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(v2.1.1.9045) fix host in animal guidelines
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Package: AMR
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Version: 2.1.1.9044
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Date: 2024-06-10
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Version: 2.1.1.9045
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Date: 2024-06-12
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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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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 2.1.1.9044
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# AMR 2.1.1.9045
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*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)*
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38
R/sir.R
38
R/sir.R
@ -545,6 +545,13 @@ as.sir.data.frame <- function(x,
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}
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# -- host
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if (missing(breakpoint_type) && any(host %in% AMR_env$host_preferred_order, na.rm = TRUE)) {
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message_("Assuming `breakpoint_type = \"animal\"` since `host` contains animal species.")
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breakpoint_type <- "animal"
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} else if (any(!convert_host(host) %in% c("human", "ECOFF"), na.rm = TRUE)) {
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message_("Assuming `breakpoint_type = \"animal\"`.")
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breakpoint_type <- "animal"
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}
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if (breakpoint_type == "animal") {
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if (is.null(host)) {
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host <- search_type_in_df(x = x, type = "host", add_col_prefix = FALSE)
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@ -936,6 +943,7 @@ as_sir_method <- function(method_short,
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}
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if (length(ab) == 1) {
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ab <- rep(ab, length(x))
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ab.bak <- rep(ab.bak, length(ab))
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}
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if (length(host) == 1) {
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host <- rep(host, length(x))
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@ -952,7 +960,7 @@ as_sir_method <- function(method_short,
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warning_("in `as.sir()`: using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
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}
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}
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agent_formatted <- paste0("'", font_bold(ab.bak, collapse = NULL), "'")
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agent_name <- ab_name(ab, tolower = TRUE, language = NULL)
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same_ab <- generalise_antibiotic_name(ab) == generalise_antibiotic_name(agent_name)
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@ -966,7 +974,7 @@ as_sir_method <- function(method_short,
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")")
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# this intro text will also be printed in the progress bar if the `progress` package is installed
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intro_txt <- paste0("Interpreting ", method_long, ": ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
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ifelse(length(unique(agent_formatted)) == 1, unique(agent_formatted), paste0("for ", vector_and(ab, quotes = FALSE, sort = FALSE))),
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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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paste0(", ", font_bold(guideline_coerced)),
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@ -1042,17 +1050,6 @@ as_sir_method <- function(method_short,
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}
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msgs <- character(0)
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if (nrow(breakpoints) == 0) {
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# apparently no breakpoints found
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message(
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paste0(font_rose_bg(" WARNING "), "\n"),
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font_black(paste0(" ", AMR_env$bullet_icon, " No ", guideline_coerced, " ", method_coerced, " breakpoints available for ",
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suppressMessages(suppressWarnings(ab_name(ab_coerced, language = NULL, tolower = TRUE))),
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" (", ab_coerced, ").")))
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load_mo_uncertainties(metadata_mo)
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return(rep(NA_sir_, nrow(df)))
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}
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if (guideline_coerced %like% "EUCAST") {
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any_is_intrinsic_resistant <- FALSE
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@ -1067,6 +1064,18 @@ as_sir_method <- function(method_short,
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has_progress_bar <- !is.null(import_fn("progress_bar", "progress", error_on_fail = FALSE)) && nrow(df_unique) >= 10
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on.exit(close(p))
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if (nrow(breakpoints) == 0) {
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# apparently no breakpoints found
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message(
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paste0(font_rose_bg(" WARNING "), "\n"),
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font_black(paste0(" ", AMR_env$bullet_icon, " No ", guideline_coerced, " ", method_coerced, " breakpoints available for ",
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suppressMessages(suppressWarnings(ab_name(unique(ab_coerced), language = NULL, tolower = TRUE))),
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" (", unique(ab_coerced), ")."), collapse = "\n"))
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load_mo_uncertainties(metadata_mo)
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return(rep(NA_sir_, nrow(df)))
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}
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# run the rules (df_unique is a row combination per mo/ab/uti/host)
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for (i in seq_len(nrow(df_unique))) {
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p$tick()
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@ -1106,7 +1115,6 @@ as_sir_method <- function(method_short,
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suppressMessages(suppressWarnings(ab_name(ab_current, language = NULL, tolower = TRUE))),
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" (", ab_current, ")"
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)
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# gather all available breakpoints for current MO
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breakpoints_current <- breakpoints %pm>%
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@ -1151,7 +1159,7 @@ as_sir_method <- function(method_short,
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subset(host_match == TRUE)
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} else {
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# no breakpoint found for this host, so sort on mostly available guidelines
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msgs <- c(msgs, paste0("No ", guideline_coerced, " breakpoints for ", font_bold(host_current), " available for ", ab_formatted, " in ", mo_formatted, " - using ", font_bold(breakpoints_current$host[1]), " breakpoints instead."))
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msgs <- c(msgs, paste0("No breakpoints available for ", font_bold(host_current), " for ", ab_formatted, " in ", mo_formatted, " - using ", font_bold(breakpoints_current$host[1]), " instead."))
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}
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}
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4
index.md
4
index.md
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# The `AMR` Package for R <a href="https://msberends.github.io/AMR/"><img src="./logo.svg" align="right" height="139" /></a>
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<img src="./endorsement_clsi_eucast.jpg" class="endorse_img" align="right" height="120" />
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* Provides an **all-in-one solution** for AMR data analysis in a One Health approach
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* Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
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* Provides the **full microbiological taxonomy** and extensive info on **all antimicrobial drugs**
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@ -15,6 +13,8 @@
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<p style="text-align:right; width: 50%;"><small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank">https://doi.org/10.18637/jss.v104.i03</a></small></p>
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</div>
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<a href="./reference/clinical_breakpoints.html#response-from-clsi-and-eucast"><img src="./endorsement_clsi_eucast.jpg" class="endorse_img" align="right" height="120" /></a>
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----
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### Introduction
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@ -292,6 +292,7 @@ expect_message(as.sir(data.frame(
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sir_history <- sir_interpretation_history(clean = TRUE)
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mics <- as.mic(2 ^ c(-4:6)) # 0.0625 to 64 in factors of 2
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vet <- data.frame(animal = c(rep("cat", 3), rep("dogs", 3), "canine", "equine", "horse", "cattle", "bird"),
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PRA = mics,
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FLR = mics,
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@ -313,12 +314,9 @@ expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA,
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sir_history <- sir_interpretation_history()
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expect_identical(sir_history$host,
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c("cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle",
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"cattle", "cattle", "cattle", "cattle", "cattle", "cats" , "cats" , "cats" , "cattle", "cattle", "cattle",
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"cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle",
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"cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle",
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"cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle",
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"cats" , "cats" , "cats" , "dogs" , "dogs" , "dogs" , "cattle", "cattle", "cattle", "cattle", "cats",
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"cats" , "cats" , "cats" , "cats" , "cats" , "cats"))
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"cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs", "dogs", "cattle", "cattle", "cats",
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"cats", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs",
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"dogs", "cattle", "cattle", "cats", "cats"))
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# ECOFF -------------------------------------------------------------------
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@ -89,13 +89,19 @@
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box-shadow: none !important;
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}
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.endorse_img {
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width: 0% !important;
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}
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.template-home img.logo {
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width: 200px;
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}
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.template-home .endorse_img {
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width: 150px;
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}
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.template-reference-index .section-desc {
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font-style: italic;
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text-align: justify;
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font-size: 16px;
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}
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@media (max-width: 575.98px) {
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.template-home img.logo {
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width: 140px;
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