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(v1.1.0.9004) lose dependencies

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dr. M.S. (Matthijs) Berends
2020-05-16 13:05:47 +02:00
parent 9fce546901
commit 7f3da74b17
111 changed files with 3211 additions and 2345 deletions
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81
R/zzz.R
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@ -19,18 +19,16 @@
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' @importFrom data.table as.data.table setkey
.onLoad <- function(libname, pkgname) {
# get new functions not available in older versions of R
backports::import(pkgname)
# register data
assign(x = "microorganismsDT",
value = make_DT(),
assign(x = "MO_lookup",
value = create_MO_lookup(),
envir = asNamespace("AMR"))
assign(x = "microorganisms.oldDT",
value = make_oldDT(),
assign(x = "MO.old_lookup",
value = create_MO.old_lookup(),
envir = asNamespace("AMR"))
assign(x = "mo_codes_v0.5.0",
@ -41,52 +39,43 @@
# maybe add survey later: "https://www.surveymonkey.com/r/AMR_for_R"
#' @importFrom data.table as.data.table setkey
#' @importFrom dplyr %>% mutate case_when
make_DT <- function() {
microorganismsDT <- AMR::microorganisms %>%
mutate(kingdom_index = case_when(kingdom == "Bacteria" ~ 1,
kingdom == "Fungi" ~ 2,
kingdom == "Protozoa" ~ 3,
kingdom == "Archaea" ~ 4,
TRUE ~ 99),
# for fullname_lower: keep only dots, letters,
# numbers, slashes, spaces and dashes
fullname_lower = gsub("[^.a-z0-9/ \\-]+", "",
# use this paste instead of `fullname` to
# work with Viridans Group Streptococci, etc.
tolower(trimws(ifelse(genus == "",
fullname,
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()
create_MO_lookup <- function() {
MO_lookup <- AMR::microorganisms
MO_lookup$kingdom_index <- 99
MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2
MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3
MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
# use this paste instead of `fullname` to
# work with Viridans Group Streptococci, etc.
MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus,
MO_lookup$species,
MO_lookup$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)
# 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
setkey(microorganismsDT,
prevalence,
kingdom_index,
fullname_lower)
microorganismsDT
MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower),]
}
#' @importFrom data.table as.data.table setkey
#' @importFrom dplyr %>% mutate
make_oldDT <- function() {
microorganisms.oldDT <- AMR::microorganisms.old %>%
mutate(
# for fullname_lower: keep only dots, letters,
# numbers, slashes, spaces and dashes
fullname_lower = gsub("[^.a-z0-9/ \\-]+", "", tolower(fullname)),
# add a column with only "e coli" like combinations
g_species = gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", fullname_lower)) %>%
as.data.table()
create_MO.old_lookup <- function() {
MO.old_lookup <- AMR::microorganisms.old
# use this paste instead of `fullname` to
# work with Viridans Group Streptococci, etc.
MO.old_lookup$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname)))
# add a column with only "e coli" like combinations
MO.old_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower)
# so arrange data on prevalence first, then full name
setkey(microorganisms.oldDT,
prevalence,
fullname)
microorganisms.oldDT
MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower),]
}
make_trans_tbl <- function() {