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Catalogue of Life, replaces ITIS

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dr. M.S. (Matthijs) Berends
2019-02-18 02:33:37 +01:00
parent 9209787a53
commit 54f8258f8c
88 changed files with 607 additions and 590 deletions
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32
R/mo_property.R
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@ -38,7 +38,7 @@
#' @rdname mo_property
#' @name mo_property
#' @return \itemize{
#' \item{An \code{integer} in case of \code{mo_TSN} and \code{mo_year}}
#' \item{An \code{integer} in case of \code{mo_year}}
#' \item{A \code{list} in case of \code{mo_taxonomy}}
#' \item{A \code{character} in all other cases}
#' }
@ -57,7 +57,6 @@
#' mo_genus("E. coli") # "Escherichia"
#' mo_species("E. coli") # "coli"
#' mo_subspecies("E. coli") # NA
#' mo_TSN("E. coli") # 285 (Taxonomic Serial Number)
#'
#' ## colloquial properties
#' mo_fullname("E. coli") # "Escherichia coli"
@ -242,17 +241,15 @@ mo_type <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_gramstain <- function(x, language = get_locale(), ...) {
mo_translate(mo_validate(x = x, property = "gramstain", ...), language = language)
}
#' @rdname mo_property
#' @export
mo_TSN <- function(x, ...) {
res <- mo_validate(x = x, property = "tsn", ...)
if (any(is.na(res))) {
warning("Some results do not have a TSN, because they are missing from ITIS and were added manually. See ?microorganisms.")
}
res
x.bak <- x
x <- mo_phylum(x, ...)
x[x %in% c("Actinobacteria",
"Chloroflexi",
"Firmicutes",
"Tenericutes")] <- "Gram positive"
x[x != "Gram positive"] <- "Gram negative"
x[mo_kingdom(x.bak) != "Bacteria"] <- NA_character_
mo_translate(x, language = language)
}
#' @rdname mo_property
@ -284,7 +281,6 @@ mo_year <- function(x, ...) {
mo_taxonomy <- function(x, ...) {
x <- AMR::as.mo(x, ...)
base::list(kingdom = mo_kingdom(x),
subkingdom = mo_subkingdom(x),
phylum = mo_phylum(x),
class = mo_class(x),
order = mo_order(x),
@ -472,11 +468,7 @@ mo_validate <- function(x, property, ...) {
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
# check onLoad() in R/zzz.R: data tables are created there.
}
if (!all(x %in% microorganismsDT[[property]])
@ -486,8 +478,6 @@ mo_validate <- function(x, property, ...) {
} else {
if (property == "mo") {
return(structure(x, class = "mo"))
} else if (property == "tsn") {
return(as.integer(x))
} else {
return(x)
}