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(v2.1.1.9082) algorithm updates

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dr. M.S. (Matthijs) Berends
2024-09-30 18:46:55 +02:00
parent ac1c40d8bb
commit 681fe011fe
25 changed files with 15593 additions and 15505 deletions
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17
R/first_isolate.R
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@ -670,6 +670,16 @@ duplicated_antibiogram <- function(antibiogram, points_threshold, ignore_I, type
# fast return, only 1 isolate
return(FALSE)
}
stop("Check R/first_isolate.R -> duplicated_antibiogram()")
# first sort on data availability - count the dots and order that ascending
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],
@ -680,11 +690,6 @@ duplicated_antibiogram <- function(antibiogram, points_threshold, ignore_I, type
return(out)
}
# sort after the second one (since we already determined AB equality of the first two)
original_sort <- c(1, 2, rank(antibiogram[3:length(antibiogram)]) + 2)
antibiogram.bak <- antibiogram
antibiogram <- c(antibiogram[1:2], sort(antibiogram[3:length(antibiogram)]))
# 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
@ -703,7 +708,7 @@ duplicated_antibiogram <- function(antibiogram, points_threshold, ignore_I, type
type = type)))
}
out <- out[original_sort]
out <- out[order(new_order)]
# rerun duplicated again
duplicates <- duplicated(antibiogram.bak)
out[duplicates == TRUE] <- TRUE