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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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2
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 2.0.0.9024 Version: 2.0.0.9024
Date: 2023-06-10 Date: 2023-06-22
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

4
NEWS.md
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@ -2,8 +2,8 @@
## New ## New
* 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. * 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.
* The EUCAST dosage guideline of v13.0 as been added to the `dosage` data set * The EUCAST dosage guideline of v13.0 has been added to the `dosage` data set
* 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. * 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.
* Added oxygen tolerance from BacDive to over 25,000 bacteria in the `microorganisms` data set * Added oxygen tolerance from BacDive to over 25,000 bacteria in the `microorganisms` data set
* Added `mo_oxygen_tolerance()` to retrieve the values * Added `mo_oxygen_tolerance()` to retrieve the values
* Added `mo_is_anaerobic()` to determine which genera/species are obligate anaerobic bacteria * Added `mo_is_anaerobic()` to determine which genera/species are obligate anaerobic bacteria

14
R/aa_globals.R
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@ -56,12 +56,6 @@ EUCAST_VERSION_BREAKPOINTS <- list(
) )
) )
EUCAST_VERSION_EXPERT_RULES <- 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( "3.3" = list(
version_txt = "v3.3", version_txt = "v3.3",
year = 2021, year = 2021,
@ -81,6 +75,14 @@ EUCAST_VERSION_EXPERT_RULES <- list(
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/" 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( TAXONOMY_VERSION <- list(
GBIF = list( GBIF = list(

10
R/eucast_rules.R
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@ -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 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 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 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_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 either `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), 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 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 ... 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()] #' @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, verbose = FALSE,
version_breakpoints = 12.0, version_breakpoints = 12.0,
version_expertrules = 3.3, version_expertrules = 3.3,
version_resistant_phenotypes = 1.2,
ampc_cephalosporin_resistance = NA, ampc_cephalosporin_resistance = NA,
only_sir_columns = FALSE, only_sir_columns = FALSE,
custom_rules = NULL, custom_rules = NULL,
@ -178,6 +180,7 @@ eucast_rules <- function(x,
meet_criteria(verbose, allow_class = "logical", has_length = 1) 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_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_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(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(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE) 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)]] 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)]] 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) # support old setting (until AMR v1.3.0)
if (missing(rules) && !is.null(getOption("AMR.eucast_rules"))) { if (missing(rules) && !is.null(getOption("AMR.eucast_rules"))) {
rules <- getOption("AMR.eucast_rules") rules <- getOption("AMR.eucast_rules")

38
R/sir.R
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@ -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 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_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 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 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 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. #' @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(...)$is_data.frame), "column ", ""), message_("=> Interpreting ", method_long, " of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
agent_formatted, agent_formatted,
mo_var_found, mo_var_found,
" according to ", ifelse(identical(reference_data, AMR::clinical_breakpoints), " according to ",
font_bold(guideline_coerced), ifelse(isTRUE(ecoff),
"manually defined 'reference_data'" "ECOFF values of ",
), ""),
"... ", ifelse(identical(reference_data, AMR::clinical_breakpoints),
appendLF = FALSE, font_bold(guideline_coerced),
as_note = FALSE "manually defined 'reference_data'"
),
"... ",
appendLF = FALSE,
as_note = FALSE
) )
msg_note <- function(messages) { msg_note <- function(messages) {
@ -876,7 +880,7 @@ as_sir_method <- function(method_short,
method_coerced <- toupper(method) method_coerced <- toupper(method)
ab_coerced <- ab ab_coerced <- ab
mo_coerced <- mo mo_coerced <- mo
if (identical(reference_data, AMR::clinical_breakpoints)) { if (identical(reference_data, AMR::clinical_breakpoints)) {
breakpoints <- reference_data %pm>% breakpoints <- reference_data %pm>%
subset(guideline == guideline_coerced & method == method_coerced & ab == ab_coerced) subset(guideline == guideline_coerced & method == method_coerced & ab == ab_coerced)
@ -900,7 +904,17 @@ as_sir_method <- function(method_short,
breakpoints <- breakpoints %pm>% breakpoints <- breakpoints %pm>%
subset(mo != "UNKNOWN" & ref_tbl %unlike% "PK.*PD") 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) msgs <- character(0)
if (nrow(breakpoints) == 0) { if (nrow(breakpoints) == 0) {
# apparently no breakpoints found # apparently no breakpoints found

0
inst/tinytest/test-ggplot_rsi.R → inst/tinytest/test-ggplot_sir.R
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4
inst/tinytest/test-mo_property.R
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@ -166,15 +166,13 @@ expect_identical(mo_ref("Chlamydia psittaci"), "Garcia-Lopez et al., 2019")
expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999") expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999")
expect_true(112283007 %in% mo_snomed("Escherichia coli")[[1]]) expect_true(112283007 %in% mo_snomed("Escherichia coli")[[1]])
# old codes must throw a warning in mo_* family
# expect_warning(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))
# outcome of mo_fullname must always return the fullname from the data set # outcome of mo_fullname must always return the fullname from the data set
x <- data.frame( x <- data.frame(
mo = microorganisms$mo, mo = microorganisms$mo,
# fullname from the original data: # fullname from the original data:
f1 = microorganisms$fullname, f1 = microorganisms$fullname,
# newly created fullname based on MO code: # newly created fullname based on MO code:
f2 = mo_fullname(microorganisms$mo, language = "en"), f2 = mo_fullname(microorganisms$mo, language = "en", keep_synonyms = TRUE),
stringsAsFactors = FALSE stringsAsFactors = FALSE
) )
expect_equal(nrow(subset(x, f1 != f2)), 0) expect_equal(nrow(subset(x, f1 != f2)), 0)

4
inst/tinytest/test-rsi.R → inst/tinytest/test-sir.R
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@ -142,6 +142,10 @@ expect_equal(
suppressMessages(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020")), suppressMessages(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020")),
as.sir("S") as.sir("S")
) )
expect_equal(
suppressMessages(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020", ecoff = TRUE)),
as.sir("S")
)
expect_equal( expect_equal(
suppressMessages(as.sir(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020")), suppressMessages(as.sir(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020")),
as.sir("R") as.sir("R")

4
man/antibiotic_class_selectors.Rd
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@ -112,7 +112,7 @@ not_intrinsic_resistant(
\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()}}.} \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()}}.}
\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".} \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".}
} }
\value{ \value{
(internally) a \link{character} vector of column names, with additional class \code{"ab_selector"} (internally) a \link{character} vector of column names, with additional class \code{"ab_selector"}
@ -133,7 +133,7 @@ The \code{\link[=ab_selector]{ab_selector()}} function can be used to internally
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. 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.
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. 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.
} }
\section{Full list of supported (antibiotic) classes}{ \section{Full list of supported (antibiotic) classes}{

2
man/as.sir.Rd
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@ -102,7 +102,7 @@ sir_interpretation_history(clean = FALSE)
\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}}.} \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}}.}
\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}}.} \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}}.}
\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()}}.} \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()}}.}

7
man/eucast_rules.Rd
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@ -27,6 +27,7 @@ eucast_rules(
verbose = FALSE, verbose = FALSE,
version_breakpoints = 12, version_breakpoints = 12,
version_expertrules = 3.3, version_expertrules = 3.3,
version_resistant_phenotypes = 1.2,
ampc_cephalosporin_resistance = NA, ampc_cephalosporin_resistance = NA,
only_sir_columns = FALSE, only_sir_columns = FALSE,
custom_rules = NULL, custom_rules = NULL,
@ -46,9 +47,11 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 13)
\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.} \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.}
\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".} \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".}
\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".} \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".}
\item{version_resistant_phenotypes}{the version number to use for the EUCAST Expected Resistant Phenotypes. Can be "1.2".}
\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}.} \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}.}