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new tibble export

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-08-27 20:49:37 +02:00
parent 164886f50b
commit 303d61b473
115 changed files with 836 additions and 996 deletions
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10
R/zzz.R
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@ -101,9 +101,13 @@ if (utf8_supported && !is_latex) {
}
}, silent = TRUE)
# be sure to print tibbles as tibbles
if (pkg_is_available("tibble", also_load = FALSE)) {
loadNamespace("tibble")
}
# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
# they cannott be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
# they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
assign(x = "AB_lookup", value = create_AB_lookup(), envir = asNamespace("AMR"))
assign(x = "MO_lookup", value = create_MO_lookup(), envir = asNamespace("AMR"))
assign(x = "MO.old_lookup", value = create_MO.old_lookup(), envir = asNamespace("AMR"))
@ -140,7 +144,7 @@ create_MO_lookup <- function() {
MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)
# so arrange data on prevalence first, then kingdom, then full name
MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), ]
MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), , drop = FALSE]
}
create_MO.old_lookup <- function() {
@ -151,7 +155,7 @@ create_MO.old_lookup <- function() {
MO.old_lookup$g_species <- trimws(gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower))
# so arrange data on prevalence first, then full name
MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), ]
MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), , drop = FALSE]
}
create_intr_resistance <- function() {