like% "expected" & reference.version == version_expected_phenotypes)
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# )
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}
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if (any(c("all", "expert") %in% rules)) {
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eucast_rules_df <- subset(
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eucast_rules_df,
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reference.rule_group %unlike% "expert" |
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(reference.rule_group %like% "expert" & reference.version == version_expertrules)
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)
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eucast_rules_df <- eucast_rules_df %pm>%
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rbind_AMR(eucast_rules_df_total %pm>%
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subset(reference.rule_group %like% "expert" & reference.version == version_expertrules))
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# eucast_rules_df <- subset(
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# eucast_rules_df,
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# reference.rule_group %unlike% "expert" |
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# (reference.rule_group %like% "expert" & reference.version == version_expertrules)
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# )
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}
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## filter out AmpC de-repressed cephalosporin-resistant mutants ----
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# no need to filter on version number here - the rules contain these version number, so are inherently filtered
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@ -657,6 +688,9 @@ eucast_rules <- function(x,
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if (rule_group_current %like% "breakpoint" && !any(c("all", "breakpoints") %in% rules)) {
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next
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}
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if (rule_group_current %like% "expected" && !any(c("all", "expected_phenotypes") %in% rules)) {
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next
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}
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if (rule_group_current %like% "expert" && !any(c("all", "expert") %in% rules)) {
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next
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}
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@ -677,6 +711,7 @@ eucast_rules <- function(x,
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)
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}
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}
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if (i == 1) {
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rule_previous <- ""
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rule_group_previous <- ""
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@ -712,15 +747,25 @@ eucast_rules <- function(x,
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)
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),
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ifelse(
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rule_group_current %like% "expert",
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rule_group_current %like% "expected",
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paste0(
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"\n",
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word_wrap(
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expertrules_info$title, " (",
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font_red(paste0(expertrules_info$version_txt, ", ", expertrules_info$year)), ")\n"
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expected_phenotypes_info$title, " (",
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font_red(paste0(expected_phenotypes_info$version_txt, ", ", expected_phenotypes_info$year)), ")\n"
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)
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),
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""
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ifelse(
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rule_group_current %like% "expert",
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paste0(
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"\n",
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word_wrap(
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expertrules_info$title, " (",
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font_red(paste0(expertrules_info$version_txt, ", ", expertrules_info$year)), ")\n"
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)
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),
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"" # Default empty string if none of the conditions are met
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)
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)
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)
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), "\n")
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@ -743,47 +788,15 @@ eucast_rules <- function(x,
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if_mo_property <- trimws(eucast_rules_df[i, "if_mo_property", drop = TRUE])
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like_is_one_of <- trimws(eucast_rules_df[i, "like.is.one_of", drop = TRUE])
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mo_value <- trimws(eucast_rules_df[i, "this_value", drop = TRUE])
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source_antibiotics <- eucast_rules_df[i, "and_these_antibiotics", drop = TRUE]
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source_value <- trimws(unlist(strsplit(eucast_rules_df[i, "have_these_values", drop = TRUE], ",", fixed = TRUE)))
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target_antibiotics <- eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE]
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target_value <- eucast_rules_df[i, "to_value", drop = TRUE]
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# be sure to comprise all coagulase-negative/-positive staphylococci when they are mentioned
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if (mo_value %like% "coagulase" && any(x$genus == "Staphylococcus", na.rm = TRUE)) {
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if (mo_value %like% "negative") {
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eucast_rules_df[i, "this_value"] <- paste0(
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"^(", paste0(
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all_staph[which(all_staph$CNS_CPS %like% "negative"),
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"fullname",
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drop = TRUE
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],
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collapse = "|"
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),
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")$"
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)
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} else {
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eucast_rules_df[i, "this_value"] <- paste0(
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"^(", paste0(
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all_staph[which(all_staph$CNS_CPS %like% "positive"),
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"fullname",
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drop = TRUE
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],
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collapse = "|"
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),
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")$"
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)
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}
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like_is_one_of <- "like"
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}
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# be sure to comprise all beta-haemolytic Streptococci (Lancefield groups A, B, C and G) when they are mentioned
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if (mo_value %like% "group [ABCG]" && any(x$genus == "Streptococcus", na.rm = TRUE)) {
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eucast_rules_df[i, "this_value"] <- paste0(
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"^(", paste0(
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all_strep[which(all_strep$Lancefield %like% "group [ABCG]"),
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"fullname",
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drop = TRUE
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],
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collapse = "|"
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),
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")$"
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)
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like_is_one_of <- "like"
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# if amo_value contains a group name, expand that name with all species in it
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if (any(trimws(strsplit(mo_value, ",")[[1]]) %in% AMR::microorganisms.groups$mo_group_name, na.rm = TRUE)) {
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like_is_one_of <- "one_of"
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mo_value <- expand_groups(mo_value)
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}
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if (like_is_one_of == "is") {
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@ -802,13 +815,8 @@ eucast_rules <- function(x,
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stop("invalid value for column 'like.is.one_of'", call. = FALSE)
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}
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source_antibiotics <- eucast_rules_df[i, "and_these_antibiotics", drop = TRUE]
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source_value <- trimws(unlist(strsplit(eucast_rules_df[i, "have_these_values", drop = TRUE], ",", fixed = TRUE)))
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target_antibiotics <- eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE]
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target_value <- eucast_rules_df[i, "to_value", drop = TRUE]
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if (is.na(source_antibiotics)) {
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rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value),
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rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value | x$fullname %like% mo_value),
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error = function(e) integer(0)
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)
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} else {
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@ -820,25 +828,17 @@ eucast_rules <- function(x,
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rows <- integer(0)
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} else if (length(source_antibiotics) == 1) {
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rows <- tryCatch(
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which(x[, if_mo_property, drop = TRUE] %like% mo_value &
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which((x[, if_mo_property, drop = TRUE] %like% mo_value | x$fullname %like% mo_value) &
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as.sir_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]),
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error = function(e) integer(0)
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)
|
||||
} else if (length(source_antibiotics) == 2) {
|
||||
rows <- tryCatch(
|
||||
which(x[, if_mo_property, drop = TRUE] %like% mo_value &
|
||||
which((x[, if_mo_property, drop = TRUE] %like% mo_value | x$fullname %like% mo_value) &
|
||||
as.sir_no_warning(x[, source_antibiotics[1L]]) == source_value[1L] &
|
||||
as.sir_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]),
|
||||
error = function(e) integer(0)
|
||||
)
|
||||
# nolint start
|
||||
# } else if (length(source_antibiotics) == 3) {
|
||||
# rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value
|
||||
# & as.sir_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]
|
||||
# & as.sir_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]
|
||||
# & as.sir_no_warning(x[, source_antibiotics[3L]]) == source_value[3L]),
|
||||
# error = function(e) integer(0))
|
||||
# nolint end
|
||||
} else {
|
||||
stop_("only 2 antimicrobials supported for source_antibiotics")
|
||||
}
|
||||
@ -855,7 +855,10 @@ eucast_rules <- function(x,
|
||||
rule_text, rule_group_current, rule_current,
|
||||
ifelse(rule_group_current %like% "breakpoint",
|
||||
paste0(breakpoints_info$title, " ", breakpoints_info$version_txt, ", ", breakpoints_info$year),
|
||||
paste0(expertrules_info$title, " ", expertrules_info$version_txt, ", ", expertrules_info$year)
|
||||
ifelse(rule_group_current %like% "expected",
|
||||
paste0(expected_phenotypes_info$title, " ", expected_phenotypes_info$version_txt, ", ", expected_phenotypes_info$year),
|
||||
paste0(expertrules_info$title, " ", expertrules_info$version_txt, ", ", expertrules_info$year)
|
||||
)
|
||||
)
|
||||
),
|
||||
rows = rows,
|
||||
@ -1130,7 +1133,12 @@ edit_sir <- function(x,
|
||||
if (any(!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.sir), na.rm = TRUE)) {
|
||||
track_changes$sir_warn <- cols[!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.sir)]
|
||||
}
|
||||
non_SIR <- is.na(new_edits[rows, cols]) | !(new_edits[rows, cols] == "S" | new_edits[rows, cols] == "I" | new_edits[rows, cols] == "R" | new_edits[rows, cols] == "SDD" | new_edits[rows, cols] == "NI")
|
||||
isNA <- is.na(new_edits[rows, cols])
|
||||
isSIR <- !isNA & (new_edits[rows, cols] == "S" | new_edits[rows, cols] == "I" | new_edits[rows, cols] == "R" | new_edits[rows, cols] == "SDD" | new_edits[rows, cols] == "NI")
|
||||
non_SIR <- !isSIR
|
||||
if (isFALSE(overwrite) && any(isSIR) && message_not_thrown_before("edit_sir.warning_overwrite")) {
|
||||
warning_("Some values had SIR values and were not overwritten, since `overwrite = FALSE`.")
|
||||
}
|
||||
tryCatch(
|
||||
# insert into original table
|
||||
if (isTRUE(overwrite)) {
|
||||
|
||||
Reference in New Issue
Block a user