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uncertainty levels, new WHONET codes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-03-12 12:19:27 +01:00
parent b319b89750
commit 504a042fba
22 changed files with 402 additions and 292 deletions
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35
R/zzz.R
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@ -25,28 +25,25 @@
backports::import(pkgname)
# register data
if (!all(c("microorganismsDT", "microorganisms.oldDT") %in% ls(envir = asNamespace("AMR")))) {
microorganisms.oldDT <- as.data.table(AMR::microorganisms.old)
microorganisms.oldDT$fullname_lower <- tolower(microorganisms.oldDT$fullname)
setkey(microorganisms.oldDT, col_id, fullname)
microorganisms.oldDT <- as.data.table(AMR::microorganisms.old)
microorganisms.oldDT$fullname_lower <- tolower(microorganisms.oldDT$fullname)
setkey(microorganisms.oldDT, col_id, fullname)
assign(x = "microorganisms",
value = make(),
envir = asNamespace("AMR"))
assign(x = "microorganisms",
value = make(),
envir = asNamespace("AMR"))
assign(x = "microorganismsDT",
value = make_DT(),
envir = asNamespace("AMR"))
assign(x = "microorganismsDT",
value = make_DT(),
envir = asNamespace("AMR"))
assign(x = "microorganisms.oldDT",
value = microorganisms.oldDT,
envir = asNamespace("AMR"))
assign(x = "microorganisms.oldDT",
value = microorganisms.oldDT,
envir = asNamespace("AMR"))
assign(x = "mo_codes_v0.5.0",
value = make_trans_tbl(),
envir = asNamespace("AMR"))
}
assign(x = "mo_codes_v0.5.0",
value = make_trans_tbl(),
envir = asNamespace("AMR"))
}
#' @importFrom dplyr mutate case_when
@ -88,8 +85,8 @@ make_DT <- function() {
microorganismsDT <- as.data.table(make())
microorganismsDT$fullname_lower <- tolower(microorganismsDT$fullname)
setkey(microorganismsDT,
kingdom,
prevalence,
kingdom,
fullname)
microorganismsDT
}