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(v2.1.1.9048) vctrs update for sir

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dr. M.S. (Matthijs) Berends
2024-06-13 20:55:17 +02:00
parent 3179216c81
commit de17de1be9
19 changed files with 35 additions and 16 deletions
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3
R/aa_globals.R
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@ -161,6 +161,7 @@ globalVariables(c(
"microorganisms",
"microorganisms.codes",
"mo",
"n",
"name",
"new",
"numerator",
@ -186,8 +187,10 @@ globalVariables(c(
"total",
"txt",
"type",
"uti_index",
"value",
"varname",
"x",
"xvar",
"y",
"year",

18
R/sir.R
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@ -362,10 +362,16 @@ as.sir.default <- function(x,
x[x.bak == 2] <- "I"
x[x.bak == 3] <- "R"
}
} else if (inherits(x.bak, "character") && all(x %in% c("1", "2", "3", "S", "SDD", "I", "R", "N", NA_character_))) {
} else if (inherits(x.bak, "character") && all(x %in% c("1", "2", "3", "S", "I", "R", NA_character_))) {
x[x.bak == "1"] <- "S"
x[x.bak == "2"] <- "I"
x[x.bak == "3"] <- "R"
} else if (inherits(x.bak, "character") && all(x %in% c("1", "2", "3", "4", "5", "S", "SDD", "I", "R", "N", NA_character_))) {
x[x.bak == "1"] <- "S"
x[x.bak == "2"] <- "SDD"
x[x.bak == "3"] <- "I"
x[x.bak == "4"] <- "R"
x[x.bak == "5"] <- "N"
} else if (!all(is.na(x)) && !identical(levels(x), c("S", "SDD", "I", "R", "N")) && !all(x %in% c("S", "SDD", "I", "R", "N", NA))) {
if (all(x %unlike% "(S|I|R)", na.rm = TRUE)) {
# check if they are actually MICs or disks
@ -1133,7 +1139,7 @@ as_sir_method <- function(method_short,
if (all(uti_current == FALSE, na.rm = TRUE)) {
breakpoints_current <- breakpoints_current %pm>%
# this will put UTI = FALSE first, then UTI = NA, then UTI = TRUE
pm_mutate(uti_index = ifelse(uti == FALSE, 1,
pm_mutate(uti_index = ifelse(is.na(uti) & uti == FALSE, 1,
ifelse(is.na(uti), 2,
3))) %pm>%
# be as specific as possible (i.e. prefer species over genus):
@ -1170,22 +1176,22 @@ as_sir_method <- function(method_short,
} else {
site <- paste0("body site '", site, "'")
}
if (nrow(breakpoints_current) == 1 && all(breakpoints_current$uti == TRUE) && any(uti_current %in% c(FALSE, NA)) && message_not_thrown_before("as.sir", "uti", ab_coerced)) {
if (nrow(breakpoints_current) == 1 && all(breakpoints_current$uti == TRUE) && any(uti_current %in% c(FALSE, NA)) && message_not_thrown_before("as.sir", "uti", ab_current)) {
# only UTI breakpoints available
warning_("in `as.sir()`: interpretation of ", font_bold(ab_formatted), " is only available for (uncomplicated) urinary tract infections (UTI) for some microorganisms, thus assuming `uti = TRUE`. See `?as.sir`.")
rise_warning <- TRUE
} else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && any(is.na(uti_current)) && all(c(TRUE, FALSE) %in% breakpoints_current$uti, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteUTI", mo_current, ab_coerced)) {
} else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && any(is.na(uti_current)) && all(c(TRUE, FALSE) %in% breakpoints_current$uti, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteUTI", mo_current, ab_current)) {
# both UTI and Non-UTI breakpoints available
msgs <- c(msgs, paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See `?as.sir`."))
breakpoints_current <- breakpoints_current %pm>%
pm_filter(uti == FALSE)
} else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_coerced)) {
} else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_current)) {
# breakpoints for multiple body sites available
msgs <- c(msgs, paste0("Multiple breakpoints available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, "."))
}
# first check if mo is intrinsic resistant
if (isTRUE(add_intrinsic_resistance) && guideline_coerced %like% "EUCAST" && paste(mo_current, ab_coerced) %in% AMR_env$intrinsic_resistant) {
if (isTRUE(add_intrinsic_resistance) && guideline_coerced %like% "EUCAST" && paste(mo_current, ab_current) %in% AMR_env$intrinsic_resistant) {
msgs <- c(msgs, paste0("Intrinsic resistance applied for ", ab_formatted, " in ", mo_formatted, ""))
new_sir <- rep(as.sir("R"), length(rows))
} else if (nrow(breakpoints_current) == 0) {

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R/sysdata.rda
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7
R/vctrs.R
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@ -179,10 +179,13 @@ vec_arith.mic <- function(op, x, y, ...) {
# S3: sir ----
vec_ptype2.sir.default <- function (x, y, ..., x_arg = "", y_arg = "") {
x
NA_sir_[0]
}
vec_ptype2.sir.sir <- function(x, y, ...) {
x
NA_sir_[0]
}
vec_ptype2.character.sir <- function(x, y, ...) {
NA_sir_[0]
}
vec_cast.character.sir <- function(x, to, ...) {
as.character(x)

1
R/zzz.R
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@ -176,6 +176,7 @@ AMR_env$sup_1_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$sup_1 %o
# S3: sir
s3_register("vctrs::vec_ptype2", "sir.default")
s3_register("vctrs::vec_ptype2", "sir.sir")
s3_register("vctrs::vec_ptype2", "character.sir")
s3_register("vctrs::vec_cast", "character.sir")
s3_register("vctrs::vec_cast", "sir.character")