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(v1.7.1.9011) subsetting taxonomy fix
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Package: AMR
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Package: AMR
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Version: 1.7.1.9010
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Version: 1.7.1.9011
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Date: 2021-07-04
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Date: 2021-07-04
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# `AMR` 1.7.1.9010
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# `AMR` 1.7.1.9011
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## <small>Last updated: 4 July 2021</small>
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## <small>Last updated: 4 July 2021</small>
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### Changed
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### Changed
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@ -25,7 +25,7 @@
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#' Determine Bug-Drug Combinations
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#' Determine Bug-Drug Combinations
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#'
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#'
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#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publicable/printable format, see *Examples*.
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#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publishable/printable format, see *Examples*.
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#' @inheritSection lifecycle Stable Lifecycle
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#' @inheritSection lifecycle Stable Lifecycle
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#' @inheritParams eucast_rules
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#' @inheritParams eucast_rules
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#' @param combine_IR a [logical] to indicate whether values R and I should be summed
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#' @param combine_IR a [logical] to indicate whether values R and I should be summed
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@ -48,11 +48,13 @@
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#'
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#'
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#' Intrinsic resistance - [mo_is_intrinsic_resistant()] - will be determined based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.2)`. The [mo_is_intrinsic_resistant()] functions can be vectorised over arguments `x` (input for microorganisms) and over `ab` (input for antibiotics).
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#' Intrinsic resistance - [mo_is_intrinsic_resistant()] - will be determined based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.2)`. The [mo_is_intrinsic_resistant()] functions can be vectorised over arguments `x` (input for microorganisms) and over `ab` (input for antibiotics).
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#'
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#'
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#' The functions [mo_family()], [mo_genus()], [mo_name()], [mo_fullname()] and [mo_shortname()] are returned with an additional class `taxonomic_name`, which allows italic printing in [tibbles][tibble::tibble()].
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#'
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#' All output [will be translated][translate] where possible.
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#' All output [will be translated][translate] where possible.
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#'
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#'
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#' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
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#' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
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#'
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#'
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#' SNOMED codes - [mo_snomed()] - are from the `r SNOMED_VERSION$current_source`. See the [microorganisms] data set for more info.
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#' SNOMED codes - [mo_snomed()] - are from the `r SNOMED_VERSION$current_source`. See *Source* and the [microorganisms] data set for more info.
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#' @inheritSection mo_matching_score Matching Score for Microorganisms
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#' @inheritSection mo_matching_score Matching Score for Microorganisms
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#' @inheritSection catalogue_of_life Catalogue of Life
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#' @inheritSection catalogue_of_life Catalogue of Life
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#' @inheritSection as.mo Source
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#' @inheritSection as.mo Source
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@ -63,9 +65,10 @@
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#' - A [list] in case of [mo_taxonomy()] and [mo_info()]
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#' - A [list] in case of [mo_taxonomy()] and [mo_info()]
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#' - A named [character] in case of [mo_url()]
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#' - A named [character] in case of [mo_url()]
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#' - A [numeric] in case of [mo_snomed()]
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#' - A [numeric] in case of [mo_snomed()]
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#' - A [character] with additional class `taxonomic_name` in case of [mo_family()], [mo_genus()], [mo_name()], [mo_fullname()] and [mo_shortname()]
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#' - A [character] in all other cases
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#' - A [character] in all other cases
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#' @export
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#' @export
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#' @seealso [microorganisms]
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#' @seealso Data set [microorganisms]
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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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@ -783,15 +786,15 @@ print.taxonomic_name <- function(x, ...) {
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as.data.frame.taxonomic_name <- function(x, ...) {
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as.data.frame.taxonomic_name <- function(x, ...) {
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nm <- deparse1(substitute(x))
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nm <- deparse1(substitute(x))
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if (!"nm" %in% names(list(...))) {
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if (!"nm" %in% names(list(...))) {
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as.data.frame.vector(x, ..., nm = nm)
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as.data.frame(unclass(x), ..., nm = nm)
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} else {
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} else {
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as.data.frame.vector(x, ...)
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as.data.frame(unclass(x), ...)
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}
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}
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}
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}
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# will be exported using s3_register() in R/zzz.R
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# will be exported using s3_register() in R/zzz.R
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type_sum.taxonomic_name <- function(x, ...) {
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type_sum.taxonomic_name <- function(x, ...) {
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"chr"
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"chr/taxon"
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}
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}
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# will be exported using s3_register() in R/zzz.R
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# will be exported using s3_register() in R/zzz.R
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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">1.7.1.9010</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9011</span>
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</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">1.7.1.9010</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9011</span>
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</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">1.7.1.9010</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9011</span>
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</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">1.7.1.9010</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9011</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">1.7.1.9010</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9011</span>
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</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">1.7.1.9010</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9011</span>
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</span>
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</div>
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<table class="table">
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<table class="table">
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<thead><tr class="header">
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<thead><tr class="header">
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<th align="left">bacteria</th>
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<th align="left">bacteria</th>
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<th align="center">AMK</th>
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<th align="center">GEN</th>
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<th align="center">GEN</th>
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<th align="center">KAN</th>
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<th align="center">TOB</th>
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<th align="center">TOB</th>
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<th align="center">AMK</th>
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<th align="center">KAN</th>
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<th align="center">IPM</th>
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<th align="center">IPM</th>
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<th align="center">MEM</th>
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<th align="center">MEM</th>
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</tr></thead>
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</tr></thead>
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<tbody>
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<tbody>
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<tr class="odd">
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<tr class="odd">
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="center"></td>
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<td align="center">I</td>
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<td align="center">I</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center"></td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center"></td>
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<td align="center"></td>
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</tr>
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</tr>
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<tr class="even">
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<tr class="even">
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="center"></td>
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<td align="center">I</td>
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<td align="center">I</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center"></td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center"></td>
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<td align="center"></td>
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</tr>
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</tr>
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<tr class="odd">
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<tr class="odd">
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="center"></td>
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<td align="center">I</td>
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<td align="center">I</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center"></td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center"></td>
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<td align="center"></td>
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</tr>
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</tr>
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center"></td>
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<td align="center"></td>
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<td align="center">S</td>
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<td align="center">S</td>
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</tr>
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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</tr>
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</tr>
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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</tr>
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</tr>
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center"></td>
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<td align="center"></td>
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<td align="center">S</td>
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<td align="center">S</td>
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</tr>
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</tr>
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center"></td>
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<td align="center"></td>
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<td align="center">S</td>
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<td align="center">S</td>
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</tr>
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</tr>
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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</tr>
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</tr>
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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">1.7.1.9010</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9011</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>
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<div id="amr-1719010" class="section level1">
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<div id="amr-1719011" class="section level1">
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<h1 class="page-header" data-toc-text="1.7.1.9010">
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<h1 class="page-header" data-toc-text="1.7.1.9011">
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<a href="#amr-1719010" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9010</h1>
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<a href="#amr-1719011" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9011</h1>
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<div id="last-updated-4-july-2021" class="section level2">
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<div id="last-updated-4-july-2021" 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-4-july-2021" class="anchor"></a><small>Last updated: 4 July 2021</small>
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<a href="#last-updated-4-july-2021" class="anchor"></a><small>Last updated: 4 July 2021</small>
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@ -12,7 +12,7 @@ articles:
|
|||||||
datasets: datasets.html
|
datasets: datasets.html
|
||||||
resistance_predict: resistance_predict.html
|
resistance_predict: resistance_predict.html
|
||||||
welcome_to_AMR: welcome_to_AMR.html
|
welcome_to_AMR: welcome_to_AMR.html
|
||||||
last_built: 2021-07-04T09:59Z
|
last_built: 2021-07-04T13:26Z
|
||||||
urls:
|
urls:
|
||||||
reference: https://msberends.github.io/AMR//reference
|
reference: https://msberends.github.io/AMR//reference
|
||||||
article: https://msberends.github.io/AMR//articles
|
article: https://msberends.github.io/AMR//articles
|
||||||
|
@ -49,7 +49,7 @@
|
|||||||
<script src="../extra.js"></script>
|
<script src="../extra.js"></script>
|
||||||
|
|
||||||
<meta property="og:title" content="Determine Bug-Drug Combinations — bug_drug_combinations" />
|
<meta property="og:title" content="Determine Bug-Drug Combinations — bug_drug_combinations" />
|
||||||
<meta property="og:description" content="Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format() on the result to prettify it to a publicable/printable format, see Examples." />
|
<meta property="og:description" content="Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use format() on the result to prettify it to a publishable/printable format, see Examples." />
|
||||||
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
|
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
|
||||||
|
|
||||||
|
|
||||||
@ -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">1.7.1</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9011</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -90,14 +90,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="../index.html">
|
<a href="../index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -106,77 +106,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/AMR.html">
|
<a href="../articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/resistance_predict.html">
|
<a href="../articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/datasets.html">
|
<a href="../articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/PCA.html">
|
<a href="../articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/MDR.html">
|
<a href="../articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/WHONET.html">
|
<a href="../articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/SPSS.html">
|
<a href="../articles/SPSS.html">
|
||||||
<span class="fas fa-file-upload"></span>
|
<span class="fa fa-file-upload"></span>
|
||||||
|
|
||||||
Import data from SPSS/SAS/Stata
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/EUCAST.html">
|
<a href="../articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/mo_property.html">
|
<a href="../reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/ab_property.html">
|
<a href="../reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/benchmarks.html">
|
<a href="../articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -185,14 +185,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/index.html">
|
<a href="../reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../authors.html">
|
<a href="../authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -215,7 +215,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../survey.html">
|
<a href="../survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
@ -239,7 +239,7 @@
|
|||||||
</div>
|
</div>
|
||||||
|
|
||||||
<div class="ref-description">
|
<div class="ref-description">
|
||||||
<p>Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use <code><a href='https://rdrr.io/r/base/format.html'>format()</a></code> on the result to prettify it to a publicable/printable format, see <em>Examples</em>.</p>
|
<p>Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use <code><a href='https://rdrr.io/r/base/format.html'>format()</a></code> on the result to prettify it to a publishable/printable format, see <em>Examples</em>.</p>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
<pre class="usage"><span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>x</span>, col_mo <span class='op'>=</span> <span class='cn'>NULL</span>, FUN <span class='op'>=</span> <span class='va'>mo_shortname</span>, <span class='va'>...</span><span class='op'>)</span>
|
<pre class="usage"><span class='fu'>bug_drug_combinations</span><span class='op'>(</span><span class='va'>x</span>, col_mo <span class='op'>=</span> <span class='cn'>NULL</span>, FUN <span class='op'>=</span> <span class='va'>mo_shortname</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||||
|
@ -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">1.7.1.9010</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9011</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">1.7.1</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9011</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -90,14 +90,14 @@
|
|||||||
<ul class="nav navbar-nav">
|
<ul class="nav navbar-nav">
|
||||||
<li>
|
<li>
|
||||||
<a href="../index.html">
|
<a href="../index.html">
|
||||||
<span class="fas fa-home"></span>
|
<span class="fa fa-home"></span>
|
||||||
|
|
||||||
Home
|
Home
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li class="dropdown">
|
<li class="dropdown">
|
||||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||||
<span class="fas fa-question-circle"></span>
|
<span class="fa fa-question-circle"></span>
|
||||||
|
|
||||||
How to
|
How to
|
||||||
|
|
||||||
@ -106,77 +106,77 @@
|
|||||||
<ul class="dropdown-menu" role="menu">
|
<ul class="dropdown-menu" role="menu">
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/AMR.html">
|
<a href="../articles/AMR.html">
|
||||||
<span class="fas fa-directions"></span>
|
<span class="fa fa-directions"></span>
|
||||||
|
|
||||||
Conduct AMR analysis
|
Conduct AMR analysis
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/resistance_predict.html">
|
<a href="../articles/resistance_predict.html">
|
||||||
<span class="fas fa-dice"></span>
|
<span class="fa fa-dice"></span>
|
||||||
|
|
||||||
Predict antimicrobial resistance
|
Predict antimicrobial resistance
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/datasets.html">
|
<a href="../articles/datasets.html">
|
||||||
<span class="fas fa-database"></span>
|
<span class="fa fa-database"></span>
|
||||||
|
|
||||||
Data sets for download / own use
|
Data sets for download / own use
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/PCA.html">
|
<a href="../articles/PCA.html">
|
||||||
<span class="fas fa-compress"></span>
|
<span class="fa fa-compress"></span>
|
||||||
|
|
||||||
Conduct principal component analysis for AMR
|
Conduct principal component analysis for AMR
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/MDR.html">
|
<a href="../articles/MDR.html">
|
||||||
<span class="fas fa-skull-crossbones"></span>
|
<span class="fa fa-skull-crossbones"></span>
|
||||||
|
|
||||||
Determine multi-drug resistance (MDR)
|
Determine multi-drug resistance (MDR)
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/WHONET.html">
|
<a href="../articles/WHONET.html">
|
||||||
<span class="fas fa-globe-americas"></span>
|
<span class="fa fa-globe-americas"></span>
|
||||||
|
|
||||||
Work with WHONET data
|
Work with WHONET data
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/SPSS.html">
|
<a href="../articles/SPSS.html">
|
||||||
<span class="fas fa-file-upload"></span>
|
<span class="fa fa-file-upload"></span>
|
||||||
|
|
||||||
Import data from SPSS/SAS/Stata
|
Import data from SPSS/SAS/Stata
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/EUCAST.html">
|
<a href="../articles/EUCAST.html">
|
||||||
<span class="fas fa-exchange-alt"></span>
|
<span class="fa fa-exchange-alt"></span>
|
||||||
|
|
||||||
Apply EUCAST rules
|
Apply EUCAST rules
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/mo_property.html">
|
<a href="../reference/mo_property.html">
|
||||||
<span class="fas fa-bug"></span>
|
<span class="fa fa-bug"></span>
|
||||||
|
|
||||||
Get properties of a microorganism
|
Get properties of a microorganism
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/ab_property.html">
|
<a href="../reference/ab_property.html">
|
||||||
<span class="fas fa-capsules"></span>
|
<span class="fa fa-capsules"></span>
|
||||||
|
|
||||||
Get properties of an antibiotic
|
Get properties of an antibiotic
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../articles/benchmarks.html">
|
<a href="../articles/benchmarks.html">
|
||||||
<span class="fas fa-shipping-fast"></span>
|
<span class="fa fa-shipping-fast"></span>
|
||||||
|
|
||||||
Other: benchmarks
|
Other: benchmarks
|
||||||
</a>
|
</a>
|
||||||
@ -185,14 +185,14 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../reference/index.html">
|
<a href="../reference/index.html">
|
||||||
<span class="fas fa-book-open"></span>
|
<span class="fa fa-book-open"></span>
|
||||||
|
|
||||||
Manual
|
Manual
|
||||||
</a>
|
</a>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../authors.html">
|
<a href="../authors.html">
|
||||||
<span class="fas fa-users"></span>
|
<span class="fa fa-users"></span>
|
||||||
|
|
||||||
Authors
|
Authors
|
||||||
</a>
|
</a>
|
||||||
@ -215,7 +215,7 @@
|
|||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<a href="../survey.html">
|
<a href="../survey.html">
|
||||||
<span class="fas fa-clipboard-list"></span>
|
<span class="fa fa-clipboard-list"></span>
|
||||||
|
|
||||||
Survey
|
Survey
|
||||||
</a>
|
</a>
|
||||||
@ -335,6 +335,7 @@
|
|||||||
<li><p>A <a href='https://rdrr.io/r/base/list.html'>list</a> in case of <code>mo_taxonomy()</code> and <code>mo_info()</code></p></li>
|
<li><p>A <a href='https://rdrr.io/r/base/list.html'>list</a> in case of <code>mo_taxonomy()</code> and <code>mo_info()</code></p></li>
|
||||||
<li><p>A named <a href='https://rdrr.io/r/base/character.html'>character</a> in case of <code>mo_url()</code></p></li>
|
<li><p>A named <a href='https://rdrr.io/r/base/character.html'>character</a> in case of <code>mo_url()</code></p></li>
|
||||||
<li><p>A <a href='https://rdrr.io/r/base/numeric.html'>numeric</a> in case of <code>mo_snomed()</code></p></li>
|
<li><p>A <a href='https://rdrr.io/r/base/numeric.html'>numeric</a> in case of <code>mo_snomed()</code></p></li>
|
||||||
|
<li><p>A <a href='https://rdrr.io/r/base/character.html'>character</a> with additional class <code>taxonomic_name</code> in case of <code>mo_family()</code>, <code>mo_genus()</code>, <code>mo_name()</code>, <code>mo_fullname()</code> and <code>mo_shortname()</code></p></li>
|
||||||
<li><p>A <a href='https://rdrr.io/r/base/character.html'>character</a> in all other cases</p></li>
|
<li><p>A <a href='https://rdrr.io/r/base/character.html'>character</a> in all other cases</p></li>
|
||||||
</ul>
|
</ul>
|
||||||
|
|
||||||
@ -351,9 +352,10 @@
|
|||||||
<p>The Gram stain - <code>mo_gramstain()</code> - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, <a href='https://pubmed.ncbi.nlm.nih.gov/11837318'>PMID 11837318</a>), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
|
<p>The Gram stain - <code>mo_gramstain()</code> - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, <a href='https://pubmed.ncbi.nlm.nih.gov/11837318'>PMID 11837318</a>), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
|
||||||
<p>Determination of yeasts - <code>mo_is_yeast()</code> - will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). <em>True yeasts</em> are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
|
<p>Determination of yeasts - <code>mo_is_yeast()</code> - will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). <em>True yeasts</em> are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
|
||||||
<p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, which 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> (2020). The <code>mo_is_intrinsic_resistant()</code> functions can be vectorised over arguments <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p>
|
<p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, which 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> (2020). The <code>mo_is_intrinsic_resistant()</code> functions can be vectorised over arguments <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p>
|
||||||
|
<p>The functions <code>mo_family()</code>, <code>mo_genus()</code>, <code>mo_name()</code>, <code>mo_fullname()</code> and <code>mo_shortname()</code> are returned with an additional class <code>taxonomic_name</code>, which allows italic printing in <a href='https://tibble.tidyverse.org/reference/tibble.html'>tibbles</a>.</p>
|
||||||
<p>All output <a href='translate.html'>will be translated</a> where possible.</p>
|
<p>All output <a href='translate.html'>will be translated</a> where possible.</p>
|
||||||
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
|
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
|
||||||
<p>SNOMED codes - <code>mo_snomed()</code> - are from the US Edition of SNOMED CT from 1 September 2020. See the <a href='microorganisms.html'>microorganisms</a> data set for more info.</p>
|
<p>SNOMED codes - <code>mo_snomed()</code> - are from the US Edition of SNOMED CT from 1 September 2020. See <em>Source</em> and the <a href='microorganisms.html'>microorganisms</a> data set for more info.</p>
|
||||||
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
|
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
|
||||||
|
|
||||||
|
|
||||||
@ -411,7 +413,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
|||||||
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
||||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||||
|
|
||||||
<div class='dont-index'><p><a href='microorganisms.html'>microorganisms</a></p></div>
|
<div class='dont-index'><p>Data set <a href='microorganisms.html'>microorganisms</a></p></div>
|
||||||
|
|
||||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||||
<pre class="examples"><span class='co'># taxonomic tree -----------------------------------------------------------</span>
|
<pre class="examples"><span class='co'># taxonomic tree -----------------------------------------------------------</span>
|
||||||
|
@ -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">1.7.1.9010</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9011</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
20
index.md
20
index.md
@ -35,18 +35,18 @@ example_isolates %>%
|
|||||||
|
|
||||||
With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (`mo_is_gram_negative()` and `mo_is_intrinsic_resistant()`) and a column selection on two antibiotic groups (`aminoglycosides()` and `carbapenems()`), the reference data about [all microorganisms](./reference/microorganisms.html) and [all antibiotics](./reference/antibiotics.html) in the `AMR` package make sure you get what you meant:
|
With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (`mo_is_gram_negative()` and `mo_is_intrinsic_resistant()`) and a column selection on two antibiotic groups (`aminoglycosides()` and `carbapenems()`), the reference data about [all microorganisms](./reference/microorganisms.html) and [all antibiotics](./reference/antibiotics.html) in the `AMR` package make sure you get what you meant:
|
||||||
|
|
||||||
|bacteria | AMK | GEN | KAN | TOB | IPM | MEM |
|
|bacteria | GEN | TOB | AMK | KAN | IPM | MEM |
|
||||||
|:------------------------------|:---:|:---:|:---:|:---:|:---:|:---:|
|
|:------------------------------|:---:|:---:|:---:|:---:|:---:|:---:|
|
||||||
|*Pseudomonas aeruginosa* | | I | R | S | S | |
|
|*Pseudomonas aeruginosa* | I | S | | R | S | |
|
||||||
|*Pseudomonas aeruginosa* | | I | R | S | S | |
|
|*Pseudomonas aeruginosa* | I | S | | R | S | |
|
||||||
|*Pseudomonas aeruginosa* | | I | R | S | S | |
|
|*Pseudomonas aeruginosa* | I | S | | R | S | |
|
||||||
|*Pseudomonas aeruginosa* | S | S | R | S | | S |
|
|*Pseudomonas aeruginosa* | S | S | S | R | | S |
|
||||||
|*Pseudomonas aeruginosa* | S | S | R | S | S | S |
|
|*Pseudomonas aeruginosa* | S | S | S | R | S | S |
|
||||||
|*Pseudomonas aeruginosa* | S | S | R | S | S | S |
|
|*Pseudomonas aeruginosa* | S | S | S | R | S | S |
|
||||||
|*Stenotrophomonas maltophilia* | R | R | R | R | R | R |
|
|*Stenotrophomonas maltophilia* | R | R | R | R | R | R |
|
||||||
|*Pseudomonas aeruginosa* | S | S | R | S | | S |
|
|*Pseudomonas aeruginosa* | S | S | S | R | | S |
|
||||||
|*Pseudomonas aeruginosa* | S | S | R | S | | S |
|
|*Pseudomonas aeruginosa* | S | S | S | R | | S |
|
||||||
|*Pseudomonas aeruginosa* | S | S | R | S | S | S |
|
|*Pseudomonas aeruginosa* | S | S | S | R | S | S |
|
||||||
|
|
||||||
A base R equivalent would be, giving the exact same results:
|
A base R equivalent would be, giving the exact same results:
|
||||||
|
|
||||||
|
@ -58,7 +58,7 @@ bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
|
|||||||
The function \code{\link[=bug_drug_combinations]{bug_drug_combinations()}} returns a \link{data.frame} with columns "mo", "ab", "S", "I", "R" and "total".
|
The function \code{\link[=bug_drug_combinations]{bug_drug_combinations()}} returns a \link{data.frame} with columns "mo", "ab", "S", "I", "R" and "total".
|
||||||
}
|
}
|
||||||
\description{
|
\description{
|
||||||
Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{\link[=format]{format()}} on the result to prettify it to a publicable/printable format, see \emph{Examples}.
|
Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{\link[=format]{format()}} on the result to prettify it to a publishable/printable format, see \emph{Examples}.
|
||||||
}
|
}
|
||||||
\details{
|
\details{
|
||||||
The function \code{\link[=format]{format()}} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
|
The function \code{\link[=format]{format()}} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
|
||||||
|
@ -106,6 +106,7 @@ mo_property(x, property = "fullname", language = get_locale(), ...)
|
|||||||
\item A \link{list} in case of \code{\link[=mo_taxonomy]{mo_taxonomy()}} and \code{\link[=mo_info]{mo_info()}}
|
\item A \link{list} in case of \code{\link[=mo_taxonomy]{mo_taxonomy()}} and \code{\link[=mo_info]{mo_info()}}
|
||||||
\item A named \link{character} in case of \code{\link[=mo_url]{mo_url()}}
|
\item A named \link{character} in case of \code{\link[=mo_url]{mo_url()}}
|
||||||
\item A \link{numeric} in case of \code{\link[=mo_snomed]{mo_snomed()}}
|
\item A \link{numeric} in case of \code{\link[=mo_snomed]{mo_snomed()}}
|
||||||
|
\item A \link{character} with additional class \code{taxonomic_name} in case of \code{\link[=mo_family]{mo_family()}}, \code{\link[=mo_genus]{mo_genus()}}, \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_fullname]{mo_fullname()}} and \code{\link[=mo_shortname]{mo_shortname()}}
|
||||||
\item A \link{character} in all other cases
|
\item A \link{character} in all other cases
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -130,11 +131,13 @@ Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be ba
|
|||||||
|
|
||||||
Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which 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} (2020). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} functions can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics).
|
Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which 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} (2020). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} functions can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics).
|
||||||
|
|
||||||
|
The functions \code{\link[=mo_family]{mo_family()}}, \code{\link[=mo_genus]{mo_genus()}}, \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_fullname]{mo_fullname()}} and \code{\link[=mo_shortname]{mo_shortname()}} are returned with an additional class \code{taxonomic_name}, which allows italic printing in \link[tibble:tibble]{tibbles}.
|
||||||
|
|
||||||
All output \link[=translate]{will be translated} where possible.
|
All output \link[=translate]{will be translated} where possible.
|
||||||
|
|
||||||
The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
|
The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
|
||||||
|
|
||||||
SNOMED codes - \code{\link[=mo_snomed]{mo_snomed()}} - are from the US Edition of SNOMED CT from 1 September 2020. See the \link{microorganisms} data set for more info.
|
SNOMED codes - \code{\link[=mo_snomed]{mo_snomed()}} - are from the US Edition of SNOMED CT from 1 September 2020. See \emph{Source} and the \link{microorganisms} data set for more info.
|
||||||
}
|
}
|
||||||
\section{Stable Lifecycle}{
|
\section{Stable Lifecycle}{
|
||||||
|
|
||||||
@ -299,5 +302,5 @@ mo_info("E. coli")
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
\seealso{
|
\seealso{
|
||||||
\link{microorganisms}
|
Data set \link{microorganisms}
|
||||||
}
|
}
|
||||||
|
Loading…
Reference in New Issue
Block a user