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implement ecoffs

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dr. M.S. (Matthijs) Berends
2023-06-22 10:07:33 +02:00
parent 55b98ede4c
commit 3083828e15
11 changed files with 57 additions and 32 deletions
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14
R/aa_globals.R
View File

@@ -56,12 +56,6 @@ EUCAST_VERSION_BREAKPOINTS <- list(
)
)
EUCAST_VERSION_EXPERT_RULES <- list(
"1.2" = list(
version_txt = "v3.3",
year = 2023,
title = "'EUCAST Expert Rules' and 'Expected Resistant Phenotypes'",
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"
),
"3.3" = list(
version_txt = "v3.3",
year = 2021,
@@ -81,6 +75,14 @@ EUCAST_VERSION_EXPERT_RULES <- list(
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"
)
)
EUCAST_VERSION_RESISTANTPHENOTYPES <- list(
"1.2" = list(
version_txt = "v1.2",
year = 2023,
title = "'Expected Resistant Phenotypes'",
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"
)
)
TAXONOMY_VERSION <- list(
GBIF = list(

10
R/eucast_rules.R
View File

@@ -63,8 +63,9 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' @param info a [logical] to indicate whether progress should be printed to the console - the default is 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"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value using the [package option][AMR-options] [`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()].
#' @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. Can be either `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), reverse = TRUE)`.
#' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`.
#' @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)`.
#' @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)`.
#' @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)`.
#' @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 = "*")`.
#' @param ... column name of an antibiotic, see section *Antibiotics* below
#' @param ab any (vector of) text that can be coerced to a valid antibiotic drug code with [as.ab()]
@@ -167,6 +168,7 @@ eucast_rules <- function(x,
verbose = FALSE,
version_breakpoints = 12.0,
version_expertrules = 3.3,
version_resistant_phenotypes = 1.2,
ampc_cephalosporin_resistance = NA,
only_sir_columns = FALSE,
custom_rules = NULL,
@@ -178,6 +180,7 @@ eucast_rules <- function(x,
meet_criteria(verbose, allow_class = "logical", has_length = 1)
meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS)))
meet_criteria(version_expertrules, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_EXPERT_RULES)))
meet_criteria(version_resistant_phenotypes, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_RESISTANTPHENOTYPES)))
meet_criteria(ampc_cephalosporin_resistance, allow_class = c("logical", "character", "sir"), has_length = 1, allow_NA = TRUE, allow_NULL = TRUE)
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
@@ -205,7 +208,8 @@ eucast_rules <- function(x,
breakpoints_info <- EUCAST_VERSION_BREAKPOINTS[[which(as.double(names(EUCAST_VERSION_BREAKPOINTS)) == version_breakpoints)]]
expertrules_info <- EUCAST_VERSION_EXPERT_RULES[[which(as.double(names(EUCAST_VERSION_EXPERT_RULES)) == version_expertrules)]]
resistantphenotypes_info <- EUCAST_VERSION_RESISTANTPHENOTYPES[[which(as.double(names(EUCAST_VERSION_RESISTANTPHENOTYPES)) == version_resistant_phenotypes)]]
# support old setting (until AMR v1.3.0)
if (missing(rules) && !is.null(getOption("AMR.eucast_rules"))) {
rules <- getOption("AMR.eucast_rules")

38
R/sir.R
View File

@@ -43,7 +43,7 @@
#' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.3)`.
#' @param include_screening a [logical] to indicate that clinical breakpoints for screening are allowed - the default is `FALSE`. Can also be set with the [package option][AMR-options] [`AMR_include_screening`][AMR-options].
#' @param include_PKPD a [logical] to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is `TRUE`. Can also be set with the [package option][AMR-options] [`AMR_include_PKPD`][AMR-options].
#' @param ecoff a [logical] to indicate that ECOFF (Epidemiological Cut-Off) values must be used - the default is `FALSE`. Can also be set with the [package option][AMR-options] [`AMR_ecoff`][AMR-options].
#' @param ecoff a [logical] to indicate that ECOFF (Epidemiological Cut-Off) values must be used **instead** of other clinical breakpoints - the default is `FALSE`. Can also be set with the [package option][AMR-options] [`AMR_ecoff`][AMR-options].
#' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [clinical_breakpoints] data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the [clinical_breakpoints] data set (same column names and column types). Please note that the `guideline` argument will be ignored when `reference_data` is manually set.
#' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, see *Examples*
#' @param ... for using on a [data.frame]: names of columns to apply [as.sir()] on (supports tidy selection such as `column1:column4`). Otherwise: arguments passed on to methods.
@@ -831,15 +831,19 @@ as_sir_method <- function(method_short,
)
}
message_("=> Interpreting ", method_long, " of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
agent_formatted,
mo_var_found,
" according to ", ifelse(identical(reference_data, AMR::clinical_breakpoints),
font_bold(guideline_coerced),
"manually defined 'reference_data'"
),
"... ",
appendLF = FALSE,
as_note = FALSE
agent_formatted,
mo_var_found,
" according to ",
ifelse(isTRUE(ecoff),
"ECOFF values of ",
""),
ifelse(identical(reference_data, AMR::clinical_breakpoints),
font_bold(guideline_coerced),
"manually defined 'reference_data'"
),
"... ",
appendLF = FALSE,
as_note = FALSE
)
msg_note <- function(messages) {
@@ -876,7 +880,7 @@ as_sir_method <- function(method_short,
method_coerced <- toupper(method)
ab_coerced <- ab
mo_coerced <- mo
if (identical(reference_data, AMR::clinical_breakpoints)) {
breakpoints <- reference_data %pm>%
subset(guideline == guideline_coerced & method == method_coerced & ab == ab_coerced)
@@ -900,7 +904,17 @@ as_sir_method <- function(method_short,
breakpoints <- breakpoints %pm>%
subset(mo != "UNKNOWN" & ref_tbl %unlike% "PK.*PD")
}
if (isFALSE(ecoff)) {
# remove ECOFF interpretations from the breakpoints table
breakpoints <- breakpoints %pm>%
subset(ref_tbl != "ECOFF")
} else {
# keep only ECOFF interpretations from the breakpoints table
breakpoints <- breakpoints %pm>%
subset(ref_tbl == "ECOFF") %pm>%
pm_mutate(breakpoint_S = ecoff, breakpoint_R = ecoff)
}
msgs <- character(0)
if (nrow(breakpoints) == 0) {
# apparently no breakpoints found