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(v2.1.1.9163) cleanup

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-02-27 14:04:29 +01:00
parent 68efddab3d
commit 07efc292bc
73 changed files with 2187 additions and 1715 deletions
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53
R/first_isolate.R
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@ -466,7 +466,7 @@ first_isolate <- function(x = NULL,
x$other_pat_or_mo <- !(x$newvar_patient_id == pm_lag(x$newvar_patient_id) & x$newvar_genus_species == pm_lag(x$newvar_genus_species))
x$newvar_episode_group <- paste(x$newvar_patient_id, x$newvar_genus_species)
x$more_than_episode_ago <- unlist(
lapply(
split(
@ -479,7 +479,7 @@ first_isolate <- function(x = NULL,
),
use.names = FALSE
)
if (!is.null(col_keyantimicrobials)) {
# using phenotypes
x$different_antibiogram <- !unlist(
@ -498,15 +498,15 @@ first_isolate <- function(x = NULL,
} else {
x$different_antibiogram <- FALSE
}
x$newvar_first_isolate <- x$newvar_row_index_sorted >= row.start &
x$newvar_row_index_sorted <= row.end &
x$newvar_genus_species != "" &
(x$other_pat_or_mo | x$more_than_episode_ago | x$different_antibiogram)
decimal.mark <- getOption("OutDec")
big.mark <- ifelse(decimal.mark != ",", ",", " ")
# first one as TRUE
x[row.start, "newvar_first_isolate"] <- TRUE
# no tests that should be included, or ICU
@ -517,7 +517,8 @@ first_isolate <- function(x = NULL,
if (icu_exclude == TRUE) {
if (isTRUE(info)) {
message_("Excluding ", format(sum(x$newvar_is_icu, na.rm = TRUE), decimal.mark = decimal.mark, big.mark = big.mark), " isolates from ICU.",
add_fn = font_red)
add_fn = font_red
)
}
x[which(x$newvar_is_icu), "newvar_first_isolate"] <- FALSE
} else if (isTRUE(info)) {
@ -673,24 +674,27 @@ duplicated_antibiogram <- function(antibiogram, points_threshold, ignore_I, type
return(FALSE)
}
# first sort on data availability - count the dots and order that ascending so that highest availability of SIR is on top
number_dots <- vapply(FUN.VALUE = integer(1),
antibiogram,
function(x) sum(strsplit(x, "", fixed = TRUE)[[1]] == "."),
USE.NAMES = FALSE)
number_dots <- vapply(
FUN.VALUE = integer(1),
antibiogram,
function(x) sum(strsplit(x, "", fixed = TRUE)[[1]] == "."),
USE.NAMES = FALSE
)
new_order <- order(number_dots, antibiogram)
antibiogram.bak <- antibiogram
antibiogram <- antibiogram[new_order]
out <- rep(NA, length(antibiogram))
out[1] <- FALSE
out[2] <- antimicrobials_equal(antibiogram[1], antibiogram[2],
ignore_I = ignore_I, points_threshold = points_threshold,
type = type)
ignore_I = ignore_I, points_threshold = points_threshold,
type = type
)
if (length(antibiogram) == 2) {
# fast return, no further check required
return(out)
}
# we can skip the duplicates - they are never unique antibiograms of course
duplicates <- duplicated(antibiogram)
out[3:length(out)][duplicates[3:length(out)] == TRUE] <- TRUE
@ -698,17 +702,24 @@ duplicated_antibiogram <- function(antibiogram, points_threshold, ignore_I, type
# fast return, no further check required
return(c(out[1:2], rep(TRUE, length(out) - 2)))
}
for (na in antibiogram[is.na(out)]) {
# check if this antibiogram has any change with other antibiograms
out[which(antibiogram == na)] <- all(
vapply(FUN.VALUE = logical(1),
antibiogram[!is.na(out) & antibiogram != na],
function(y) antimicrobials_equal(y = y, z = na,
ignore_I = ignore_I, points_threshold = points_threshold,
type = type)))
vapply(
FUN.VALUE = logical(1),
antibiogram[!is.na(out) & antibiogram != na],
function(y) {
antimicrobials_equal(
y = y, z = na,
ignore_I = ignore_I, points_threshold = points_threshold,
type = type
)
}
)
)
}
out <- out[order(new_order)]
# rerun duplicated again
duplicates <- duplicated(antibiogram.bak)