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(v1.1.0.9011) lose dependencies

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dr. M.S. (Matthijs) Berends
2020-05-18 13:59:34 +02:00
parent d659c9baef
commit 218fd08097
18 changed files with 110 additions and 65 deletions
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10
R/zzz.R
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@ -20,9 +20,6 @@
# ==================================================================== #
.onLoad <- function(libname, pkgname) {
# get new functions not available in older versions of R
backports::import(pkgname)
assign(x = "MO_lookup",
value = create_MO_lookup(),
envir = asNamespace("AMR"))
@ -34,7 +31,6 @@
assign(x = "mo_codes_v0.5.0",
value = make_trans_tbl(),
envir = asNamespace("AMR"))
}
# maybe add survey later: "https://www.surveymonkey.com/r/AMR_for_R"
@ -55,13 +51,13 @@ create_MO_lookup <- function() {
MO_lookup$subspecies)))
MO_lookup[MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname), "fullname_lower"] <- tolower(trimws(MO_lookup[MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname),
"fullname"]))
MO_lookup$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "",MO_lookup$fullname_lower)
MO_lookup$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower)
# add a column with only "e coli" like combinations
MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower)
# so arrange data on prevalence first, then kingdom, then full name
MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower),]
MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), ]
}
create_MO.old_lookup <- function() {
@ -75,7 +71,7 @@ create_MO.old_lookup <- function() {
MO.old_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower)
# so arrange data on prevalence first, then full name
MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower),]
MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), ]
}
make_trans_tbl <- function() {