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support new mo codes

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dr. M.S. (Matthijs) Berends
2022-12-27 15:16:15 +01:00
parent e493248ea5
commit f619fb683b
127 changed files with 859 additions and 443 deletions
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28
R/mo_property.R
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@ -11,9 +11,9 @@
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
@ -676,9 +676,9 @@ mo_synonyms <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio
metadata <- get_mo_uncertainties()
syns <- lapply(x.mo, function(y) {
gbif <- AMR::microorganisms$gbif[match(y, AMR::microorganisms$mo)]
lpsn <- AMR::microorganisms$lpsn[match(y, AMR::microorganisms$mo)]
out <- AMR::microorganisms[which(AMR::microorganisms$lpsn_renamed_to == lpsn | AMR::microorganisms$gbif_renamed_to == gbif), "fullname", drop = TRUE]
gbif <- AMR_env$MO_lookup$gbif[match(y, AMR_env$MO_lookup$mo)]
lpsn <- AMR_env$MO_lookup$lpsn[match(y, AMR_env$MO_lookup$mo)]
out <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$lpsn_renamed_to == lpsn | AMR_env$MO_lookup$gbif_renamed_to == gbif), "fullname", drop = TRUE]
if (length(out) == 0) {
NULL
} else {
@ -760,10 +760,10 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms =
x.mo <- as.mo(x = x, language = language, keep_synonyms = keep_synonyms, ... = ...)
metadata <- get_mo_uncertainties()
x.rank <- AMR::microorganisms$rank[match(x.mo, AMR::microorganisms$mo)]
x.name <- AMR::microorganisms$fullname[match(x.mo, AMR::microorganisms$mo)]
x.lpsn <- AMR::microorganisms$lpsn[match(x.mo, AMR::microorganisms$mo)]
x.gbif <- AMR::microorganisms$gbif[match(x.mo, AMR::microorganisms$mo)]
x.rank <- AMR_env$MO_lookup$rank[match(x.mo, AMR_env$MO_lookup$mo)]
x.name <- AMR_env$MO_lookup$fullname[match(x.mo, AMR_env$MO_lookup$mo)]
x.lpsn <- AMR_env$MO_lookup$lpsn[match(x.mo, AMR_env$MO_lookup$mo)]
x.gbif <- AMR_env$MO_lookup$gbif[match(x.mo, AMR_env$MO_lookup$mo)]
u <- character(length(x))
u[!is.na(x.gbif)] <- paste0(TAXONOMY_VERSION$GBIF$url, "/species/", x.gbif[!is.na(x.gbif)])
@ -792,7 +792,7 @@ mo_property <- function(x, property = "fullname", language = get_AMR_locale(), k
x <- find_mo_col(fn = "mo_property")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(AMR::microorganisms))
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(AMR_env$MO_lookup))
language <- validate_language(language)
meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
@ -803,7 +803,7 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ..
# try to catch an error when inputting an invalid argument
# so the 'call.' can be set to FALSE
tryCatch(x[1L] %in% unlist(AMR::microorganisms[1, property, drop = TRUE]),
tryCatch(x[1L] %in% unlist(AMR_env$MO_lookup[1, property, drop = TRUE]),
error = function(e) stop(e$message, call. = FALSE)
)
@ -819,7 +819,7 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ..
has_Becker_or_Lancefield <- Becker %in% c(TRUE, "all") || Lancefield %in% c(TRUE, "all")
# get microorganisms data set, but remove synonyms if keep_synonyms is FALSE
mo_data_check <- AMR::microorganisms[which(AMR::microorganisms$status %in% if (isTRUE(keep_synonyms)) c("synonym", "accepted") else "accepted"), , drop = FALSE]
mo_data_check <- AMR_env$MO_lookup[which(AMR_env$MO_lookup$status %in% if (isTRUE(keep_synonyms)) c("synonym", "accepted") else "accepted"), , drop = FALSE]
if (all(x %in% c(mo_data_check$mo, NA)) && !has_Becker_or_Lancefield) {
# do nothing, just don't run the other if-else's
@ -833,7 +833,7 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ..
}
# get property reeaaally fast using match()
x <- AMR::microorganisms[[property]][match(x, AMR::microorganisms$mo)]
x <- AMR_env$MO_lookup[[property]][match(x, AMR_env$MO_lookup$mo)]
if (property == "mo") {
return(set_clean_class(x, new_class = c("mo", "character")))