diff --git a/.github/workflows/check-old.yaml b/.github/workflows/check-old.yaml index b4293492..77b7e59c 100644 --- a/.github/workflows/check-old.yaml +++ b/.github/workflows/check-old.yaml @@ -47,7 +47,7 @@ jobs: matrix: config: # Test all old versions of R >= 3.0, we support them all! - # For these old versions, dependencies will not be installed and checked. + # For these old versions, dependencies and vignettes will not be checked. # For recent R versions, see check-recent.yaml (r-lib and tidyverse support the latest 5 major R versions). - {os: ubuntu-22.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - {os: ubuntu-22.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} @@ -82,8 +82,8 @@ jobs: as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] shell: Rscript {0} - - name: Remove vignettes on R without knitr support - if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' || matrix.config.r == '3.3' + - name: Remove vignettes + if: always() # matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' || matrix.config.r == '3.3' # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R <= 3.3 as writeLines() cannot overwrite run: | rm -rf vignettes @@ -101,7 +101,7 @@ jobs: _R_CHECK_LENGTH_1_CONDITION_: verbose _R_CHECK_LENGTH_1_LOGIC2_: verbose # no check for old R versions - these packages require higher R versions - _R_CHECK_RD_XREFS_: ${{ matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' && matrix.config.r != '3.3' && matrix.config.r != '3.4' }} + _R_CHECK_RD_XREFS_: false _R_CHECK_FORCE_SUGGESTS_: false R_CHECK_CONSTANTS: 5 R_JIT_STRATEGY: 3 diff --git a/.github/workflows/check-recent.yaml b/.github/workflows/check-recent.yaml index 48d6c23e..4775ad33 100644 --- a/.github/workflows/check-recent.yaml +++ b/.github/workflows/check-recent.yaml @@ -99,6 +99,5 @@ jobs: - name: Show tinytest output if: always() run: | - ls -lh find . -name 'tinytest.Rout*' -exec cat '{}' \; || true shell: bash diff --git a/DESCRIPTION b/DESCRIPTION index baf24f44..adbb10cd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.2.9083 +Version: 1.8.2.9084 Date: 2023-01-06 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NAMESPACE b/NAMESPACE index 2dbd4df3..77232b4f 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -313,6 +313,7 @@ export(mo_lpsn) export(mo_matching_score) export(mo_name) export(mo_order) +export(mo_pathogenicity) export(mo_phylum) export(mo_property) export(mo_rank) diff --git a/NEWS.md b/NEWS.md index 37191378..63d53705 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.2.9083 +# AMR 1.8.2.9084 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)* diff --git a/R/mo_property.R b/R/mo_property.R index 09148905..192490fa 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -45,17 +45,19 @@ #' #' Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions [mo_kingdom()] and [mo_domain()] return the exact same results. #' -#' Determination of the Gram stain - [mo_gramstain()] - will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, [PMID 34694987](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria in these phyla are considered Gram-positive in this `AMR` package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (or `NA` when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria. +#' Determination of human pathogenicity ([mo_pathogenicity()]) is strongly based on Bartlett *et al.* (2022, \doi{10.1099/mic.0.001269}). This function returns a [factor] with the levels *Pathogenic*, *Potentially pathogenic*, *Non-pathogenic*, and *Unknown*. #' -#' Determination of yeasts - [mo_is_yeast()] - will be based on the taxonomic kingdom and class. *Budding yeasts* are fungi of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes). *True yeasts* are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (or `NA` when the input is `NA` or the MO code is `UNKNOWN`). +#' Determination of the Gram stain ([mo_gramstain()]) will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, [PMID 34694987](https://pubmed.ncbi.nlm.nih.gov/34694987/)). Bacteria in these phyla are considered Gram-positive in this `AMR` package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (or `NA` when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria. #' -#' Determination of intrinsic resistance - [mo_is_intrinsic_resistant()] - will be based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.3)`. The [mo_is_intrinsic_resistant()] function can be vectorised over both argument `x` (input for microorganisms) and `ab` (input for antibiotics). +#' Determination of yeasts ([mo_is_yeast()]) will be based on the taxonomic kingdom and class. *Budding yeasts* are fungi of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes). *True yeasts* are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (or `NA` when the input is `NA` or the MO code is `UNKNOWN`). +#' +#' Determination of intrinsic resistance ([mo_is_intrinsic_resistant()]) will be based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.3)`. The [mo_is_intrinsic_resistant()] function can be vectorised over both argument `x` (input for microorganisms) and `ab` (input for antibiotics). #' #' All output [will be translated][translate] where possible. #' #' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. #' -#' SNOMED codes - [mo_snomed()] - are from the version of `r documentation_date(TAXONOMY_VERSION$SNOMED$accessed_date)`. See *Source* and the [microorganisms] data set for more info. +#' SNOMED codes ([mo_snomed()]) are from the version of `r documentation_date(TAXONOMY_VERSION$SNOMED$accessed_date)`. See *Source* and the [microorganisms] data set for more info. #' #' Old taxonomic names (so-called 'synonyms') can be retrieved with [mo_synonyms()], the current taxonomic name can be retrieved with [mo_current()]. Both functions return full names. #' @inheritSection mo_matching_score Matching Score for Microorganisms @@ -64,6 +66,7 @@ #' @name mo_property #' @return #' - An [integer] in case of [mo_year()] +#' - An [ordered factor][factor] in case of [mo_pathogenicity()] #' - A [list] in case of [mo_taxonomy()], [mo_synonyms()] and [mo_info()] #' - A named [character] in case of [mo_url()] #' - A [numeric] in case of [mo_snomed()] @@ -73,6 +76,7 @@ #' @inheritSection AMR Reference Data Publicly Available #' @examples #' # taxonomic tree ----------------------------------------------------------- +#' #' mo_kingdom("Klebsiella pneumoniae") #' mo_phylum("Klebsiella pneumoniae") #' mo_class("Klebsiella pneumoniae") @@ -82,27 +86,37 @@ #' mo_species("Klebsiella pneumoniae") #' mo_subspecies("Klebsiella pneumoniae") #' -#' # colloquial properties ---------------------------------------------------- +#' +#' # full names and short names ----------------------------------------------- +#' #' mo_name("Klebsiella pneumoniae") #' mo_fullname("Klebsiella pneumoniae") #' mo_shortname("Klebsiella pneumoniae") #' +#' #' # other properties --------------------------------------------------------- +#' +#' mo_pathogenicity("Klebsiella pneumoniae") #' mo_gramstain("Klebsiella pneumoniae") #' mo_snomed("Klebsiella pneumoniae") #' mo_type("Klebsiella pneumoniae") #' mo_rank("Klebsiella pneumoniae") #' mo_url("Klebsiella pneumoniae") -#' mo_synonyms("Klebsiella pneumoniae") +#' mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella")) +#' #' #' # scientific reference ----------------------------------------------------- +#' #' mo_ref("Klebsiella pneumoniae") #' mo_authors("Klebsiella pneumoniae") #' mo_year("Klebsiella pneumoniae") #' mo_lpsn("Klebsiella pneumoniae") #' mo_gbif("Klebsiella pneumoniae") +#' mo_synonyms("Klebsiella pneumoniae") +#' #' #' # abbreviations known in the field ----------------------------------------- +#' #' mo_genus("MRSA") #' mo_species("MRSA") #' mo_shortname("VISA") @@ -111,18 +125,24 @@ #' mo_genus("EHEC") #' mo_species("EHEC") #' +#' #' # known subspecies --------------------------------------------------------- +#' #' mo_fullname("K. pneu rh") #' mo_shortname("K. pneu rh") #' +#' #' \donttest{ #' # Becker classification, see ?as.mo ---------------------------------------- +#' #' mo_fullname("Staph. epidermidis") #' mo_fullname("Staph. epidermidis", Becker = TRUE) #' mo_shortname("Staph. epidermidis") #' mo_shortname("Staph. epidermidis", Becker = TRUE) #' +#' #' # Lancefield classification, see ?as.mo ------------------------------------ +#' #' mo_fullname("S. pyo") #' mo_fullname("S. pyo", Lancefield = TRUE) #' mo_shortname("S. pyo") @@ -130,6 +150,7 @@ #' #' #' # language support -------------------------------------------------------- +#' #' mo_gramstain("Klebsiella pneumoniae", language = "de") # German #' mo_gramstain("Klebsiella pneumoniae", language = "nl") # Dutch #' mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish @@ -148,8 +169,6 @@ #' #' # other -------------------------------------------------------------------- #' -#' mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella")) -#' #' # gram stains and intrinsic resistance can be used as a filter in dplyr verbs #' if (require("dplyr")) { #' example_isolates %>% @@ -162,7 +181,6 @@ #' count(mo_genus(), sort = TRUE) #' } #' -#' #' # get a list with the complete taxonomy (from kingdom to subspecies) #' mo_taxonomy("Klebsiella pneumoniae") #' @@ -386,6 +404,40 @@ mo_status <- function(x, language = get_AMR_locale(), keep_synonyms = getOption( translate_into_language(mo_validate(x = x, property = "status", language = language, keep_synonyms = keep_synonyms, ...), language = language, only_unknown = TRUE) } +#' @rdname mo_property +#' @export +mo_pathogenicity <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { + if (missing(x)) { + # this tries to find the data and an 'mo' column + x <- find_mo_col(fn = "mo_pathogenicity") + } + meet_criteria(x, allow_NA = TRUE) + language <- validate_language(language) + meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1) + + x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...) + metadata <- get_mo_uncertainties() + + prev <- AMR_env$MO_lookup$prevalence[match(x.mo, AMR_env$MO_lookup$mo)] + kngd <- AMR_env$MO_lookup$kingdom[match(x.mo, AMR_env$MO_lookup$mo)] + rank <- AMR_env$MO_lookup$rank[match(x.mo, AMR_env$MO_lookup$mo)] + + out <- factor(ifelse(prev == 1 & kngd == "Bacteria" & rank != "genus", + "Pathogenic", + ifelse(prev < 2 & kngd == "Fungi", + "Potentially pathogenic", + ifelse(prev == 2 & kngd == "Bacteria", + "Non-pathogenic", + ifelse(kngd == "Bacteria", + "Potentially pathogenic", + "Unknown")))), + levels = c("Pathogenic", "Potentially pathogenic", "Non-pathogenic", "Unknown"), + ordered = TRUE) + + load_mo_uncertainties(metadata) + out +} + #' @rdname mo_property #' @export mo_gramstain <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { diff --git a/inst/tinytest/test-mo_property.R b/inst/tinytest/test-mo_property.R index 5fc27749..7b1f7680 100644 --- a/inst/tinytest/test-mo_property.R +++ b/inst/tinytest/test-mo_property.R @@ -102,6 +102,9 @@ expect_equal(names(mo_info("Escherichia coli")), c( )) expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list") +expect_equal(as.character(table(mo_pathogenicity(example_isolates$mo))) + c("1561", "422", "1", "16")) + expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919") expect_equal(mo_authors("Escherichia coli"), "Castellani et al.") expect_equal(mo_year("Escherichia coli"), 1919) diff --git a/man/mo_property.Rd b/man/mo_property.Rd index 2770d980..22738e84 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -16,6 +16,7 @@ \alias{mo_domain} \alias{mo_type} \alias{mo_status} +\alias{mo_pathogenicity} \alias{mo_gramstain} \alias{mo_is_gram_negative} \alias{mo_is_gram_positive} @@ -133,6 +134,13 @@ mo_status( ... ) +mo_pathogenicity( + x, + language = get_AMR_locale(), + keep_synonyms = getOption("AMR_keep_synonyms", FALSE), + ... +) + mo_gramstain( x, language = get_AMR_locale(), @@ -275,6 +283,7 @@ mo_property( \value{ \itemize{ \item An \link{integer} in case of \code{\link[=mo_year]{mo_year()}} +\item An \link[=factor]{ordered factor} in case of \code{\link[=mo_pathogenicity]{mo_pathogenicity()}} \item A \link{list} in case of \code{\link[=mo_taxonomy]{mo_taxonomy()}}, \code{\link[=mo_synonyms]{mo_synonyms()}} and \code{\link[=mo_info]{mo_info()}} \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()}} @@ -296,17 +305,19 @@ The short name - \code{\link[=mo_shortname]{mo_shortname()}} - almost always ret Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions \code{\link[=mo_kingdom]{mo_kingdom()}} and \code{\link[=mo_domain]{mo_domain()}} return the exact same results. -Determination of the Gram stain - \code{\link[=mo_gramstain]{mo_gramstain()}} - will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, \href{https://pubmed.ncbi.nlm.nih.gov/11837318/}{PMID 11837318}), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, \href{https://pubmed.ncbi.nlm.nih.gov/34694987/}{PMID 34694987}). Bacteria in these phyla are considered Gram-positive in this \code{AMR} package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value \code{NA}. Functions \code{\link[=mo_is_gram_negative]{mo_is_gram_negative()}} and \code{\link[=mo_is_gram_positive]{mo_is_gram_positive()}} always return \code{TRUE} or \code{FALSE} (or \code{NA} when the input is \code{NA} or the MO code is \code{UNKNOWN}), thus always return \code{FALSE} for species outside the taxonomic kingdom of Bacteria. +Determination of human pathogenicity (\code{\link[=mo_pathogenicity]{mo_pathogenicity()}}) is strongly based on Bartlett \emph{et al.} (2022, \doi{10.1099/mic.0.001269}). This function returns a \link{factor} with the levels \emph{Pathogenic}, \emph{Potentially pathogenic}, \emph{Non-pathogenic}, and \emph{Unknown}. -Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are fungi of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes). \emph{True yeasts} are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (or \code{NA} when the input is \code{NA} or the MO code is \code{UNKNOWN}). +Determination of the Gram stain (\code{\link[=mo_gramstain]{mo_gramstain()}}) will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, \href{https://pubmed.ncbi.nlm.nih.gov/11837318/}{PMID 11837318}), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, \href{https://pubmed.ncbi.nlm.nih.gov/34694987/}{PMID 34694987}). Bacteria in these phyla are considered Gram-positive in this \code{AMR} package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value \code{NA}. Functions \code{\link[=mo_is_gram_negative]{mo_is_gram_negative()}} and \code{\link[=mo_is_gram_positive]{mo_is_gram_positive()}} always return \code{TRUE} or \code{FALSE} (or \code{NA} when the input is \code{NA} or the MO code is \code{UNKNOWN}), thus always return \code{FALSE} for species outside the taxonomic kingdom of Bacteria. -Determination of intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} function can be vectorised over both argument \code{x} (input for microorganisms) and \code{ab} (input for antibiotics). +Determination of yeasts (\code{\link[=mo_is_yeast]{mo_is_yeast()}}) will be based on the taxonomic kingdom and class. \emph{Budding yeasts} are fungi of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes). \emph{True yeasts} are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes, the function will return \code{TRUE}. It returns \code{FALSE} otherwise (or \code{NA} when the input is \code{NA} or the MO code is \code{UNKNOWN}). + +Determination of intrinsic resistance (\code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}}) will be based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} function can be vectorised over both argument \code{x} (input for microorganisms) and \code{ab} (input for antibiotics). 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. -SNOMED codes - \code{\link[=mo_snomed]{mo_snomed()}} - are from the version of 1 July, 2021. See \emph{Source} and the \link{microorganisms} data set for more info. +SNOMED codes (\code{\link[=mo_snomed]{mo_snomed()}}) are from the version of 1 July, 2021. See \emph{Source} and the \link{microorganisms} data set for more info. Old taxonomic names (so-called 'synonyms') can be retrieved with \code{\link[=mo_synonyms]{mo_synonyms()}}, the current taxonomic name can be retrieved with \code{\link[=mo_current]{mo_current()}}. Both functions return full names. } @@ -369,6 +380,7 @@ All data sets in this \code{AMR} package (about microorganisms, antibiotics, R/S \examples{ # taxonomic tree ----------------------------------------------------------- + mo_kingdom("Klebsiella pneumoniae") mo_phylum("Klebsiella pneumoniae") mo_class("Klebsiella pneumoniae") @@ -378,27 +390,37 @@ mo_genus("Klebsiella pneumoniae") mo_species("Klebsiella pneumoniae") mo_subspecies("Klebsiella pneumoniae") -# colloquial properties ---------------------------------------------------- + +# full names and short names ----------------------------------------------- + mo_name("Klebsiella pneumoniae") mo_fullname("Klebsiella pneumoniae") mo_shortname("Klebsiella pneumoniae") + # other properties --------------------------------------------------------- + +mo_pathogenicity("Klebsiella pneumoniae") mo_gramstain("Klebsiella pneumoniae") mo_snomed("Klebsiella pneumoniae") mo_type("Klebsiella pneumoniae") mo_rank("Klebsiella pneumoniae") mo_url("Klebsiella pneumoniae") -mo_synonyms("Klebsiella pneumoniae") +mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella")) + # scientific reference ----------------------------------------------------- + mo_ref("Klebsiella pneumoniae") mo_authors("Klebsiella pneumoniae") mo_year("Klebsiella pneumoniae") mo_lpsn("Klebsiella pneumoniae") mo_gbif("Klebsiella pneumoniae") +mo_synonyms("Klebsiella pneumoniae") + # abbreviations known in the field ----------------------------------------- + mo_genus("MRSA") mo_species("MRSA") mo_shortname("VISA") @@ -407,18 +429,24 @@ mo_gramstain("VISA") mo_genus("EHEC") mo_species("EHEC") + # known subspecies --------------------------------------------------------- + mo_fullname("K. pneu rh") mo_shortname("K. pneu rh") + \donttest{ # Becker classification, see ?as.mo ---------------------------------------- + mo_fullname("Staph. epidermidis") mo_fullname("Staph. epidermidis", Becker = TRUE) mo_shortname("Staph. epidermidis") mo_shortname("Staph. epidermidis", Becker = TRUE) + # Lancefield classification, see ?as.mo ------------------------------------ + mo_fullname("S. pyo") mo_fullname("S. pyo", Lancefield = TRUE) mo_shortname("S. pyo") @@ -426,6 +454,7 @@ mo_shortname("S. pyo", Lancefield = TRUE) # language support -------------------------------------------------------- + mo_gramstain("Klebsiella pneumoniae", language = "de") # German mo_gramstain("Klebsiella pneumoniae", language = "nl") # Dutch mo_gramstain("Klebsiella pneumoniae", language = "es") # Spanish @@ -444,8 +473,6 @@ mo_fullname("S. pyogenes", Lancefield = TRUE, language = "uk") # other -------------------------------------------------------------------- -mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella")) - # gram stains and intrinsic resistance can be used as a filter in dplyr verbs if (require("dplyr")) { example_isolates \%>\% @@ -458,7 +485,6 @@ if (require("dplyr")) { count(mo_genus(), sort = TRUE) } - # get a list with the complete taxonomy (from kingdom to subspecies) mo_taxonomy("Klebsiella pneumoniae")