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speed improvement as.mo, freq title

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dr. M.S. (Matthijs) Berends
2018-10-31 12:10:49 +01:00
parent 3d4c4c678b
commit 9cd4ab928a
27 changed files with 289 additions and 224 deletions
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32
R/zzz.R
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@ -50,21 +50,25 @@ NULL
.onAttach <- function(libname, pkgname) {
# save data.tables to improve speed of as.mo:
MOs <- data.table::as.data.table(AMR::microorganisms)
data.table::setkey(MOs, prevalence, tsn)
base::assign(x = "MOs",
value = MOs,
envir = base::as.environment("package:AMR"))
base::assign(x = "MOs_mostprevalent",
value = MOs[prevalence != 9999,],
envir = base::as.environment("package:AMR"))
base::assign(x = "MOs_allothers",
value = MOs[prevalence == 9999,],
envir = base::as.environment("package:AMR"))
# microorganismsDT <- data.table::as.data.table(AMR::microorganisms)
# microorganisms.oldDT <- data.table::as.data.table(AMR::microorganisms.old)
#
# data.table::setkey(microorganismsDT, prevalence, tsn)
# data.table::setkey(microorganisms.oldDT, tsn, name)
base::assign(x = "MOs_old",
value = data.table::as.data.table(AMR::microorganisms.old),
envir = base::as.environment("package:AMR"))
base::assign(x = "microorganismsDT",
value = microorganismsDT,
envir = base::as.environment("package:AMR"))
base::assign(x = "microorganisms.prevDT",
value = microorganismsDT[prevalence != 9999,],
envir = base::as.environment("package:AMR"))
base::assign(x = "microorganisms.unprevDT",
value = microorganismsDT[prevalence == 9999,],
envir = base::as.environment("package:AMR"))
base::assign(x = "microorganisms.oldDT",
value = microorganisms.oldDT,
envir = base::as.environment("package:AMR"))
}