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(v1.8.0.9010) as.mo improvement

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dr. M.S. (Matthijs) Berends
2022-03-15 17:35:02 +01:00
parent 0fb9a1b194
commit 7b0f1596bd
13 changed files with 76 additions and 41 deletions
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29
R/mo.R
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@ -1003,6 +1003,35 @@ exec_as.mo <- function(x,
}
}
# try splitting of characters in the middle and then find ID based on old names ----
# only when text length is 6 or lower
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus
if (nchar(g.x_backup_without_spp) <= 6) {
x_length <- nchar(g.x_backup_without_spp)
x_split <- paste0("^",
g.x_backup_without_spp %pm>% substr(1, x_length / 2),
".* ",
g.x_backup_without_spp %pm>% substr((x_length / 2) + 1, x_length))
found <- lookup(fullname_lower %like_case% x_split,
haystack = MO.old_lookup,
column = NULL)
if (!all(is.na(found))) {
# it's an old name, so return it
if (property == "ref") {
x[i] <- found["ref"]
} else {
x[i] <- lookup(fullname == found["fullname_new"], haystack = MO_lookup)
}
pkg_env$mo_renamed_last_run <- found["fullname"]
was_renamed(name_old = found["fullname"],
name_new = lookup(fullname == found["fullname_new"], "fullname", haystack = MO_lookup),
ref_old = found["ref"],
ref_new = lookup(fullname == found["fullname_new"], "ref", haystack = MO_lookup),
mo = lookup(fullname == found["fullname_new"], "mo", haystack = MO_lookup))
return(x[i])
}
}
# try fullname without start and without nchar limit of >= 6 ----
# like "K. pneu rhino" >> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
found <- lookup(fullname_lower %like_case% e.x_withspaces_start_only,