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(v1.3.0.9035) mdro() for EUCAST 3.2, examples cleanup

This commit is contained in:
2020-09-29 23:35:46 +02:00
parent 68e6e1e329
commit 4e0374af29
94 changed files with 1143 additions and 1165 deletions

51
R/zzz.R
View File

@ -35,9 +35,18 @@
assign(x = "LANGUAGES_SUPPORTED",
value = sort(c("en", unique(translations_file$lang))),
envir = asNamespace("AMR"))
assign(x = "MO_CONS",
value = create_species_cons_cops("CoNS"),
envir = asNamespace("AMR"))
assign(x = "MO_COPS",
value = create_species_cons_cops("CoPS"),
envir = asNamespace("AMR"))
# support for tibble headers (type_sum) and tibble columns content (pillar_shaft) without the need to depend on other packages
# this was suggested by the developers of the vctrs package:
# Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
# without the need to depend on other packages. This was suggested by the
# developers of the vctrs package:
# https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
s3_register("pillar::pillar_shaft", "ab")
s3_register("tibble::type_sum", "ab")
@ -49,10 +58,10 @@
s3_register("tibble::type_sum", "mic")
s3_register("pillar::pillar_shaft", "disk")
s3_register("tibble::type_sum", "disk")
# support for frequency tables from the cleaner package
# Support for frequency tables from the cleaner package
s3_register("cleaner::freq", "mo")
s3_register("cleaner::freq", "rsi")
# support from skim from the skimr package
# Support from skim() from the skimr package
s3_register("skimr::get_skimmers", "mo")
s3_register("skimr::get_skimmers", "rsi")
s3_register("skimr::get_skimmers", "mic")
@ -60,6 +69,7 @@
}
.onAttach <- function(...) {
# show notice in 10% of cases in interactive session
if (!interactive() || stats::runif(1) > 0.1 || isTRUE(as.logical(getOption("AMR_silentstart", FALSE)))) {
return()
}
@ -69,6 +79,39 @@
"\n[ prevent his notice with suppressPackageStartupMessages(library(AMR)) or use options(AMR_silentstart = TRUE) ]")
}
create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
# Determination of which staphylococcal species are CoNS/CoPS according to Becker et al.:
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/figure/F3/
# returns class <mo>
MO_staph <- AMR::microorganisms
MO_staph <- MO_staph[which(MO_staph$genus == "Staphylococcus"), , drop = FALSE]
if (type == "CoNS") {
MO_staph[which(MO_staph$species %in% c("coagulase-negative",
"arlettae", "auricularis", "capitis",
"caprae", "carnosus", "chromogenes", "cohnii", "condimenti",
"devriesei", "epidermidis", "equorum", "felis",
"fleurettii", "gallinarum", "haemolyticus",
"hominis", "jettensis", "kloosii", "lentus",
"lugdunensis", "massiliensis", "microti",
"muscae", "nepalensis", "pasteuri", "petrasii",
"pettenkoferi", "piscifermentans", "rostri",
"saccharolyticus", "saprophyticus", "sciuri",
"stepanovicii", "simulans", "succinus",
"vitulinus", "warneri", "xylosus")
| (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
"mo", drop = TRUE]
} else if (type == "CoPS") {
MO_staph[which(MO_staph$species %in% c("coagulase-positive",
"simiae", "agnetis",
"delphini", "lutrae",
"hyicus", "intermedius",
"pseudintermedius", "pseudointermedius",
"schweitzeri", "argenteus")
| (MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
"mo", drop = TRUE]
}
}
create_AB_lookup <- function() {
AB_lookup <- AMR::antibiotics
AB_lookup$generalised_name <- generalise_antibiotic_name(AB_lookup$name)