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(v2.1.1.9042) update translations and example isolates

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dr. M.S. (Matthijs) Berends
2024-06-09 11:31:04 +02:00
parent af74e1d4f2
commit a3071cf58b
8 changed files with 42 additions and 23 deletions
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14
R/sir.R
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@ -327,9 +327,15 @@ is_sir_eligible <- function(x, threshold = 0.05) {
#' @rdname as.sir
#' @export
#' @param S,I,R,N,SDD a case-independent [regular expression][base::regex] to translate input to this result. This regular expression will be run *after* all non-letters are removed from the input.
#' @param S,I,R,N,SDD a case-independent [regular expression][base::regex] to translate input to this result. This regular expression will be run *after* all non-letters and whitespaces are removed from the input.
# extra param: warn (logical, to never throw a warning)
as.sir.default <- function(x, S = "^(S|U)+$", I = "^(I|H)+$", R = "^(R)+$", N = "^(N|V)+$", SDD = "^(SDD|D)+$", ...) {
as.sir.default <- function(x,
S = "^(S|U)+$",
I = "^(I)+$",
R = "^(R)+$",
N = "^(N|V)+$",
SDD = "^(SDD|D|H)+$",
...) {
if (inherits(x, "sir")) {
return(as_sir_structure(x))
}
@ -349,7 +355,7 @@ as.sir.default <- function(x, S = "^(S|U)+$", I = "^(I|H)+$", R = "^(R)+$", N =
x[x.bak == 2] <- "I"
x[x.bak == 3] <- "R"
}
} else if (inherits(x.bak, "character") && all(x %in% c("1", "2", "3", c("S", "SDD", "I", "R", "N"), NA_character_))) {
} else if (inherits(x.bak, "character") && all(x %in% c("1", "2", "3", "S", "SDD", "I", "R", "N", NA_character_))) {
x[x.bak == "1"] <- "S"
x[x.bak == "2"] <- "I"
x[x.bak == "3"] <- "R"
@ -389,7 +395,9 @@ as.sir.default <- function(x, S = "^(S|U)+$", I = "^(I|H)+$", R = "^(R)+$", N =
# replace all English textual input
x[x %like% "([^a-z]|^)res(is(tant)?)?"] <- "R"
x[x %like% "([^a-z]|^)sus(cep(tible)?)?"] <- "S"
x[x %like% "not|non"] <- "N"
x[x %like% "([^a-z]|^)int(er(mediate)?)?|incr.*exp"] <- "I"
x[x %like% "dose"] <- "SDD"
x <- gsub("[^A-Z]+", "", x, perl = TRUE)
# apply regexes set by user
x[x %like% S] <- "S"