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Generalise interpretive rules for multi-guideline support (#268)
- Rename data-raw/eucast_rules.tsv → interpretive_rules.tsv; add rule.provider column (value: "EUCAST") to distinguish future CLSI rows - Rename EUCAST_RULES_DF → INTERPRETIVE_RULES_DF in _pre_commit_checks.R; filter by rule.provider == guideline when applying rules in interpretive_rules() - Rename custom_eucast_rules() → custom_interpretive_rules() with new S3 class "custom_interpretive_rules"; old function becomes a deprecated wrapper in zz_deprecated.R; backward-compat S3 dispatch shims added for old class - Remove stop_if(guideline == "CLSI", ...) so clsi_rules() no longer errors - Add .onLoad shim in zzz.R to create INTERPRETIVE_RULES_DF from EUCAST_RULES_DF for transitional compatibility until sysdata.rda is regenerated https://claude.ai/code/session_01D46BTsfJSPo3HnLWp3PRkP
This commit is contained in:
Claude
@@ -62,17 +62,17 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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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 guideline A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option [`AMR_guideline`][AMR-options].
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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_interpretive_rules`][AMR-options]: `options(AMR_interpretive_rules = "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_interpretive_rules`][AMR-options]: `options(AMR_interpretive_rules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_interpretive_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), documentation = TRUE, 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), documentation = TRUE, 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), documentation = TRUE, reverse = TRUE)`.
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#' @param ampc_cephalosporin_resistance (only applies when `rules` contains `"expert"` or `"all"`) 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 versions 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 ampc_cephalosporin_resistance (only applies when `rules` contains `"expert"` or `"all"`) 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 versions 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(INTERPRETIVE_RULES_DF[which(INTERPRETIVE_RULES_DF$reference.version %in% c(3.2, 3.3) & INTERPRETIVE_RULES_DF$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`.
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#' @param ... Column names of antimicrobials. To automatically detect antimicrobial column names, do not provide any named arguments; [guess_ab_col()] will then be used for detection. To manually specify a column, provide its name (case-insensitive) as an argument, e.g. `AMX = "amoxicillin"`. To skip a specific antimicrobial, set it to `NULL`, e.g. `TIC = NULL` to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.
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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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#' @param administration Route of administration, either `r vector_or(dosage$administration, documentation = TRUE)`.
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#' @param only_sir_columns A [logical] to indicate whether only antimicrobial columns must be included that were transformed to class [sir][as.sir()] on beforehand. Defaults to `FALSE` if no columns of `x` have a class [sir][as.sir()].
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#' @param custom_rules Custom rules to apply, created with [custom_eucast_rules()].
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#' @param custom_rules Custom rules to apply, created with [custom_interpretive_rules()].
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#' @param overwrite A [logical] indicating whether to overwrite existing SIR values (default: `FALSE`). When `FALSE`, only non-SIR values are modified (i.e., any value that is not already S, I or R). To ensure compliance with EUCAST guidelines, **this should remain** `FALSE`, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant".
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#' @param add_if_missing A [logical] indicating whether rules should also be applied to missing (`NA`) values (default: `TRUE`). When `FALSE`, rules are only applied to cells that already contain an SIR value; cells with `NA` are left untouched. This is particularly useful when using `overwrite = TRUE` with custom rules and you want to update reported results without imputing values for untested drugs.
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#' @inheritParams first_isolate
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@@ -80,15 +80,15 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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#' **Note:** This function does not translate MIC or disk values to SIR values. Use [as.sir()] for that. \cr
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#' **Note:** When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. \cr
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#'
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#' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv>. **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The `AMR` package contains the full microbial taxonomy updated until `r documentation_date(max(TAXONOMY_VERSION$GBIF$accessed_date, TAXONOMY_VERSION$LPSN$accessed_date))`, see [microorganisms].
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#' The file containing all interpretive rules is located here: <https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv>. **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The `AMR` package contains the full microbial taxonomy updated until `r documentation_date(max(TAXONOMY_VERSION$GBIF$accessed_date, TAXONOMY_VERSION$LPSN$accessed_date))`, see [microorganisms].
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#'
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#' ### Custom Rules
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#'
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#' Custom rules can be created using [custom_eucast_rules()], e.g.:
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#' Custom rules can be created using [custom_interpretive_rules()], e.g.:
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#'
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#' ```r
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#' x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
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#' AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
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#' x <- custom_interpretive_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
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#' AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
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#'
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#' eucast_rules(example_isolates, rules = "custom", custom_rules = x)
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#' ```
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@@ -184,7 +184,7 @@ interpretive_rules <- function(x,
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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(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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meet_criteria(custom_rules, allow_class = c("custom_interpretive_rules", "custom_eucast_rules"), allow_NULL = TRUE)
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meet_criteria(overwrite, allow_class = "logical", has_length = 1)
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meet_criteria(add_if_missing, allow_class = "logical", has_length = 1)
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@@ -193,11 +193,6 @@ interpretive_rules <- function(x,
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"Either set {.arg overwrite} or {.arg add_if_missing} to {.code TRUE}, or both."
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)
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stop_if(
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guideline == "CLSI",
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"CLSI guideline is not yet supported."
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)
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stop_if(
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!is.na(ampc_cephalosporin_resistance) && !any(c("expert", "all") %in% rules),
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"For the {.arg ampc_cephalosporin_resistance} argument to work, the {.arg rules} argument must contain {.code \"expert\"} or {.code \"all\"}."
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@@ -206,7 +201,7 @@ interpretive_rules <- function(x,
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add_MO_lookup_to_AMR_env()
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if ("custom" %in% rules && is.null(custom_rules)) {
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warning_("in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: no custom rules were set with the {.arg custom_rules} argument",
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warning_("in {.help [{.fun interpretive_rules}](AMR::interpretive_rules)}: no custom rules were set with the {.arg custom_rules} argument",
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immediate = TRUE
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)
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rules <- rules[rules != "custom"]
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@@ -611,59 +606,62 @@ interpretive_rules <- function(x,
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if (!any(c("all", "custom") %in% rules) && !is.null(custom_rules)) {
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if (isTRUE(info)) {
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message_("Skipping custom EUCAST rules, since the {.arg rules} argument does not contain {.code \"custom\"}.")
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message_("Skipping custom interpretive rules, since the {.arg rules} argument does not contain {.code \"custom\"}.")
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}
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custom_rules <- NULL
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}
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# >>> Apply Official EUCAST rules <<< ---------------------------------------------------
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# >>> Apply Official interpretive rules <<< ---------------------------------------------------
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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_total <- list(...)$eucast_rules_df
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if (!is.null(list(...)$interpretive_rules_df)) {
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# this allows: interpretive_rules(x, interpretive_rules_df = AMR:::INTERPRETIVE_RULES_DF |> filter(is.na(have_these_values)))
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interpretive_rules_df_total <- list(...)$interpretive_rules_df
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} else if (!is.null(list(...)$eucast_rules_df)) {
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# deprecated parameter name kept for backward compatibility
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interpretive_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_total <- EUCAST_RULES_DF
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interpretive_rules_df_total <- INTERPRETIVE_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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## filter on guideline provider and user-set guideline versions ----
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interpretive_rules_df <- data.frame()
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if (any(c("all", "breakpoints") %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% "breakpoint" & reference.version == version_breakpoints))
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interpretive_rules_df <- interpretive_rules_df %pm>%
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rbind_AMR(interpretive_rules_df_total %pm>%
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subset(rule.provider == guideline & reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints))
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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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interpretive_rules_df <- interpretive_rules_df %pm>%
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rbind_AMR(interpretive_rules_df_total %pm>%
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subset(rule.provider == guideline & reference.rule_group %like% "expected" & reference.version == version_expected_phenotypes))
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}
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if (any(c("all", "expert") %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% "expert" & reference.version == version_expertrules))
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interpretive_rules_df <- interpretive_rules_df %pm>%
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rbind_AMR(interpretive_rules_df_total %pm>%
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subset(rule.provider == guideline & reference.rule_group %like% "expert" & reference.version == version_expertrules))
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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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# cefotaxime, ceftriaxone, ceftazidime
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if (is.null(ampc_cephalosporin_resistance) || isFALSE(ampc_cephalosporin_resistance)) {
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eucast_rules_df <- subset(
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eucast_rules_df,
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interpretive_rules_df <- subset(
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interpretive_rules_df,
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reference.rule %unlike% "ampc"
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)
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} else {
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if (isTRUE(ampc_cephalosporin_resistance)) {
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ampc_cephalosporin_resistance <- "R"
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}
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if (!is.null(eucast_rules_df$reference.rule)) {
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eucast_rules_df[which(eucast_rules_df$reference.rule %like% "ampc"), "to_value"] <- as.character(ampc_cephalosporin_resistance)
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if (!is.null(interpretive_rules_df$reference.rule)) {
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interpretive_rules_df[which(interpretive_rules_df$reference.rule %like% "ampc"), "to_value"] <- as.character(ampc_cephalosporin_resistance)
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}
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}
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# sometimes, the screenings are missing but the names are actually available
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# we only hints on remaining rows in `eucast_rules_df`
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# we only hints on remaining rows in `interpretive_rules_df`
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screening_abx <- as.character(AMR::antimicrobials$ab[which(AMR::antimicrobials$ab %like% "-S$")])
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screening_abx <- screening_abx[screening_abx %in% unique(unlist(strsplit(EUCAST_RULES_DF$and_these_antibiotics[!is.na(EUCAST_RULES_DF$and_these_antibiotics)], ", *")))]
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screening_abx <- screening_abx[screening_abx %in% unique(unlist(strsplit(INTERPRETIVE_RULES_DF$and_these_antibiotics[!is.na(INTERPRETIVE_RULES_DF$and_these_antibiotics)], ", *")))]
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if (isTRUE(info)) {
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cat("\n")
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}
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@@ -682,12 +680,12 @@ interpretive_rules <- function(x,
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}
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## Go over all rules and apply them ----
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for (i in seq_len(nrow(eucast_rules_df))) {
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rule_previous <- eucast_rules_df[max(1, i - 1), "reference.rule", drop = TRUE]
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rule_current <- eucast_rules_df[i, "reference.rule", drop = TRUE]
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rule_next <- eucast_rules_df[min(nrow(eucast_rules_df), i + 1), "reference.rule", drop = TRUE]
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rule_group_previous <- eucast_rules_df[max(1, i - 1), "reference.rule_group", drop = TRUE]
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rule_group_current <- eucast_rules_df[i, "reference.rule_group", drop = TRUE]
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for (i in seq_len(nrow(interpretive_rules_df))) {
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rule_previous <- interpretive_rules_df[max(1, i - 1), "reference.rule", drop = TRUE]
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rule_current <- interpretive_rules_df[i, "reference.rule", drop = TRUE]
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rule_next <- interpretive_rules_df[min(nrow(interpretive_rules_df), i + 1), "reference.rule", drop = TRUE]
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rule_group_previous <- interpretive_rules_df[max(1, i - 1), "reference.rule_group", drop = TRUE]
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rule_group_current <- interpretive_rules_df[i, "reference.rule_group", drop = TRUE]
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# don't apply rules if user doesn't want to apply them
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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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@@ -702,16 +700,16 @@ interpretive_rules <- function(x,
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if (isFALSE(info) || isFALSE(verbose)) {
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rule_text <- ""
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} else {
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if (is.na(eucast_rules_df[i, "and_these_antibiotics", drop = TRUE])) {
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rule_text <- paste0("always report as '", eucast_rules_df[i, "to_value", drop = TRUE], "': ", get_antibiotic_names(eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE]))
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if (is.na(interpretive_rules_df[i, "and_these_antibiotics", drop = TRUE])) {
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rule_text <- paste0("always report as '", interpretive_rules_df[i, "to_value", drop = TRUE], "': ", get_antibiotic_names(interpretive_rules_df[i, "then_change_these_antibiotics", drop = TRUE]))
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} else {
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rule_text <- paste0(
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"report as '", eucast_rules_df[i, "to_value", drop = TRUE], "' when ",
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"report as '", interpretive_rules_df[i, "to_value", drop = TRUE], "' when ",
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format_antibiotic_names(
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ab_names = get_antibiotic_names(eucast_rules_df[i, "and_these_antibiotics", drop = TRUE]),
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ab_results = eucast_rules_df[i, "have_these_values", drop = TRUE]
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ab_names = get_antibiotic_names(interpretive_rules_df[i, "and_these_antibiotics", drop = TRUE]),
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ab_results = interpretive_rules_df[i, "have_these_values", drop = TRUE]
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), ": ",
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get_antibiotic_names(eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE])
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get_antibiotic_names(interpretive_rules_df[i, "then_change_these_antibiotics", drop = TRUE])
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)
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}
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}
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@@ -720,7 +718,7 @@ interpretive_rules <- function(x,
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rule_previous <- ""
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rule_group_previous <- ""
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}
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if (i == nrow(eucast_rules_df)) {
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if (i == nrow(interpretive_rules_df)) {
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rule_next <- ""
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}
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@@ -789,13 +787,13 @@ interpretive_rules <- function(x,
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}
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## Get rule from file ------------------------------------------------------
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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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if_mo_property <- trimws(interpretive_rules_df[i, "if_mo_property", drop = TRUE])
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like_is_one_of <- trimws(interpretive_rules_df[i, "like.is.one_of", drop = TRUE])
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mo_value <- trimws(interpretive_rules_df[i, "this_value", drop = TRUE])
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source_antibiotics <- interpretive_rules_df[i, "and_these_antibiotics", drop = TRUE]
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source_value <- trimws(unlist(strsplit(interpretive_rules_df[i, "have_these_values", drop = TRUE], ",", fixed = TRUE)))
|
||||
target_antibiotics <- interpretive_rules_df[i, "then_change_these_antibiotics", drop = TRUE]
|
||||
target_value <- interpretive_rules_df[i, "to_value", drop = TRUE]
|
||||
|
||||
# if amo_value contains a group name, expand that name with all species in it
|
||||
if (any(trimws(strsplit(mo_value, ",")[[1]]) %in% AMR::microorganisms.groups$mo_group_name, na.rm = TRUE)) {
|
||||
@@ -894,7 +892,7 @@ interpretive_rules <- function(x,
|
||||
if (!is.null(custom_rules)) {
|
||||
if (isTRUE(info)) {
|
||||
cat("\n")
|
||||
cat(font_bold("Custom EUCAST rules, set by user"), "\n")
|
||||
cat(font_bold("Custom interpretive rules, set by user"), "\n")
|
||||
}
|
||||
for (i in seq_len(length(custom_rules))) {
|
||||
rule <- custom_rules[[i]]
|
||||
@@ -929,8 +927,8 @@ interpretive_rules <- function(x,
|
||||
to = target_value,
|
||||
rule = c(
|
||||
rule_text,
|
||||
"Custom EUCAST rules",
|
||||
paste0("Custom EUCAST rule ", i),
|
||||
"Custom interpretive rules",
|
||||
paste0("Custom interpretive rule ", i),
|
||||
paste0(
|
||||
"Object '", deparse(substitute(custom_rules)),
|
||||
"' consisting of ", length(custom_rules), " custom rules"
|
||||
|
||||
Reference in New Issue
Block a user