mirror of https://github.com/msberends/AMR.git
264 lines
11 KiB
R
264 lines
11 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This program is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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# ==================================================================== #
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#' Key antibiotics for first \emph{weighted} isolates
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#'
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#' These function can be used to determine first isolates (see \code{\link{first_isolate}}). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first \emph{weighted} isolates.
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#' @param tbl table with antibiotics coloms, like \code{amox} and \code{amcl}.
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#' @param x,y characters to compare
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#' @inheritParams first_isolate
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#' @param universal_1,universal_2,universal_3,universal_4,universal_5,universal_6 column names of \strong{broad-spectrum} antibiotics, case-insensitive
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#' @param GramPos_1,GramPos_2,GramPos_3,GramPos_4,GramPos_5,GramPos_6 column names of antibiotics for \strong{Gram positives}, case-insensitive
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#' @param GramNeg_1,GramNeg_2,GramNeg_3,GramNeg_4,GramNeg_5,GramNeg_6 column names of antibiotics for \strong{Gram negatives}, case-insensitive
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#' @param warnings give warning about missing antibiotic columns, they will anyway be ignored
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#' @details The function \code{key_antibiotics} returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using \code{key_antibiotics_equal}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}). The \code{\link{first_isolate}} function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible \emph{S. aureus} (MSSA) found within the same episode (see \code{episode} parameter of \code{\link{first_isolate}}). Without key antibiotic comparison it wouldn't.
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#'
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#' At default, the antibiotics that are used for \strong{Gram positive bacteria} are (colum names): \cr
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#' \code{"amox"}, \code{"amcl"}, \code{"cfur"}, \code{"pita"}, \code{"cipr"}, \code{"trsu"} (until here is universal), \code{"vanc"}, \code{"teic"}, \code{"tetr"}, \code{"eryt"}, \code{"oxac"}, \code{"rifa"}.
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#'
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#' At default, the antibiotics that are used for \strong{Gram negative bacteria} are (colum names): \cr
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#' \code{"amox"}, \code{"amcl"}, \code{"cfur"}, \code{"pita"}, \code{"cipr"}, \code{"trsu"} (until here is universal), \code{"gent"}, \code{"tobr"}, \code{"coli"}, \code{"cfot"}, \code{"cfta"}, \code{"mero"}.
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#'
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#'
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#' The function \code{key_antibiotics_equal} checks the characters returned by \code{key_antibiotics} for equality, and returns a logical vector.
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#' @inheritSection first_isolate Key antibiotics
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#' @rdname key_antibiotics
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#' @export
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#' @importFrom dplyr %>% mutate if_else
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#' @seealso \code{\link{first_isolate}}
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#' @examples
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#' # septic_patients is a dataset available in the AMR package
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#' ?septic_patients
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#' my_patients <- septic_patients
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#'
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#' library(dplyr)
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#' # set key antibiotics to a new variable
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#' my_patients <- my_patients %>%
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#' mutate(keyab = key_antibiotics(.)) %>%
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#' mutate(
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#' # now calculate first isolates
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#' first_regular = first_isolate(., "date", "patient_id", "mo"),
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#' # and first WEIGHTED isolates
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#' first_weighted = first_isolate(., "date", "patient_id", "mo",
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#' col_keyantibiotics = "keyab")
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#' )
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#'
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#' # Check the difference, in this data set it results in 7% more isolates:
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#' sum(my_patients$first_regular, na.rm = TRUE)
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#' sum(my_patients$first_weighted, na.rm = TRUE)
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#'
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#'
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#' # output of the `key_antibiotics` function could be like this:
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#' strainA <- "SSSRR.S.R..S"
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#' strainB <- "SSSIRSSSRSSS"
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#'
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#' key_antibiotics_equal(strainA, strainB)
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#' # TRUE, because I is ignored (as are missing values)
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#'
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#' key_antibiotics_equal(strainA, strainB, ignore_I = FALSE)
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#' # FALSE, because I is not ignored and so the 4th value differs
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key_antibiotics <- function(tbl,
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col_mo = "mo",
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universal_1 = "amox",
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universal_2 = "amcl",
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universal_3 = "cfur",
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universal_4 = "pita",
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universal_5 = "cipr",
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universal_6 = "trsu",
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GramPos_1 = "vanc",
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GramPos_2 = "teic",
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GramPos_3 = "tetr",
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GramPos_4 = "eryt",
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GramPos_5 = "oxac",
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GramPos_6 = "rifa",
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GramNeg_1 = "gent",
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GramNeg_2 = "tobr",
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GramNeg_3 = "coli",
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GramNeg_4 = "cfot",
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GramNeg_5 = "cfta",
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GramNeg_6 = "mero",
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warnings = TRUE,
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col_bactid = "bactid") {
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if (col_bactid %in% colnames(tbl)) {
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col_mo <- col_bactid
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warning("Use of `col_bactid` is deprecated. Use `col_mo` instead.")
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}
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if (!col_mo %in% colnames(tbl)) {
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stop('Column ', col_mo, ' not found.', call. = FALSE)
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}
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# check columns
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col.list <- c(universal_1, universal_2, universal_3, universal_4, universal_5, universal_6,
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GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6,
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GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6)
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col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = warnings)
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universal_1 <- col.list[universal_1]
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universal_2 <- col.list[universal_2]
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universal_3 <- col.list[universal_3]
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universal_4 <- col.list[universal_4]
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universal_5 <- col.list[universal_5]
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universal_6 <- col.list[universal_6]
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GramPos_1 <- col.list[GramPos_1]
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GramPos_2 <- col.list[GramPos_2]
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GramPos_3 <- col.list[GramPos_3]
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GramPos_4 <- col.list[GramPos_4]
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GramPos_5 <- col.list[GramPos_5]
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GramPos_6 <- col.list[GramPos_6]
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GramNeg_1 <- col.list[GramNeg_1]
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GramNeg_2 <- col.list[GramNeg_2]
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GramNeg_3 <- col.list[GramNeg_3]
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GramNeg_4 <- col.list[GramNeg_4]
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GramNeg_5 <- col.list[GramNeg_5]
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GramNeg_6 <- col.list[GramNeg_6]
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universal <- c(universal_1, universal_2, universal_3,
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universal_4, universal_5, universal_6)
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gram_positive = c(universal,
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GramPos_1, GramPos_2, GramPos_3,
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GramPos_4, GramPos_5, GramPos_6)
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gram_positive <- gram_positive[!is.na(gram_positive)]
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gram_negative = c(universal,
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GramNeg_1, GramNeg_2, GramNeg_3,
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GramNeg_4, GramNeg_5, GramNeg_6)
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gram_negative <- gram_negative[!is.na(gram_negative)]
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if (!tbl %>% pull(col_mo) %>% is.mo()) {
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tbl[, col_mo] <- as.mo(tbl[, col_mo])
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}
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# join microorganisms
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tbl <- tbl %>% left_join_microorganisms(col_mo)
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tbl$key_ab <- NA_character_
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# Gram +
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tbl <- tbl %>% mutate(key_ab =
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if_else(gramstain == "Gram positive",
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apply(X = tbl[, gram_positive],
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MARGIN = 1,
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FUN = function(x) paste(x, collapse = "")),
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key_ab))
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# Gram -
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tbl <- tbl %>% mutate(key_ab =
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if_else(gramstain == "Gram negative",
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apply(X = tbl[, gram_negative],
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MARGIN = 1,
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FUN = function(x) paste(x, collapse = "")),
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key_ab))
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# format
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key_abs <- tbl %>%
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pull(key_ab) %>%
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gsub('(NA|NULL)', '.', .) %>%
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gsub('[^SIR]', '.', ., ignore.case = TRUE)
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key_abs
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}
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#' @importFrom dplyr progress_estimated %>%
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#' @rdname key_antibiotics
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#' @export
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key_antibiotics_equal <- function(x,
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y,
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type = c("keyantibiotics", "points"),
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ignore_I = TRUE,
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points_threshold = 2,
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info = FALSE) {
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# x is active row, y is lag
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type <- type[1]
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if (length(x) != length(y)) {
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stop('Length of `x` and `y` must be equal.')
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}
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# only show progress bar on points or when at least 5000 isolates
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info_needed <- info == TRUE & (type == "points" | length(x) > 5000)
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result <- logical(length(x))
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if (info_needed == TRUE) {
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p <- dplyr::progress_estimated(length(x))
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}
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for (i in 1:length(x)) {
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if (info_needed == TRUE) {
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p$tick()$print()
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}
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if (is.na(x[i])) {
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x[i] <- ''
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}
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if (is.na(y[i])) {
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y[i] <- ''
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}
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if (x[i] == y[i]) {
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result[i] <- TRUE
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} else if (nchar(x[i]) != nchar(y[i])) {
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result[i] <- FALSE
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} else {
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x_split <- strsplit(x[i], "")[[1]]
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y_split <- strsplit(y[i], "")[[1]]
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if (type == 'keyantibiotics') {
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if (ignore_I == TRUE) {
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x_split[x_split == "I"] <- "."
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y_split[y_split == "I"] <- "."
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}
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y_split[x_split == "."] <- "."
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x_split[y_split == "."] <- "."
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result[i] <- all(x_split == y_split)
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} else if (type == 'points') {
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# count points for every single character:
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# - no change is 0 points
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# - I <-> S|R is 0.5 point
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# - S|R <-> R|S is 1 point
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# use the levels of as.rsi (S = 1, I = 2, R = 3)
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suppressWarnings(x_split <- x_split %>% as.rsi() %>% as.double())
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suppressWarnings(y_split <- y_split %>% as.rsi() %>% as.double())
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points <- (x_split - y_split) %>% abs() %>% sum(na.rm = TRUE) / 2
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result[i] <- points >= points_threshold
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} else {
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stop('`', type, '` is not a valid value for type, must be "points" or "keyantibiotics". See ?first_isolate.')
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}
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}
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}
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if (info_needed == TRUE) {
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cat('\n')
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}
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result
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}
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