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40d9658e06 | |
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f781998904 |
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@ -100,7 +100,6 @@ jobs:
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- name: Unpack AMR and install R dependencies
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if: always()
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run: |
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tar -xf data-raw/AMR_latest.tar.gz
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Rscript -e "source('data-raw/_install_deps.R')"
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shell: bash
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.8.1.9033
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Version: 1.8.1.9034
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Date: 2022-08-28
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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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3
NEWS.md
3
NEWS.md
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@ -1,4 +1,4 @@
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# AMR 1.8.1.9033
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# AMR 1.8.1.9034
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### New
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* EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.
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@ -20,6 +20,7 @@
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* Fix for using `info = FALSE` in `mdro()`
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* All data sets in this package are now exported as `tibble`, instead of base R `data.frame`s. Older R versions are still supported.
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* Automatic language determination will give a note once a session
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* For all interpretation guidelines using `as.rsi()` on amoxicillin, the rules for ampicillin will be used if amoxicillin rules are not available
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### Other
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* New website to make use of the new Bootstrap 5 and pkgdown v2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions
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25
R/rsi.R
25
R/rsi.R
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@ -722,7 +722,12 @@ as_rsi_method <- function(method_short,
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agent_formatted <- paste0("'", font_bold(ab), "'")
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agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
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if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
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agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
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agent_formatted <- paste0(
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agent_formatted,
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" (", ifelse(ab == ab_coerced, "",
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paste0(ab_coerced, ", ")
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), agent_name, ")"
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)
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}
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message_("=> Interpreting ", method_long, " of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
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agent_formatted,
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@ -799,19 +804,31 @@ exec_as.rsi <- function(method,
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new_rsi <- rep(NA_character_, length(x))
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ab_param <- ab
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if (ab_param == "AMX") {
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if (identical(reference_data, AMR::rsi_translation)) {
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trans <- reference_data %pm>%
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subset(guideline == guideline_coerced & method == method_param & ab == ab_param)
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if (ab_param == "AMX" && nrow(trans) == 0) {
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ab_param <- "AMP"
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if (message_not_thrown_before("as.rsi", "AMP_for_AMX")) {
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message_("(using ampicillin rules)", appendLF = FALSE, as_note = FALSE)
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}
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}
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if (identical(reference_data, AMR::rsi_translation)) {
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trans <- reference_data %pm>%
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subset(guideline == guideline_coerced & method == method_param & ab == ab_param)
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}
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} else {
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trans <- reference_data %pm>%
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subset(method == method_param & ab == ab_param)
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}
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if (nrow(trans) == 0) {
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message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
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load_mo_failures_uncertainties_renamed(metadata_mo)
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return(set_clean_class(factor(new_rsi, levels = c("S", "I", "R"), ordered = TRUE),
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new_class = c("rsi", "ordered", "factor")
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))
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}
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trans$lookup <- paste(trans$mo, trans$ab)
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lookup_mo <- paste(mo, ab_param)
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@ -494,4 +494,4 @@ invisible(capture.output(styler::style_dir(
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# Finished ----------------------------------------------------------------
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usethis::ui_info("All done")
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usethis::ui_done("All done")
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