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* Fix custom reference_data support in as.sir() (#239) - custom guideline names now correctly classify values as R: CLSI convention (>= breakpoint_R for MIC, <= for disk) applies only when guideline contains "CLSI"; all other guidelines including custom ones use the EUCAST convention (> breakpoint_R for MIC, < for disk) - guideline argument is now optional when reference_data is manually set: if omitted or if its value does not match any row in the custom data, all rows in reference_data are used; if set to a value present in the data, only matching rows are filtered — useful for multi-guideline custom tables - host = NA in custom reference_data now acts as a host-agnostic fallback when no host-specific breakpoint row exists for the current animal species - updated reference_data argument documentation to explain these conventions https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U * Refactor R-classification logic using custom_breakpoints_set flag Introduce custom_breakpoints_set <- !identical(reference_data, AMR::clinical_breakpoints) at the top of as_sir_method() and replace all identical() calls inside that function with this variable. In the case_when_AMR interpretation blocks (MIC and disk), the R-classification now has three explicit arms: - !custom_breakpoints_set & EUCAST guideline -> open interval (> / <) - !custom_breakpoints_set & CLSI guideline -> closed interval (>= / <=) - custom_breakpoints_set -> open interval (> / <), always, regardless of the guideline name in the custom data (e.g. "CLSI_custom" must not accidentally trigger CLSI convention) https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U * Fix unit tests for custom reference_data (#239) - Do not override my_bp$mo / my_bp$ab in tests: assigning plain character strips the <mo>/<ab> class, which check_reference_data() rejects. Use the mo/ab values already present in the source row instead. - Use NA_character_ instead of NA for my_bp$host so the host column keeps its character class. - Pass breakpoint_type = "animal" explicitly in the host-fallback test since the custom reference_data only contains animal-type breakpoints. https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U * Add coerce_reference_data_columns() for lenient reference_data validation check_reference_data() now returns the (possibly coerced) reference_data and the call site captures the result so downstream code sees the fixed columns. A new coerce_reference_data_columns() helper is called before the strict class check inside check_reference_data(). It coerces columns to the expected types: - mo -> as.mo() if not already <mo> class - ab -> as.ab() if not already <ab> class - character columns -> as.character() (e.g. host = NA becomes NA_character_) - numeric columns -> as.double() - logical columns -> as.logical() This allows users to build a custom reference_data from a plain data.frame without having to pre-apply as.mo()/as.ab() or worry about NA column types. Updated the reference_data roxygen argument to document the auto-coercion and restored the tests to the simpler form that uses plain character assignments, relying on the new coercion instead of workarounds. https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U --------- Co-authored-by: Claude <noreply@anthropic.com>
This commit is contained in:
Matthijs Berends
GitHub
@@ -1,6 +1,6 @@
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Package: AMR
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Version: 3.0.1.9050
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Date: 2026-04-24
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Date: 2026-04-25
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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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1
NEWS.md
1
NEWS.md
@@ -21,6 +21,7 @@
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* Two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R's `NA_character_` and `NA_integer_`, for use in pipelines that require typed missing values
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### Fixes
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* `as.sir()` with `reference_data`: custom guideline names now correctly classify values as R using EUCAST convention (`> breakpoint_R` for MIC, `< breakpoint_R` for disk); custom breakpoints with `host = NA` now serve as a host-agnostic fallback when no host-specific row matches (fixes #239)
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* Fixed multiple bugs in the `parallel = TRUE` mode of `as.sir()` for data frames: (1) PSOCK workers (Windows / R < 4.0) now correctly load the AMR package before processing, with a graceful fallback to sequential mode when the package cannot be loaded; (2) resolved stale-environment issue where the PSOCK path read a frozen copy of `AMR_env` instead of the live one, causing the wrong log entries to be captured; (3) fixed log-entry duplication in the fork-based path (`mclapply`) where pre-existing `sir_interpretation_history` rows were included in every worker's captured log; (4) removed use of non-exported internal functions (`%pm>%`, `pm_pull`, `as.sir.default`) from the worker closure, which made PSOCK workers fail; (5) suppressed per-column progress messages inside workers to prevent interleaved console output; (6) fixed a malformed Unicode escape `\u00a` (3 digits) in the "DONE" status message
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* Fixed a bug in `as.sir()` where values that were purely numeric (e.g., `"1"`) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter
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* Fixed a bug in `as.mic()` where MIC values in scientific notation (e.g., `"1e-3"`) were incorrectly handled because the letter `e` was removed along with other Unicode letters; scientific notation `e` is now preserved
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71
R/sir.R
71
R/sir.R
@@ -69,7 +69,7 @@ VALID_SIR_LEVELS <- c("S", "SDD", "I", "R", "NI", "WT", "NWT", "NS")
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#' @param host A vector (or column name) with [character]s to indicate the host. Only useful for veterinary breakpoints, as it requires `breakpoint_type = "animal"`. The values can be any text resembling the animal species, even in any of the `r length(LANGUAGES_SUPPORTED)` supported languages of this package. For foreign languages, be sure to set the language with [set_AMR_locale()] (though it will be automatically guessed based on the system language).
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#' @param language Language to convert values set in `host` when using animal breakpoints. Use one of these supported language names or [ISO 639-1 codes](https://en.wikipedia.org/wiki/ISO_639-1): `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`.
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#' @param verbose A [logical] to indicate that all notes should be printed during interpretation of MIC values or disk diffusion values.
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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 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 have the same column names as the [clinical_breakpoints] data set. Column types are coerced automatically where possible: the `mo` column is passed through [as.mo()], the `ab` column through [as.ab()], and plain character, numeric, or logical columns are cast to the expected type. When `reference_data` is manually set, the `guideline` argument is optional: if omitted (or if its value does not match any row in the custom data), all rows in `reference_data` are considered. If `guideline` is set to a value that exists in the `guideline` column of the custom data, only matching rows are used — useful when a single custom table contains multiple guidelines. For the R classification, the EUCAST convention is used by default: MIC values `> breakpoint_R` and disk diffusion values `< breakpoint_R` are classified as R, with values between `breakpoint_S` and `breakpoint_R` classified as I (or SDD). Only when using the standard [clinical_breakpoints] with a CLSI guideline are the closed-interval rules (`>= breakpoint_R` for MIC, `<= breakpoint_R` for disk) applied; custom `reference_data` always uses the open-interval (EUCAST) convention regardless of the guideline name.
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#' @param threshold Maximum fraction of invalid antimicrobial interpretations of `x`, see *Examples*.
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#' @param conserve_capped_values Deprecated, use `capped_mic_handling` instead.
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#' @param ... For using on a [data.frame]: selection of columns to apply `as.sir()` to. Supports [tidyselect language][tidyselect::starts_with()] such as `where(is.mic)`, `starts_with(...)`, or `column1:column4`, and can thus also be [antimicrobial selectors][amr_selector()], e.g. `as.sir(df, penicillins())`.
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@@ -1271,7 +1271,7 @@ as_sir_method <- function(method_short,
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meet_criteria(substitute_missing_r_breakpoint, allow_class = "logical", has_length = 1, .call_depth = -2)
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meet_criteria(include_screening, allow_class = "logical", has_length = 1, .call_depth = -2)
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meet_criteria(include_PKPD, allow_class = "logical", has_length = 1, .call_depth = -2)
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check_reference_data(reference_data, .call_depth = -2)
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reference_data <- check_reference_data(reference_data, .call_depth = -2)
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meet_criteria(breakpoint_type, allow_class = "character", is_in = reference_data$type, has_length = 1, .call_depth = -2)
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meet_criteria(host, allow_class = c("character", "factor"), allow_NULL = TRUE, allow_NA = TRUE, .call_depth = -2)
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language <- validate_language(language)
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@@ -1286,6 +1286,7 @@ as_sir_method <- function(method_short,
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}
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current_sir_interpretation_history <- NROW(AMR_env$sir_interpretation_history)
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custom_breakpoints_set <- !identical(reference_data, AMR::clinical_breakpoints)
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if (isTRUE(info) && message_not_thrown_before("as.sir", "sir_interpretation_history")) {
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message_("Run {.help [{.fun sir_interpretation_history}](AMR::sir_interpretation_history)} afterwards to retrieve a logbook with all details of the breakpoint interpretations.\n\n")
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@@ -1490,7 +1491,7 @@ as_sir_method <- function(method_short,
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"\u00a0\u00a0", AMR_env$bullet_icon, " Interpreting ", method_long, ": ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
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ifelse(length(unique(agent_formatted)) == 1, unique(agent_formatted), paste0(vector_and(agent_formatted, quotes = FALSE, sort = FALSE))),
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mo_var_found,
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ifelse(identical(reference_data, AMR::clinical_breakpoints),
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ifelse(!custom_breakpoints_set,
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paste0(", ", vector_and(font_bold(guideline_coerced, collapse = NULL), quotes = FALSE)),
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""
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),
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@@ -1507,7 +1508,7 @@ as_sir_method <- function(method_short,
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method_coerced <- toupper(method)
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ab_coerced <- as.ab(ab, info = FALSE)
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if (identical(reference_data, AMR::clinical_breakpoints)) {
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if (!custom_breakpoints_set) {
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breakpoints <- reference_data %pm>%
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subset(guideline %in% guideline_coerced & method == method_coerced & ab %in% ab_coerced)
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if (any(ab_coerced == "AMX") && nrow(breakpoints[breakpoints$ab == "AMX", , drop = FALSE]) == 0) {
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@@ -1690,8 +1691,15 @@ as_sir_method <- function(method_short,
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# gather all available breakpoints for current MO
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# TODO for VET09 do not filter out E. coli and such
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# For custom reference_data: skip guideline filter when guideline_current is not in the data (#239)
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guideline_filter_current <- if (custom_breakpoints_set &&
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!guideline_current %in% breakpoints$guideline) {
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unique(breakpoints$guideline)
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} else {
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guideline_current
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}
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breakpoints_current <- breakpoints %pm>%
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subset(ab == ab_current & guideline == guideline_current) %pm>%
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subset(ab == ab_current & guideline %in% guideline_filter_current) %pm>%
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subset(mo %in% c(
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mo_current, mo_current_genus, mo_current_family,
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mo_current_order, mo_current_class,
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@@ -1701,8 +1709,13 @@ as_sir_method <- function(method_short,
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))
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if (breakpoint_type == "animal") {
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# 2025-03-13/ for now, only strictly follow guideline for current host, no extrapolation
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breakpoints_current <- breakpoints_current[which(breakpoints_current$host == host_current), , drop = FALSE]
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host_matched <- breakpoints_current[which(breakpoints_current$host == host_current), , drop = FALSE]
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if (nrow(host_matched) > 0) {
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breakpoints_current <- host_matched
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} else {
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# fall back to host-agnostic rows (host = NA) for custom breakpoint tables (#239)
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breakpoints_current <- breakpoints_current[which(is.na(breakpoints_current$host)), , drop = FALSE]
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}
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}
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## fall-back methods for veterinary guidelines ----
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@@ -1978,8 +1991,11 @@ as_sir_method <- function(method_short,
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# otherwise: the normal (uncapped or ignored) interpretation
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input_clean <= breakpoints_current$breakpoint_S ~ as.sir("S"),
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guideline_current %like% "EUCAST" & input_clean > breakpoints_current$breakpoint_R ~ as.sir("R"),
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guideline_current %like% "CLSI" & input_clean >= breakpoints_current$breakpoint_R ~ as.sir("R"),
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# standard data: EUCAST open interval (>), CLSI closed interval (>=)
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!custom_breakpoints_set & guideline_current %like% "EUCAST" & input_clean > breakpoints_current$breakpoint_R ~ as.sir("R"),
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!custom_breakpoints_set & guideline_current %like% "CLSI" & input_clean >= breakpoints_current$breakpoint_R ~ as.sir("R"),
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# custom reference_data: always EUCAST open interval (>), regardless of guideline name
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custom_breakpoints_set & input_clean > breakpoints_current$breakpoint_R ~ as.sir("R"),
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# return "I" or "SDD" when breakpoints are in the middle
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!is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == TRUE ~ as.sir("SDD"),
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@@ -1992,8 +2008,11 @@ as_sir_method <- function(method_short,
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new_sir <- case_when_AMR(
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is.na(input_clean) ~ NA_sir_,
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as.double(input_clean) >= as.double(breakpoints_current$breakpoint_S) ~ as.sir("S"),
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guideline_current %like% "EUCAST" & as.double(input_clean) < as.double(breakpoints_current$breakpoint_R) ~ as.sir("R"),
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guideline_current %like% "CLSI" & as.double(input_clean) <= as.double(breakpoints_current$breakpoint_R) ~ as.sir("R"),
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# standard data: EUCAST open interval (<), CLSI closed interval (<=)
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!custom_breakpoints_set & guideline_current %like% "EUCAST" & as.double(input_clean) < as.double(breakpoints_current$breakpoint_R) ~ as.sir("R"),
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!custom_breakpoints_set & guideline_current %like% "CLSI" & as.double(input_clean) <= as.double(breakpoints_current$breakpoint_R) ~ as.sir("R"),
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# custom reference_data: always EUCAST open interval (<), regardless of guideline name
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custom_breakpoints_set & as.double(input_clean) < as.double(breakpoints_current$breakpoint_R) ~ as.sir("R"),
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# return "I" or "SDD" when breakpoints are in the middle
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!is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == TRUE ~ as.sir("SDD"),
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!is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == FALSE ~ as.sir("I"),
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@@ -2340,13 +2359,36 @@ rep.sir <- function(x, ...) {
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y
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}
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coerce_reference_data_columns <- function(x) {
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ref <- AMR::clinical_breakpoints
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for (col in names(ref)) {
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col_ref <- ref[[col]]
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col_x <- x[[col]]
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if (identical(class(col_ref), class(col_x))) next
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if (col == "mo") {
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x[[col]] <- suppressMessages(as.mo(col_x))
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} else if (col == "ab") {
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x[[col]] <- suppressMessages(as.ab(col_x))
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} else if (is.character(col_ref)) {
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x[[col]] <- as.character(col_x)
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} else if (is.numeric(col_ref)) {
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x[[col]] <- as.double(col_x)
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} else if (is.logical(col_ref)) {
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x[[col]] <- as.logical(col_x)
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}
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}
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x
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}
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check_reference_data <- function(reference_data, .call_depth) {
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if (!identical(reference_data, AMR::clinical_breakpoints)) {
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class_sir <- vapply(FUN.VALUE = character(1), AMR::clinical_breakpoints, function(x) paste0("<", class(x), ">", collapse = " and "))
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class_ref <- vapply(FUN.VALUE = character(1), reference_data, function(x) paste0("<", class(x), ">", collapse = " and "))
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if (!all(names(class_sir) == names(class_ref))) {
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if (!all(names(AMR::clinical_breakpoints) == names(reference_data))) {
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stop_("{.arg reference_data} must have the same column names as the {.help [clinical_breakpoints](AMR::clinical_breakpoints)} data set.", call = .call_depth)
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}
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# coerce mo, ab, and other columns to the expected types where possible
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reference_data <- coerce_reference_data_columns(reference_data)
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class_sir <- vapply(FUN.VALUE = character(1), AMR::clinical_breakpoints, function(x) paste0("<", class(x), ">", collapse = " and "))
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class_ref <- vapply(FUN.VALUE = character(1), reference_data, function(x) paste0("<", class(x), ">", collapse = " and "))
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if (!all(class_sir == class_ref)) {
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bad_col <- names(class_ref[class_sir != class_ref][1])
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bad_cls <- gsub("<|>", "", class_ref[class_sir != class_ref][1])
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@@ -2354,4 +2396,5 @@ check_reference_data <- function(reference_data, .call_depth) {
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stop_("{.arg reference_data} must be the same structure as the {.help [clinical_breakpoints](AMR::clinical_breakpoints)} data set. Column ", paste0("{.field ", font_bold(bad_col, collapse = NULL), "}"), " is of class ", paste0("{.cls ", bad_cls, "}"), ", but should be of class ", paste0("{.cls ", exp_cls, "}"), call = .call_depth)
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}
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}
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reference_data
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}
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@@ -529,3 +529,53 @@ test_that("test-sir.R", {
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expect_lte(n_mentions, 1L)
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}
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})
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# issue #239 — custom reference_data support
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test_that("custom reference_data: non-EUCAST/CLSI guideline produces R", {
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# Build a minimal one-row custom breakpoint table from a plain data.frame.
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# coerce_reference_data_columns() will coerce mo/ab to the right class.
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my_bp <- clinical_breakpoints[clinical_breakpoints$method == "MIC" &
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clinical_breakpoints$type == "human", ][1, ]
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my_bp$guideline <- "MyLab 2025"
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my_bp$mo <- "B_ACHRMB_XYLS" # plain character — coerced to <mo>
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my_bp$ab <- "MEM" # plain character — coerced to <ab>
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my_bp$breakpoint_S <- 8
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my_bp$breakpoint_R <- 32
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# guideline omitted: all rows in reference_data are used; R via open interval (>)
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expect_equal(as.character(suppressMessages(
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as.sir(as.mic(64), mo = "B_ACHRMB_XYLS", ab = "MEM", reference_data = my_bp)
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)), "R")
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expect_equal(as.character(suppressMessages(
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as.sir(as.mic(16), mo = "B_ACHRMB_XYLS", ab = "MEM", reference_data = my_bp)
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)), "I")
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# at R breakpoint value must be I (open interval: > not >=)
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expect_equal(as.character(suppressMessages(
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as.sir(as.mic(32), mo = "B_ACHRMB_XYLS", ab = "MEM", reference_data = my_bp)
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)), "I")
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# guideline explicitly set: same result when it matches the data
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expect_equal(as.character(suppressMessages(
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as.sir(as.mic(64), mo = "B_ACHRMB_XYLS", ab = "MEM",
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guideline = "MyLab 2025", reference_data = my_bp)
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)), "R")
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})
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test_that("custom reference_data: host = NA acts as host-agnostic fallback", {
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my_bp <- clinical_breakpoints[clinical_breakpoints$method == "MIC" &
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clinical_breakpoints$type == "human", ][1, ]
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my_bp$guideline <- "MyLab 2025"
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my_bp$mo <- "B_ACHRMB_XYLS"
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my_bp$ab <- "MEM"
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my_bp$type <- "animal"
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my_bp$host <- NA # logical NA — coerced to character by coerce_reference_data_columns()
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my_bp$breakpoint_S <- 8
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my_bp$breakpoint_R <- 32
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# NA host should match when no species-specific row exists
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result <- suppressMessages(
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as.sir(as.mic(64), mo = "B_ACHRMB_XYLS", ab = "MEM",
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host = "dogs", breakpoint_type = "animal", reference_data = my_bp)
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)
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expect_equal(as.character(result), "R")
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})
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