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(v1.4.0.9019) documentation update
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Package: AMR
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Package: AMR
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Version: 1.4.0.9018
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Version: 1.4.0.9019
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Date: 2020-11-11
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Date: 2020-11-12
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Title: Antimicrobial Resistance Analysis
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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Authors@R: c(
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person(role = c("aut", "cre"),
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person(role = c("aut", "cre"),
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4
NEWS.md
4
NEWS.md
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# AMR 1.4.0.9018
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# AMR 1.4.0.9019
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## <small>Last updated: 11 November 2020</small>
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## <small>Last updated: 12 November 2020</small>
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### New
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### New
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* Functions `is_gram_negative()` and `is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria. If you have the `dplyr` package installed, they can even determine the column with microorganisms themselves inside `dplyr` functions:
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* Functions `is_gram_negative()` and `is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria. If you have the `dplyr` package installed, they can even determine the column with microorganisms themselves inside `dplyr` functions:
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2
R/data.R
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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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#' - `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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#' @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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#'
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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 Reference data publicly available
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#' @inheritSection AMR Read more on our website!
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' @examples
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# (running "data-raw/internals.R" will process that TSV file)
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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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EUCAST_VERSION_BREAKPOINTS <- list("10.0" = list(version_txt = "v10.0",
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year = 2020,
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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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EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1",
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year = 2016,
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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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"3.2" = list(version_txt = "v3.2",
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year = 2020,
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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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#' Apply EUCAST rules
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#'
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#'
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R/rsi.R
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R/rsi.R
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#' @inheritParams first_isolate
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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 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 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 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 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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#' @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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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
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<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9019</span>
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9019</span>
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9019</span>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9019</span>
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9019</span>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9019</span>
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</span>
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1409018" class="section level1">
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<div id="amr-1409019" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9018">
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<h1 class="page-header" data-toc-text="1.4.0.9019">
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<a href="#amr-1409018" class="anchor"></a>AMR 1.4.0.9018<small> Unreleased </small>
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<a href="#amr-1409019" class="anchor"></a>AMR 1.4.0.9019<small> Unreleased </small>
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</h1>
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</h1>
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<div id="last-updated-11-november-2020" class="section level2">
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<div id="last-updated-12-november-2020" class="section level2">
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<h2 class="hasAnchor">
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<h2 class="hasAnchor">
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<a href="#last-updated-11-november-2020" class="anchor"></a><small>Last updated: 11 November 2020</small>
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<a href="#last-updated-12-november-2020" class="anchor"></a><small>Last updated: 12 November 2020</small>
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</h2>
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</h2>
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<div id="new" class="section level3">
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<h3 class="hasAnchor">
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datasets: datasets.html
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2020-11-11T17:53Z
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last_built: 2020-11-12T10:02Z
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urls:
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urls:
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reference: https://msberends.github.io/AMR//reference
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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article: https://msberends.github.io/AMR//articles
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9019</span>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9013</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9019</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
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</tr>
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</tr>
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<tr>
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<th>add_intrinsic_resistance</th>
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<th>add_intrinsic_resistance</th>
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<td><p><em>(only useful when using a EUCAST guideline)</em> 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 <em>Klebsiella</em> species. Determination is based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, that itself is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version list(version_txt = "v3.1", year = 2016, title = "EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes")
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<td><p><em>(only useful when using a EUCAST guideline)</em> 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 <em>Klebsiella</em> species. Determination is based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, that itself is based on <a href='https://www.eucast.org/expert_rules_and_intrinsic_resistance/'>'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> from 2020.</p></td>
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list(version_txt = "v3.2", year = 2020, title = "EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes").</p></td>
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<th>reference_data</th>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9019</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt'>https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt</a>. This file <strong>allows for machine reading EUCAST guidelines about intrinsic resistance</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.</p>
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<p>The repository of this <code>AMR</code> package contains a file comprising this exact data set: <a href='https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt'>https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt</a>. This file <strong>allows for machine reading EUCAST guidelines about intrinsic resistance</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.</p>
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<p>This data set is based on 'EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes', v3.2 from 2020.</p>
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<p>This data set is based on <a href='https://www.eucast.org/expert_rules_and_intrinsic_resistance/'>'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> from 2020.</p>
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<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>
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<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>
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<span class="navbar-brand">
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<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9012</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9019</span>
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</span>
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</span>
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@ -82,7 +82,7 @@
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</button>
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</button>
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<span class="navbar-brand">
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<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9012</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9019</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -82,7 +82,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9014</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9019</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -81,7 +81,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9018</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9019</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
@ -67,8 +67,7 @@ is.rsi.eligible(x, threshold = 0.05)
|
|||||||
|
|
||||||
\item{conserve_capped_values}{a logical to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"}
|
\item{conserve_capped_values}{a logical to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"}
|
||||||
|
|
||||||
\item{add_intrinsic_resistance}{\emph{(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 \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on 'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes', version list(version_txt = "v3.1", year = 2016, title = "EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes")
|
\item{add_intrinsic_resistance}{\emph{(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 \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2} from 2020.}
|
||||||
list(version_txt = "v3.2", year = 2020, title = "EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes").}
|
|
||||||
|
|
||||||
\item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{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 \link{rsi_translation} data set (same column names and column types). Please note that the \code{guideline} parameter will be ignored when \code{reference_data} is manually set.}
|
\item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{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 \link{rsi_translation} data set (same column names and column types). Please note that the \code{guideline} parameter will be ignored when \code{reference_data} is manually set.}
|
||||||
|
|
||||||
|
@ -20,7 +20,7 @@ Data set containing defined intrinsic resistance by EUCAST of all bug-drug combi
|
|||||||
\details{
|
\details{
|
||||||
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt}. This file \strong{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.
|
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt}. This file \strong{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.
|
||||||
|
|
||||||
This data set is based on 'EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes', v3.2 from 2020.
|
This data set is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2} from 2020.
|
||||||
}
|
}
|
||||||
\section{Reference data publicly available}{
|
\section{Reference data publicly available}{
|
||||||
|
|
||||||
|
Loading…
Reference in New Issue
Block a user