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(v0.9.0.9005) as.mo for G. species

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dr. M.S. (Matthijs) Berends
2019-12-21 10:56:06 +01:00
parent cc8cd043e1
commit ba3ce77f02
21 changed files with 501 additions and 361 deletions
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34
R/zzz.R
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@ -21,21 +21,18 @@
#' @importFrom data.table as.data.table setkey
.onLoad <- function(libname, pkgname) {
# packageStartupMessage("Loading taxonomic reference data")
# get new functions not available in older versions of R
backports::import(pkgname)
# register data
microorganisms.oldDT <- as.data.table(AMR::microorganisms.old)
# for fullname_lower: keep only dots, letters, numbers, slashes, spaces and dashes
microorganisms.oldDT$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", tolower(microorganisms.oldDT$fullname))
setkey(microorganisms.oldDT, prevalence, fullname)
assign(x = "microorganismsDT",
value = make_DT(),
envir = asNamespace("AMR"))
assign(x = "microorganisms.oldDT",
value = microorganisms.oldDT,
value = make_oldDT(),
envir = asNamespace("AMR"))
assign(x = "mo_codes_v0.5.0",
@ -62,7 +59,9 @@ make_DT <- function() {
# work with Viridans Group Streptococci, etc.
tolower(trimws(ifelse(genus == "",
fullname,
paste(genus, species, subspecies)))))) %>%
paste(genus, species, subspecies))))),
# add a column with only "e coli" like combinations
g_species = gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", fullname_lower)) %>%
as.data.table()
# so arrange data on prevalence first, then kingdom, then full name
@ -73,6 +72,25 @@ make_DT <- function() {
microorganismsDT
}
#' @importFrom data.table as.data.table setkey
#' @importFrom dplyr %>% mutate
make_oldDT <- function() {
microorganisms.oldDT <- AMR::microorganisms.old %>%
mutate(
# for fullname_lower: keep only dots, letters,
# numbers, slashes, spaces and dashes
fullname_lower = gsub("[^.a-z0-9/ \\-]+", "", tolower(fullname)),
# add a column with only "e coli" like combinations
g_species = gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", fullname_lower)) %>%
as.data.table()
# so arrange data on prevalence first, then full name
setkey(microorganisms.oldDT,
prevalence,
fullname)
microorganisms.oldDT
}
make_trans_tbl <- function() {
# conversion of old MO codes from v0.5.0 (ITIS) to later versions (Catalogue of Life)
c(B_ACHRMB = "B_ACHRM", B_ANNMA = "B_ACTNS", B_ACLLS = "B_ALCYC",