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(v1.1.0.9004) lose dependencies
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81
R/zzz.R
81
R/zzz.R
@ -19,18 +19,16 @@
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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#' @importFrom data.table as.data.table setkey
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.onLoad <- function(libname, pkgname) {
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# get new functions not available in older versions of R
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backports::import(pkgname)
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# register data
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assign(x = "microorganismsDT",
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value = make_DT(),
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assign(x = "MO_lookup",
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value = create_MO_lookup(),
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envir = asNamespace("AMR"))
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assign(x = "microorganisms.oldDT",
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value = make_oldDT(),
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assign(x = "MO.old_lookup",
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value = create_MO.old_lookup(),
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envir = asNamespace("AMR"))
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assign(x = "mo_codes_v0.5.0",
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@ -41,52 +39,43 @@
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# maybe add survey later: "https://www.surveymonkey.com/r/AMR_for_R"
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#' @importFrom data.table as.data.table setkey
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#' @importFrom dplyr %>% mutate case_when
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make_DT <- function() {
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microorganismsDT <- AMR::microorganisms %>%
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mutate(kingdom_index = case_when(kingdom == "Bacteria" ~ 1,
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kingdom == "Fungi" ~ 2,
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kingdom == "Protozoa" ~ 3,
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kingdom == "Archaea" ~ 4,
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TRUE ~ 99),
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# for fullname_lower: keep only dots, letters,
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# numbers, slashes, spaces and dashes
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fullname_lower = gsub("[^.a-z0-9/ \\-]+", "",
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# use this paste instead of `fullname` to
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# work with Viridans Group Streptococci, etc.
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tolower(trimws(ifelse(genus == "",
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fullname,
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paste(genus, species, subspecies))))),
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# add a column with only "e coli" like combinations
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g_species = gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", fullname_lower)) %>%
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as.data.table()
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create_MO_lookup <- function() {
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MO_lookup <- AMR::microorganisms
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MO_lookup$kingdom_index <- 99
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MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
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MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2
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MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3
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MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
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# use this paste instead of `fullname` to
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# work with Viridans Group Streptococci, etc.
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MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus,
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MO_lookup$species,
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MO_lookup$subspecies)))
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MO_lookup[MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname), "fullname_lower"] <- tolower(trimws(MO_lookup[MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname),
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"fullname"]))
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MO_lookup$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "",MO_lookup$fullname_lower)
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# add a column with only "e coli" like combinations
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MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower)
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# so arrange data on prevalence first, then kingdom, then full name
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setkey(microorganismsDT,
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prevalence,
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kingdom_index,
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fullname_lower)
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microorganismsDT
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MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower),]
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}
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#' @importFrom data.table as.data.table setkey
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#' @importFrom dplyr %>% mutate
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make_oldDT <- function() {
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microorganisms.oldDT <- AMR::microorganisms.old %>%
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mutate(
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# for fullname_lower: keep only dots, letters,
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# numbers, slashes, spaces and dashes
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fullname_lower = gsub("[^.a-z0-9/ \\-]+", "", tolower(fullname)),
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# add a column with only "e coli" like combinations
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g_species = gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", fullname_lower)) %>%
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as.data.table()
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create_MO.old_lookup <- function() {
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MO.old_lookup <- AMR::microorganisms.old
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# use this paste instead of `fullname` to
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# work with Viridans Group Streptococci, etc.
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MO.old_lookup$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname)))
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# add a column with only "e coli" like combinations
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MO.old_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower)
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# so arrange data on prevalence first, then full name
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setkey(microorganisms.oldDT,
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prevalence,
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fullname)
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microorganisms.oldDT
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MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower),]
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}
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make_trans_tbl <- function() {
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