P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-09-06 02:09:37 +02:00
Code Releases Activity

(v1.3.0.9010) S3 extensions without dependencies

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-08-28 21:55:47 +02:00
parent 81af0b001c
commit 74a172ef55
49 changed files with 227 additions and 156 deletions
Download Patch File Download Diff File Expand all files Collapse all files

61
R/zzz.R
View File

@@ -29,6 +29,7 @@
envir = asNamespace("AMR"))
# support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
# without the need to depend on other packages
s3_register("pillar::pillar_shaft", "ab")
s3_register("tibble::type_sum", "ab")
s3_register("pillar::pillar_shaft", "mo")
@@ -39,9 +40,10 @@
s3_register("tibble::type_sum", "mic")
s3_register("pillar::pillar_shaft", "disk")
s3_register("tibble::type_sum", "disk")
# support for frequency tables
s3_register("cleaner::freq", "mo")
s3_register("cleaner::freq", "rsi")
}
pillar_shaft <- import_fn("pillar_shaft", "pillar", error_on_fail = FALSE)
type_sum <- import_fn("type_sum", "tibble", error_on_fail = FALSE)
.onAttach <- function(...) {
if (!interactive() || stats::runif(1) > 0.1 || isTRUE(as.logical(Sys.getenv("AMR_silentstart", FALSE)))) {
@@ -66,9 +68,9 @@ create_MO_lookup <- function() {
MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus,
MO_lookup$species,
MO_lookup$subspecies)))
MO_lookup[MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname), "fullname_lower"] <- tolower(trimws(MO_lookup[MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname),
"fullname"]))
MO_lookup$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower)
ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname)
MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower))
# add a column with only "e coli" like combinations
MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower)
@@ -79,54 +81,11 @@ create_MO_lookup <- function() {
create_MO.old_lookup <- function() {
MO.old_lookup <- AMR::microorganisms.old
MO.old_lookup$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname)))
MO.old_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname))))
# add a column with only "e coli" like combinations
MO.old_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower)
# add a column with only "e coli"-like combinations
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), ]
}
# copied from vctrs::s3_register
s3_register <- function(generic, class, method = NULL) {
stopifnot(is.character(generic), length(generic) == 1)
stopifnot(is.character(class), length(class) == 1)
pieces <- strsplit(generic, "::")[[1]]
stopifnot(length(pieces) == 2)
package <- pieces[[1]]
generic <- pieces[[2]]
caller <- parent.frame()
get_method_env <- function() {
top <- topenv(caller)
if (isNamespace(top)) {
asNamespace(environmentName(top))
}
else {
caller
}
}
get_method <- function(method, env) {
if (is.null(method)) {
get(paste0(generic, ".", class), envir = get_method_env())
}
else {
method
}
}
method_fn <- get_method(method)
stopifnot(is.function(method_fn))
setHook(packageEvent(package, "onLoad"), function(...) {
ns <- asNamespace(package)
method_fn <- get_method(method)
registerS3method(generic, class, method_fn, envir = ns)
})
if (!isNamespaceLoaded(package)) {
return(invisible())
}
envir <- asNamespace(package)
if (exists(generic, envir)) {
registerS3method(generic, class, method_fn, envir = envir)
}
invisible()
}