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implement ecoffs
This commit is contained in:
parent
55b98ede4c
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3083828e15
@ -1,6 +1,6 @@
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Package: AMR
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Version: 2.0.0.9024
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Date: 2023-06-10
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Date: 2023-06-22
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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4
NEWS.md
4
NEWS.md
@ -2,8 +2,8 @@
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## New
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* Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for `as.sir()`. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for `eucast_rules()` to apply EUCAST Expert Rules.
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* The EUCAST dosage guideline of v13.0 as been added to the `dosage` data set
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* ECOFF: the `clinical_breakpoints` data set now contains the new column `ecoff`, in which the epidemiological cut-off (ECOFF) are available. These ECOFFs can now also be used in `as.sir()`, which is an important new addition for veterinary microbiology.
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* The EUCAST dosage guideline of v13.0 has been added to the `dosage` data set
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* ECOFF: the `clinical_breakpoints` data set now contains the new column `ecoff`, in which the epidemiological cut-off (ECOFF) are available. These ECOFFs can be used for MIC/disk interpretation using `as.sir(..., ecoff = TRUE)`, which is an important new addition for veterinary microbiology.
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* Added oxygen tolerance from BacDive to over 25,000 bacteria in the `microorganisms` data set
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* Added `mo_oxygen_tolerance()` to retrieve the values
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* Added `mo_is_anaerobic()` to determine which genera/species are obligate anaerobic bacteria
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@ -56,12 +56,6 @@ EUCAST_VERSION_BREAKPOINTS <- list(
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)
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)
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EUCAST_VERSION_EXPERT_RULES <- list(
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"1.2" = list(
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version_txt = "v3.3",
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year = 2023,
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title = "'EUCAST Expert Rules' and 'Expected Resistant Phenotypes'",
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url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"
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),
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"3.3" = list(
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version_txt = "v3.3",
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year = 2021,
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@ -81,6 +75,14 @@ EUCAST_VERSION_EXPERT_RULES <- list(
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url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"
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)
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)
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EUCAST_VERSION_RESISTANTPHENOTYPES <- list(
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"1.2" = list(
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version_txt = "v1.2",
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year = 2023,
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title = "'Expected Resistant Phenotypes'",
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url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"
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)
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)
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TAXONOMY_VERSION <- list(
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GBIF = list(
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@ -63,8 +63,9 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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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-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()].
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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 either `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), 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 either `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`.
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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_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 antibiotic, see section *Antibiotics* below
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#' @param ab any (vector of) text that can be coerced to a valid antibiotic drug code with [as.ab()]
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@ -167,6 +168,7 @@ eucast_rules <- function(x,
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verbose = FALSE,
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version_breakpoints = 12.0,
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version_expertrules = 3.3,
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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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@ -178,6 +180,7 @@ eucast_rules <- function(x,
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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_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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@ -205,7 +208,8 @@ eucast_rules <- function(x,
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breakpoints_info <- EUCAST_VERSION_BREAKPOINTS[[which(as.double(names(EUCAST_VERSION_BREAKPOINTS)) == version_breakpoints)]]
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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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38
R/sir.R
38
R/sir.R
@ -43,7 +43,7 @@
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#' @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)`.
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#' @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].
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#' @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].
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#' @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].
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#' @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].
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#' @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.
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#' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, see *Examples*
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#' @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.
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@ -831,15 +831,19 @@ as_sir_method <- function(method_short,
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)
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}
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message_("=> Interpreting ", method_long, " of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
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agent_formatted,
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mo_var_found,
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" according to ", ifelse(identical(reference_data, AMR::clinical_breakpoints),
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font_bold(guideline_coerced),
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"manually defined 'reference_data'"
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),
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"... ",
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appendLF = FALSE,
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as_note = FALSE
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agent_formatted,
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mo_var_found,
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" according to ",
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ifelse(isTRUE(ecoff),
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"ECOFF values of ",
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""),
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ifelse(identical(reference_data, AMR::clinical_breakpoints),
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font_bold(guideline_coerced),
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"manually defined 'reference_data'"
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),
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"... ",
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appendLF = FALSE,
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as_note = FALSE
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)
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msg_note <- function(messages) {
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@ -876,7 +880,7 @@ as_sir_method <- function(method_short,
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method_coerced <- toupper(method)
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ab_coerced <- ab
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mo_coerced <- mo
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if (identical(reference_data, AMR::clinical_breakpoints)) {
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breakpoints <- reference_data %pm>%
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subset(guideline == guideline_coerced & method == method_coerced & ab == ab_coerced)
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@ -900,7 +904,17 @@ as_sir_method <- function(method_short,
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breakpoints <- breakpoints %pm>%
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subset(mo != "UNKNOWN" & ref_tbl %unlike% "PK.*PD")
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}
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if (isFALSE(ecoff)) {
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# remove ECOFF interpretations from the breakpoints table
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breakpoints <- breakpoints %pm>%
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subset(ref_tbl != "ECOFF")
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} else {
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# keep only ECOFF interpretations from the breakpoints table
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breakpoints <- breakpoints %pm>%
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subset(ref_tbl == "ECOFF") %pm>%
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pm_mutate(breakpoint_S = ecoff, breakpoint_R = ecoff)
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}
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msgs <- character(0)
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if (nrow(breakpoints) == 0) {
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# apparently no breakpoints found
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@ -166,15 +166,13 @@ expect_identical(mo_ref("Chlamydia psittaci"), "Garcia-Lopez et al., 2019")
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expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999")
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expect_true(112283007 %in% mo_snomed("Escherichia coli")[[1]])
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# old codes must throw a warning in mo_* family
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# expect_warning(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))
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# outcome of mo_fullname must always return the fullname from the data set
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x <- data.frame(
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mo = microorganisms$mo,
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# fullname from the original data:
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f1 = microorganisms$fullname,
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# newly created fullname based on MO code:
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f2 = mo_fullname(microorganisms$mo, language = "en"),
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f2 = mo_fullname(microorganisms$mo, language = "en", keep_synonyms = TRUE),
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stringsAsFactors = FALSE
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)
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expect_equal(nrow(subset(x, f1 != f2)), 0)
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@ -142,6 +142,10 @@ expect_equal(
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suppressMessages(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020")),
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as.sir("S")
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)
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expect_equal(
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suppressMessages(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020", ecoff = TRUE)),
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as.sir("S")
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)
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expect_equal(
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suppressMessages(as.sir(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020")),
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as.sir("R")
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@ -112,7 +112,7 @@ not_intrinsic_resistant(
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\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
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\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2", "3.1", or "1.2".}
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\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".}
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}
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\value{
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(internally) a \link{character} vector of column names, with additional class \code{"ab_selector"}
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@ -133,7 +133,7 @@ The \code{\link[=ab_selector]{ab_selector()}} function can be used to internally
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The \code{\link[=administrable_per_os]{administrable_per_os()}} and \code{\link[=administrable_iv]{administrable_iv()}} functions also rely on the \link{antibiotics} data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the \link{antibiotics} data set.
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The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function can be used to only select antibiotic columns that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of \emph{E. coli} and \emph{K. pneumoniae} and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies \href{https://www.eucast.org/expert_rules_and_expected_phenotypes/}{'EUCAST Expert Rules' and 'Expected Resistant Phenotypes' v3.3} (2023) to determine intrinsic resistance, using the \code{\link[=eucast_rules]{eucast_rules()}} function internally. Because of this determination, this function is quite slow in terms of performance.
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The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function can be used to only select antibiotic columns that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of \emph{E. coli} and \emph{K. pneumoniae} and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies \href{https://www.eucast.org/expert_rules_and_expected_phenotypes/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021) to determine intrinsic resistance, using the \code{\link[=eucast_rules]{eucast_rules()}} function internally. Because of this determination, this function is quite slow in terms of performance.
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}
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\section{Full list of supported (antibiotic) classes}{
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@ -102,7 +102,7 @@ sir_interpretation_history(clean = FALSE)
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\item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_include_PKPD}}.}
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\item{ecoff}{a \link{logical} to indicate that ECOFF (Epidemiological Cut-Off) values must be used - the default is \code{FALSE}. Can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_ecoff}}.}
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\item{ecoff}{a \link{logical} to indicate that ECOFF (Epidemiological Cut-Off) values must be used \strong{instead} of other clinical breakpoints - the default is \code{FALSE}. Can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_ecoff}}.}
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\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
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@ -27,6 +27,7 @@ eucast_rules(
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verbose = FALSE,
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version_breakpoints = 12,
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version_expertrules = 3.3,
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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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@ -46,9 +47,11 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 13)
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\item{verbose}{a \link{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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\item{version_breakpoints}{the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either "13.0", "12.0", "11.0", or "10.0".}
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\item{version_breakpoints}{the version number to use for the EUCAST Clinical Breakpoints guideline. Can be "13.0", "12.0", "11.0", or "10.0".}
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\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2", "3.1", or "1.2".}
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\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".}
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\item{version_resistant_phenotypes}{the version number to use for the EUCAST Expected Resistant Phenotypes. Can be "1.2".}
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\item{ampc_cephalosporin_resistance}{a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these version of '\emph{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 \code{NA} (the default) for this argument will remove results for these three drugs, while e.g. a value of \code{"R"} will make the results for these drugs resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia}, and \emph{Serratia}.}
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