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as.mo improvement

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dr. M.S. (Matthijs) Berends
2019-02-23 21:49:02 +01:00
parent f16a152d06
commit e65d1a3036
10 changed files with 321 additions and 352 deletions
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6
R/mo.R
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@ -219,7 +219,6 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
# conversion of old MO codes from v0.5.0 (ITIS) to later versions (Catalogue of Life)
if (any(x %like% "^[BFP]_[A-Z]{3,7}")) {
print("is any")
leftpart <- gsub("^([BFP]_[A-Z]{3,7}).*", "\\1", x)
if (any(leftpart %in% names(mo_codes_v0.5.0))) {
rightpart <- gsub("^[BFP]_[A-Z]{3,7}(.*)", "\\1", x)
@ -267,9 +266,12 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
x <- microorganismsDT[data.table(mo = x), on = "mo", ..property][[1]]
} else if (all(x %in% microorganismsDT[prevalence == 1, "fullname"][[1]])) {
# we need special treatment for prevalent full names, they are likely!
# we need special treatment for very prevalent full names, they are likely!
# e.g. as.mo("Staphylococcus aureus")
x <- microorganismsDT[prevalence == 1][data.table(fullname = x), on = "fullname", ..property][[1]]
} else if (all(x %in% microorganismsDT[prevalence == 2, "fullname"][[1]])) {
# same for common full names, they are also likely
x <- microorganismsDT[prevalence == 2][data.table(fullname = x), on = "fullname", ..property][[1]]
} else if (all(toupper(x) %in% microorganisms.codes[, "code"])) {
# commonly used MO codes