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(v1.4.0.9019) documentation update
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2
R/data.R
2
R/data.R
@ -258,7 +258,7 @@ catalogue_of_life <- list(
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#' - `antibiotic`\cr Name of the antibiotic drug
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#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt>. This file **allows for machine reading EUCAST guidelines about intrinsic resistance**, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
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#'
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#' This data set is based on '`r EUCAST_VERSION_EXPERT_RULES[["3.2"]]$title`', `r EUCAST_VERSION_EXPERT_RULES[["3.2"]]$version_txt` from `r EUCAST_VERSION_EXPERT_RULES[["3.2"]]$year`.
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#' This data set is based on `r format_eucast_version_nr(3.2)`.
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#' @inheritSection AMR Reference data publicly available
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#' @inheritSection AMR Read more on our website!
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#' @examples
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@ -27,13 +27,24 @@
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# (running "data-raw/internals.R" will process that TSV file)
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EUCAST_VERSION_BREAKPOINTS <- list("10.0" = list(version_txt = "v10.0",
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year = 2020,
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title = "EUCAST Clinical Breakpoints"))
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title = "'EUCAST Clinical Breakpoints'",
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url = "https://www.eucast.org/clinical_breakpoints/"))
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EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1",
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year = 2016,
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title = "EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes"),
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title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'",
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url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"),
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"3.2" = list(version_txt = "v3.2",
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year = 2020,
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title = "EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes"))
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title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
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url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"))
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format_eucast_version_nr <- function(version) {
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# for documentation - adds title, version number, year and url in markdown language
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lst <- c(EUCAST_VERSION_BREAKPOINTS, EUCAST_VERSION_EXPERT_RULES)
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version <- format(version, nsmall = 1)
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paste0("[", lst[[version]]$title, " ", lst[[version]]$version_txt, "](", lst[[version]]$url, ")",
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" from ", lst[[version]]$year)
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}
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#' Apply EUCAST rules
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#'
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2
R/rsi.R
2
R/rsi.R
@ -35,7 +35,7 @@
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#' @inheritParams first_isolate
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#' @param guideline defaults to the latest included EUCAST guideline, see Details for all options
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#' @param conserve_capped_values a logical to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
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#' @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 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version `r EUCAST_VERSION_EXPERT_RULES`.
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#' @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(3.2)`.
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#' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [rsi_translation] data set. Changing this parameter allows for using own interpretation guidelines. This parameter must contain a data set that is equal in structure to the [rsi_translation] data set (same column names and column types). Please note that the `guideline` parameter will be ignored when `reference_data` is manually set.
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#' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, please see *Examples*
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#' @param ... for using on a [data.frame]: names of columns to apply [as.rsi()] on (supports tidy selection like `AMX:VAN`). Otherwise: parameters passed on to methods.
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