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keyab fixes

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dr. M.S. (Matthijs) Berends
2018-07-17 19:51:09 +02:00
parent 2a4d759fbc
commit 0d64c166f0
5 changed files with 42 additions and 39 deletions
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46
R/key_antibiotics.R
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@ -136,7 +136,8 @@ key_antibiotics <- function(tbl,
# format
key_abs <- tbl %>%
pull(key_ab) %>%
gsub('(NA|NULL)', '-', .)
gsub('(NA|NULL)', '.', .) %>%
gsub('[^SIR]', '.', ., ignore.case = TRUE)
key_abs
@ -162,22 +163,24 @@ key_antibiotics_equal <- function(x,
if (type == "keyantibiotics") {
if (ignore_I == TRUE) {
# evaluation using regular expression will treat '?' as any character
# evaluation using regular expression will treat '.' as any character
# so I is actually ignored then
x <- gsub('I', '?', x, ignore.case = TRUE)
y <- gsub('I', '?', y, ignore.case = TRUE)
x <- gsub('I', '.', x, ignore.case = TRUE)
y <- gsub('I', '.', y, ignore.case = TRUE)
}
for (i in 1:length(x)) {
result[i] <- grepl(x = x[i],
pattern = y[i],
ignore.case = TRUE) |
grepl(x = y[i],
pattern = x[i],
ignore.case = TRUE)
result[i] <- nchar(x[i]) == nchar(y[i]) &
(x[i] %like% paste0("^", y[i], "$") |
y[i] %like% paste0("^", x[i], "$"))
}
return(result)
} else {
if (type != 'points') {
stop('`', type, '` is not a valid value for type, must be "points" or "keyantibiotics". See ?first_isolate.')
}
if (info == TRUE) {
p <- dplyr::progress_estimated(length(x))
}
@ -208,22 +211,17 @@ key_antibiotics_equal <- function(x,
x2 <- strsplit(x[i], "")[[1]]
y2 <- strsplit(y[i], "")[[1]]
if (type == 'points') {
# count points for every single character:
# - no change is 0 points
# - I <-> S|R is 0.5 point
# - S|R <-> R|S is 1 point
# use the levels of as.rsi (S = 1, I = 2, R = 3)
# count points for every single character:
# - no change is 0 points
# - I <-> S|R is 0.5 point
# - S|R <-> R|S is 1 point
# use the levels of as.rsi (S = 1, I = 2, R = 3)
suppressWarnings(x2 <- x2 %>% as.rsi() %>% as.double())
suppressWarnings(y2 <- y2 %>% as.rsi() %>% as.double())
suppressWarnings(x2 <- x2 %>% as.rsi() %>% as.double())
suppressWarnings(y2 <- y2 %>% as.rsi() %>% as.double())
points <- (x2 - y2) %>% abs() %>% sum(na.rm = TRUE)
result[i] <- ((points / 2) >= points_threshold)
} else {
stop('`', type, '` is not a valid value for type, must be "points" or "keyantibiotics". See ?first_isolate.')
}
points <- (x2 - y2) %>% abs() %>% sum(na.rm = TRUE)
result[i] <- ((points / 2) >= points_threshold)
}
}
if (info == TRUE) {