mirror of https://github.com/msberends/AMR.git
496 lines
22 KiB
R
Executable File
496 lines
22 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitab.io/AMR. #
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# ==================================================================== #
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#' Property of a microorganism
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#'
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#' Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set. All input values will be evaluated internally with \code{\link{as.mo}}.
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#' @param x any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}}
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#' @param property one of the column names of one of the \code{\link{microorganisms}} data set or \code{"shortname"}
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#' @param language language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.
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#' @param ... other parameters passed on to \code{\link{as.mo}}
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#' @details All functions will return the most recently known taxonomic property according to ITIS, except for \code{mo_ref}, \code{mo_authors} and \code{mo_year}. This leads to the following results:
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#' \itemize{
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#' \item{\code{mo_fullname("Chlamydia psittaci")} will return \code{"Chlamydophila psittaci"} (with a warning about the renaming)}
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#' \item{\code{mo_ref("Chlamydia psittaci")} will return \code{"Page, 1968"} (with a warning about the renaming)}
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#' \item{\code{mo_ref("Chlamydophila psittaci")} will return \code{"Everett et al., 1999"} (without a warning)}
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#' }
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#' @inheritSection get_locale Supported languages
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#' @inheritSection ITIS ITIS
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#' @inheritSection as.mo Source
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#' @rdname mo_property
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#' @name mo_property
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#' @return \itemize{
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#' \item{An \code{integer} in case of \code{mo_TSN} and \code{mo_year}}
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#' \item{A \code{list} in case of \code{mo_taxonomy}}
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#' \item{A \code{character} in all other cases}
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#' }
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#' @export
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#' @seealso \code{\link{microorganisms}}
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' # All properties of Escherichia coli
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#' ## taxonomic properties
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#' mo_kingdom("E. coli") # "Bacteria"
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#' mo_subkingdom("E. coli") # "Negibacteria"
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#' mo_phylum("E. coli") # "Proteobacteria"
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#' mo_class("E. coli") # "Gammaproteobacteria"
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#' mo_order("E. coli") # "Enterobacteriales"
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#' mo_family("E. coli") # "Enterobacteriaceae"
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#' mo_genus("E. coli") # "Escherichia"
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#' mo_species("E. coli") # "coli"
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#' mo_subspecies("E. coli") # NA
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#' mo_TSN("E. coli") # 285 (Taxonomic Serial Number)
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#'
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#' ## colloquial properties
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#' mo_fullname("E. coli") # "Escherichia coli"
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#' mo_shortname("E. coli") # "E. coli"
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#'
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#' ## other properties
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#' mo_gramstain("E. coli") # "Gram negative"
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#' mo_type("E. coli") # "Bacteria" (equal to kingdom)
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#'
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#' ## scientific reference
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#' mo_ref("E. coli") # "Castellani and Chalmers, 1919"
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#' mo_authors("E. coli") # "Castellani and Chalmers"
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#' mo_year("E. coli") # 1919
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#'
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#'
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#' # Abbreviations known in the field
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#' mo_genus("MRSA") # "Staphylococcus"
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#' mo_species("MRSA") # "aureus"
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#' mo_shortname("MRSA") # "S. aureus"
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#' mo_gramstain("MRSA") # "Gram positive"
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#'
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#' mo_genus("VISA") # "Staphylococcus"
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#' mo_species("VISA") # "aureus"
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#'
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#'
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#' # Known subspecies
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#' mo_genus("doylei") # "Campylobacter"
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#' mo_species("doylei") # "jejuni"
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#' mo_fullname("doylei") # "Campylobacter jejuni doylei"
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#'
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#' mo_fullname("K. pneu rh") # "Klebsiella pneumoniae rhinoscleromatis"
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#' mo_shortname("K. pneu rh") # "K. pneumoniae"
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#'
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#'
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#' # Becker classification, see ?as.mo
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#' mo_fullname("S. epi") # "Staphylococcus epidermidis"
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#' mo_fullname("S. epi", Becker = TRUE) # "Coagulase Negative Staphylococcus (CoNS)"
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#' mo_shortname("S. epi") # "S. epidermidis"
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#' mo_shortname("S. epi", Becker = TRUE) # "CoNS"
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#'
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#' # Lancefield classification, see ?as.mo
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#' mo_fullname("S. pyo") # "Streptococcus pyogenes"
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#' mo_fullname("S. pyo", Lancefield = TRUE) # "Streptococcus group A"
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#' mo_shortname("S. pyo") # "S. pyogenes"
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#' mo_shortname("S. pyo", Lancefield = TRUE) # "GAS" ('Group A streptococci')
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#'
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#'
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#' # Language support for German, Dutch, Spanish, Portuguese, Italian and French
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#' mo_gramstain("E. coli", language = "de") # "Gramnegativ"
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#' mo_gramstain("E. coli", language = "nl") # "Gram-negatief"
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#' mo_gramstain("E. coli", language = "es") # "Gram negativo"
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#'
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#' # mo_type is equal to mo_kingdom, but mo_kingdom will remain official
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#' mo_kingdom("E. coli") # "Bacteria" on a German system
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#' mo_type("E. coli") # "Bakterien" on a German system
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#' mo_type("E. coli") # "Bacteria" on an English system
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#'
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#' mo_fullname("S. pyogenes",
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#' Lancefield = TRUE,
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#' language = "de") # "Streptococcus Gruppe A"
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#' mo_fullname("S. pyogenes",
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#' Lancefield = TRUE,
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#' language = "nl") # "Streptococcus groep A"
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#'
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#'
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#' # Get a list with the complete taxonomy (subkingdom to subspecies)
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#' mo_taxonomy("E. coli")
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mo_fullname <- function(x, language = get_locale(), ...) {
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x <- mo_validate(x = x, property = "fullname", ...)
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mo_translate(x, language = language)
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}
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#' @rdname mo_property
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#' @importFrom dplyr %>% left_join mutate pull
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#' @export
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mo_shortname <- function(x, language = get_locale(), ...) {
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dots <- list(...)
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Becker <- dots$Becker
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if (is.null(Becker)) {
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Becker <- FALSE
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}
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Lancefield <- dots$Lancefield
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if (is.null(Lancefield)) {
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Lancefield <- FALSE
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}
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if (Becker %in% c(TRUE, "all") | Lancefield == TRUE) {
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res1 <- AMR::as.mo(x, Becker = FALSE, Lancefield = FALSE, reference_df = dots$reference_df)
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res2 <- suppressWarnings(AMR::as.mo(res1, ...))
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res2_fullname <- mo_fullname(res2, language = language)
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res2_fullname[res2_fullname %like% " \\(CoNS\\)"] <- "CoNS"
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res2_fullname[res2_fullname %like% " \\(CoPS\\)"] <- "CoPS"
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res2_fullname[res2_fullname %like% " \\(KNS\\)"] <- "KNS"
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res2_fullname[res2_fullname %like% " \\(KPS\\)"] <- "KPS"
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res2_fullname[res2_fullname %like% " \\(CNS\\)"] <- "CNS"
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res2_fullname[res2_fullname %like% " \\(CPS\\)"] <- "CPS"
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res2_fullname <- gsub("Streptococcus (group|Gruppe|gruppe|groep|grupo|gruppo|groupe) (.)",
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"G\\2S",
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res2_fullname) # turn "Streptococcus group A" and "Streptococcus grupo A" to "GAS"
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res2_fullname_vector <- res2_fullname[res2_fullname == mo_fullname(res1)]
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res2_fullname[res2_fullname == mo_fullname(res1)] <- paste0(substr(mo_genus(res2_fullname_vector), 1, 1),
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". ",
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suppressWarnings(mo_species(res2_fullname_vector)))
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if (sum(res1 == res2, na.rm = TRUE) > 0) {
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res1[res1 == res2] <- paste0(substr(mo_genus(res1[res1 == res2]), 1, 1),
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". ",
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suppressWarnings(mo_species(res1[res1 == res2])))
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}
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res1[res1 != res2] <- res2_fullname
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result <- as.character(res1)
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} else {
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x <- AMR::as.mo(x, ...)
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suppressWarnings(
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result <- data.frame(mo = x) %>%
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left_join(AMR::microorganisms, by = "mo") %>%
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mutate(shortname = ifelse(!is.na(genus) & !is.na(species), paste0(substr(genus, 1, 1), ". ", species), NA_character_)) %>%
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pull(shortname)
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)
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}
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mo_translate(result, language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_subspecies <- function(x, language = get_locale(), ...) {
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mo_translate(mo_validate(x = x, property = "subspecies", ...), language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_species <- function(x, language = get_locale(), ...) {
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mo_translate(mo_validate(x = x, property = "species", ...), language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_genus <- function(x, language = get_locale(), ...) {
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mo_translate(mo_validate(x = x, property = "genus", ...), language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_family <- function(x, ...) {
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mo_validate(x = x, property = "family", ...)
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}
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#' @rdname mo_property
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#' @export
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mo_order <- function(x, ...) {
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mo_validate(x = x, property = "order", ...)
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}
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#' @rdname mo_property
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#' @export
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mo_class <- function(x, ...) {
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mo_validate(x = x, property = "class", ...)
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}
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#' @rdname mo_property
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#' @export
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mo_phylum <- function(x, ...) {
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mo_validate(x = x, property = "phylum", ...)
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}
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#' @rdname mo_property
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#' @export
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mo_subkingdom <- function(x, ...) {
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mo_validate(x = x, property = "subkingdom", ...)
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}
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#' @rdname mo_property
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#' @export
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mo_kingdom <- function(x, ...) {
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mo_validate(x = x, property = "kingdom", ...)
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}
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#' @rdname mo_property
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#' @export
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mo_type <- function(x, language = get_locale(), ...) {
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mo_translate(mo_validate(x = x, property = "kingdom", ...), language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_gramstain <- function(x, language = get_locale(), ...) {
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mo_translate(mo_validate(x = x, property = "gramstain", ...), language = language)
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}
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#' @rdname mo_property
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#' @export
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mo_TSN <- function(x, ...) {
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res <- mo_validate(x = x, property = "tsn", ...)
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if (any(is.na(res))) {
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warning("Some results do not have a TSN, because they are missing from ITIS and were added manually. See ?microorganisms.")
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}
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res
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}
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#' @rdname mo_property
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#' @export
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mo_ref <- function(x, ...) {
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mo_validate(x = x, property = "ref", ...)
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}
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#' @rdname mo_property
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#' @export
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mo_authors <- function(x, ...) {
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x <- mo_validate(x = x, property = "ref", ...)
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# remove last 4 digits and presumably the comma and space that preceed them
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x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)])
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x
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}
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#' @rdname mo_property
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#' @export
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mo_year <- function(x, ...) {
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x <- mo_validate(x = x, property = "ref", ...)
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# get last 4 digits
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x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)])
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as.integer(x)
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}
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#' @rdname mo_property
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#' @export
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mo_taxonomy <- function(x, ...) {
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x <- AMR::as.mo(x, ...)
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base::list(kingdom = mo_kingdom(x),
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subkingdom = mo_subkingdom(x),
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phylum = mo_phylum(x),
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class = mo_class(x),
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order = mo_order(x),
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family = mo_family(x),
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genus = mo_genus(x),
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species = mo_species(x),
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subspecies = mo_subspecies(x))
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}
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#' @rdname mo_property
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#' @importFrom data.table data.table as.data.table setkey
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#' @export
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mo_property <- function(x, property = 'fullname', language = get_locale(), ...) {
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if (length(property) != 1L) {
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stop("'property' must be of length 1.")
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}
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if (!property %in% colnames(AMR::microorganisms)) {
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stop("invalid property: '", property, "' - use a column name of the `microorganisms` data set")
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}
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mo_translate(mo_validate(x = x, property = property, ...), language = language)
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}
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#' @importFrom dplyr %>% case_when
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mo_translate <- function(x, language) {
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if (is.null(language)) {
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return(x)
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}
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if (language %in% c("en", "")) {
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return(x)
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}
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supported <- c("en", "de", "nl", "es", "pt", "it", "fr")
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if (!language %in% supported) {
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stop("Unsupported language: '", language, "' - use one of: ", paste0("'", sort(supported), "'", collapse = ", "), call. = FALSE)
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}
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x_tobetranslated <- grepl(x = x,
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pattern = "(Coagulase Negative Staphylococcus|Coagulase Positive Staphylococcus|Beta-haemolytic Streptococcus|unknown Gram negatives|unknown Gram positives|CoNS|CoPS|no MO|Gram negative|Gram positive|Bacteria|Fungi|Protozoa|biogroup|biotype|vegetative|group|Group)")
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if (sum(x_tobetranslated, na.rm = TRUE) == 0) {
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return(x)
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}
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# only translate the ones that need translation
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x[x_tobetranslated] <- case_when(
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# German
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language == "de" ~ x[x_tobetranslated] %>%
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gsub("Coagulase Negative Staphylococcus","Koagulase-negative Staphylococcus", ., fixed = TRUE) %>%
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gsub("Coagulase Positive Staphylococcus","Koagulase-positive Staphylococcus", ., fixed = TRUE) %>%
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gsub("Beta-haemolytic Streptococcus", "Beta-h\u00e4molytischer Streptococcus", ., fixed = TRUE) %>%
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gsub("unknown Gram negatives", "unbekannte Gramnegativen", ., fixed = TRUE) %>%
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gsub("unknown Gram positives", "unbekannte Grampositiven", ., fixed = TRUE) %>%
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gsub("(CoNS)", "(KNS)", ., fixed = TRUE) %>%
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gsub("(CoPS)", "(KPS)", ., fixed = TRUE) %>%
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gsub("(no MO)", "(kein MO)", ., fixed = TRUE) %>%
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gsub("Gram negative", "Gramnegativ", ., fixed = TRUE) %>%
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gsub("Gram positive", "Grampositiv", ., fixed = TRUE) %>%
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gsub("Bacteria", "Bakterien", ., fixed = TRUE) %>%
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gsub("Fungi", "Hefen/Pilze", ., fixed = TRUE) %>%
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gsub("Protozoa", "Protozoen", ., fixed = TRUE) %>%
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gsub("biogroup", "Biogruppe", ., fixed = TRUE) %>%
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gsub("biotype", "Biotyp", ., fixed = TRUE) %>%
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gsub("vegetative", "vegetativ", ., fixed = TRUE) %>%
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gsub("([([ ]*?)group", "\\1Gruppe", .) %>%
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gsub("([([ ]*?)Group", "\\1Gruppe", .) %>%
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iconv(to = "UTF-8"),
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# Dutch
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language == "nl" ~ x[x_tobetranslated] %>%
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gsub("Coagulase Negative Staphylococcus","Coagulase-negatieve Staphylococcus", ., fixed = TRUE) %>%
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gsub("Coagulase Positive Staphylococcus","Coagulase-positieve Staphylococcus", ., fixed = TRUE) %>%
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gsub("Beta-haemolytic Streptococcus", "Beta-hemolytische Streptococcus", ., fixed = TRUE) %>%
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gsub("unknown Gram negatives", "onbekende Gram-negatieven", ., fixed = TRUE) %>%
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gsub("unknown Gram positives", "onbekende Gram-positieven", ., fixed = TRUE) %>%
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gsub("(no MO)", "(geen MO)", ., fixed = TRUE) %>%
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gsub("(CoNS)", "(CNS)", ., fixed = TRUE) %>%
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gsub("(CoPS)", "(CPS)", ., fixed = TRUE) %>%
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gsub("Gram negative", "Gram-negatief", ., fixed = TRUE) %>%
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gsub("Gram positive", "Gram-positief", ., fixed = TRUE) %>%
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gsub("Bacteria", "Bacteri\u00ebn", ., fixed = TRUE) %>%
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gsub("Fungi", "Schimmels/gisten", ., fixed = TRUE) %>%
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gsub("Protozoa", "protozo\u00ebn", ., fixed = TRUE) %>%
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gsub("biogroup", "biogroep", ., fixed = TRUE) %>%
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# gsub("biotype", "biotype", ., fixed = TRUE) %>%
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gsub("vegetative", "vegetatief", ., fixed = TRUE) %>%
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gsub("([([ ]*?)group", "\\1groep", .) %>%
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gsub("([([ ]*?)Group", "\\1Groep", .) %>%
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iconv(to = "UTF-8"),
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# Spanish
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language == "es" ~ x[x_tobetranslated] %>%
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gsub("Coagulase Negative Staphylococcus","Staphylococcus coagulasa negativo", ., fixed = TRUE) %>%
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gsub("Coagulase Positive Staphylococcus","Staphylococcus coagulasa positivo", ., fixed = TRUE) %>%
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gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-hemol\u00edtico", ., fixed = TRUE) %>%
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gsub("unknown Gram negatives", "Gram negativos desconocidos", ., fixed = TRUE) %>%
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gsub("unknown Gram positives", "Gram positivos desconocidos", ., fixed = TRUE) %>%
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gsub("(no MO)", "(sin MO)", ., fixed = TRUE) %>%
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gsub("Gram negative", "Gram negativo", ., fixed = TRUE) %>%
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gsub("Gram positive", "Gram positivo", ., fixed = TRUE) %>%
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gsub("Bacteria", "Bacterias", ., fixed = TRUE) %>%
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gsub("Fungi", "Hongos", ., fixed = TRUE) %>%
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gsub("Protozoa", "Protozoarios", ., fixed = TRUE) %>%
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gsub("biogroup", "biogrupo", ., fixed = TRUE) %>%
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gsub("biotype", "biotipo", ., fixed = TRUE) %>%
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gsub("vegetative", "vegetativo", ., fixed = TRUE) %>%
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gsub("([([ ]*?)group", "\\1grupo", .) %>%
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gsub("([([ ]*?)Group", "\\1Grupo", .) %>%
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iconv(to = "UTF-8"),
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# Italian
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language == "it" ~ x[x_tobetranslated] %>%
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gsub("Coagulase Negative Staphylococcus","Staphylococcus negativo coagulasi", ., fixed = TRUE) %>%
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gsub("Coagulase Positive Staphylococcus","Staphylococcus positivo coagulasi", ., fixed = TRUE) %>%
|
|
gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-emolitico", ., fixed = TRUE) %>%
|
|
gsub("unknown Gram negatives", "Gram negativi sconosciuti", ., fixed = TRUE) %>%
|
|
gsub("unknown Gram positives", "Gram positivi sconosciuti", ., fixed = TRUE) %>%
|
|
gsub("(no MO)", "(non MO)", ., fixed = TRUE) %>%
|
|
gsub("Gram negative", "Gram negativo", ., fixed = TRUE) %>%
|
|
gsub("Gram positive", "Gram positivo", ., fixed = TRUE) %>%
|
|
gsub("Bacteria", "Batteri", ., fixed = TRUE) %>%
|
|
gsub("Fungi", "Fungo", ., fixed = TRUE) %>%
|
|
gsub("Protozoa", "Protozoi", ., fixed = TRUE) %>%
|
|
gsub("biogroup", "biogruppo", ., fixed = TRUE) %>%
|
|
gsub("biotype", "biotipo", ., fixed = TRUE) %>%
|
|
gsub("vegetative", "vegetativo", ., fixed = TRUE) %>%
|
|
gsub("([([ ]*?)group", "\\1gruppo", .) %>%
|
|
gsub("([([ ]*?)Group", "\\1Gruppo", .),
|
|
|
|
# French
|
|
language == "fr" ~ x[x_tobetranslated] %>%
|
|
gsub("Coagulase Negative Staphylococcus","Staphylococcus \u00e0 coagulase n\u00e9gative", ., fixed = TRUE) %>%
|
|
gsub("Coagulase Positive Staphylococcus","Staphylococcus \u00e0 coagulase positif", ., fixed = TRUE) %>%
|
|
gsub("Beta-haemolytic Streptococcus", "Streptococcus B\u00eata-h\u00e9molytique", ., fixed = TRUE) %>%
|
|
gsub("unknown Gram negatives", "Gram n\u00e9gatifs inconnus", ., fixed = TRUE) %>%
|
|
gsub("unknown Gram positives", "Gram positifs inconnus", ., fixed = TRUE) %>%
|
|
gsub("(no MO)", "(pas MO)", ., fixed = TRUE) %>%
|
|
gsub("Gram negative", "Gram n\u00e9gatif", ., fixed = TRUE) %>%
|
|
gsub("Gram positive", "Gram positif", ., fixed = TRUE) %>%
|
|
gsub("Bacteria", "Bact\u00e9ries", ., fixed = TRUE) %>%
|
|
gsub("Fungi", "Champignons", ., fixed = TRUE) %>%
|
|
gsub("Protozoa", "Protozoaires", ., fixed = TRUE) %>%
|
|
gsub("biogroup", "biogroupe", ., fixed = TRUE) %>%
|
|
# gsub("biotype", "biotype", ., fixed = TRUE) %>%
|
|
gsub("vegetative", "v\u00e9g\u00e9tatif", ., fixed = TRUE) %>%
|
|
gsub("([([ ]*?)group", "\\1groupe", .) %>%
|
|
gsub("([([ ]*?)Group", "\\1Groupe", .) %>%
|
|
iconv(to = "UTF-8"),
|
|
|
|
# Portuguese
|
|
language == "pt" ~ x[x_tobetranslated] %>%
|
|
gsub("Coagulase Negative Staphylococcus","Staphylococcus coagulase negativo", ., fixed = TRUE) %>%
|
|
gsub("Coagulase Positive Staphylococcus","Staphylococcus coagulase positivo", ., fixed = TRUE) %>%
|
|
gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-hemol\u00edtico", ., fixed = TRUE) %>%
|
|
gsub("unknown Gram negatives", "Gram negativos desconhecidos", ., fixed = TRUE) %>%
|
|
gsub("unknown Gram positives", "Gram positivos desconhecidos", ., fixed = TRUE) %>%
|
|
gsub("(no MO)", "(sem MO)", ., fixed = TRUE) %>%
|
|
gsub("Gram negative", "Gram negativo", ., fixed = TRUE) %>%
|
|
gsub("Gram positive", "Gram positivo", ., fixed = TRUE) %>%
|
|
gsub("Bacteria", "Bact\u00e9rias", ., fixed = TRUE) %>%
|
|
gsub("Fungi", "Fungos", ., fixed = TRUE) %>%
|
|
gsub("Protozoa", "Protozo\u00e1rios", ., fixed = TRUE) %>%
|
|
gsub("biogroup", "biogrupo", ., fixed = TRUE) %>%
|
|
gsub("biotype", "bi\u00f3tipo", ., fixed = TRUE) %>%
|
|
gsub("vegetative", "vegetativo", ., fixed = TRUE) %>%
|
|
gsub("([([ ]*?)group", "\\1grupo", .) %>%
|
|
gsub("([([ ]*?)Group", "\\1Grupo", .) %>%
|
|
iconv(to = "UTF-8"))
|
|
|
|
x
|
|
|
|
}
|
|
|
|
mo_validate <- function(x, property, ...) {
|
|
|
|
dots <- list(...)
|
|
Becker <- dots$Becker
|
|
if (is.null(Becker)) {
|
|
Becker <- FALSE
|
|
}
|
|
Lancefield <- dots$Lancefield
|
|
if (is.null(Lancefield)) {
|
|
Lancefield <- FALSE
|
|
}
|
|
|
|
if (!"AMR" %in% base::.packages()) {
|
|
library("AMR")
|
|
# These data.tables are available as data sets when the AMR package is loaded:
|
|
# microorganismsDT # this one is sorted by kingdom (B<F<P), prevalence, TSN
|
|
# microorganisms.prevDT # same as microorganismsDT, but with prevalence != 9999
|
|
# microorganisms.unprevDT # same as microorganismsDT, but with prevalence == 9999
|
|
# microorganisms.oldDT # old taxonomic names, sorted by name (genus+species), TSN
|
|
}
|
|
|
|
if (!all(x %in% microorganismsDT[[property]])
|
|
| Becker %in% c(TRUE, "all")
|
|
| Lancefield %in% c(TRUE, "all")) {
|
|
exec_as.mo(x, property = property, ...)
|
|
} else {
|
|
if (property == "mo") {
|
|
return(structure(x, class = "mo"))
|
|
} else if (property == "tsn") {
|
|
return(as.integer(x))
|
|
} else {
|
|
return(x)
|
|
}
|
|
}
|
|
}
|