mirror of https://github.com/msberends/AMR.git
fix for keyab, more examples
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.2.0.9014
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Date: 2018-07-19
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Version: 0.2.0.9015
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Date: 2018-07-23
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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@ -254,3 +254,4 @@ ratio <- function(x, ratio) {
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}
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base::sum(x, na.rm = TRUE) * (ratio / base::sum(ratio, na.rm = TRUE))
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}
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@ -25,7 +25,8 @@
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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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#' @details The function \code{key_antibiotics} returns a character vector with antibiotic results.
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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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@ -34,7 +35,7 @@
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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 value.
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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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@ -54,6 +55,16 @@
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#' first_isolate(tbl,
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#' col_keyantibiotics = 'keyab')
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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_bactid = "bactid",
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universal_1 = "amox",
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@ -74,7 +85,7 @@ key_antibiotics <- function(tbl,
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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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info = TRUE) {
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warnings = TRUE) {
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if (!col_bactid %in% colnames(tbl)) {
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stop('Column ', col_bactid, ' not found.', call. = FALSE)
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@ -84,7 +95,7 @@ key_antibiotics <- function(tbl,
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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 = info)
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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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@ -173,10 +184,17 @@ key_antibiotics_equal <- function(x,
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x <- gsub('I', '.', x, ignore.case = TRUE)
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y <- gsub('I', '.', y, ignore.case = TRUE)
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}
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for (i in 1:length(x)) {
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x_split <- strsplit(x[i], "")[[1]]
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y_split <- strsplit(y[i], "")[[1]]
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y_split[x_split == "."] <- "."
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x_split[y_split == "."] <- "."
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x_checkfor <- paste(x_split, collapse = "")
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y_checkfor <- paste(y_split, collapse = "")
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result[i] <- nchar(x[i]) == nchar(y[i]) &
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(x[i] %like% paste0("^", y[i], "$") |
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y[i] %like% paste0("^", x[i], "$"))
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(x_checkfor %like% y_checkfor |
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y_checkfor %like% x_checkfor)
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}
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return(result)
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@ -41,7 +41,7 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
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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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}
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\details{
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The function \code{key_antibiotics} returns a character vector with antibiotic results.
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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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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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@ -50,7 +50,7 @@ The function \code{key_antibiotics} returns a character vector with antibiotic r
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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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The function \code{key_antibiotics_equal} checks the characters returned by \code{key_antibiotics} for equality, and returns a logical value.
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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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}
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\section{Key antibiotics}{
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@ -77,6 +77,16 @@ tbl$first_isolate_weighed <-
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first_isolate(tbl,
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col_keyantibiotics = 'keyab')
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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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key_antibiotics_equal(strainA, strainB)
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# TRUE, because I is ignored (as are missing values)
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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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}
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\seealso{
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\code{\link{first_isolate}}
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@ -1,13 +1,5 @@
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context("first_isolates.R")
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test_that("keyantibiotics work", {
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expect_equal(length(key_antibiotics(septic_patients, info = FALSE)), nrow(septic_patients))
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expect_true(key_antibiotics_equal("SSS", "SSS"))
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expect_false(key_antibiotics_equal("SSS", "SRS"))
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expect_true(key_antibiotics_equal("SSS", "SIS", ignore_I = TRUE))
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expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
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})
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test_that("first isolates work", {
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# septic_patients contains 1959 out of 2000 first isolates
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expect_equal(
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@ -0,0 +1,11 @@
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context("key_antibiotics.R")
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test_that("keyantibiotics work", {
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expect_equal(length(key_antibiotics(septic_patients, warnings = FALSE)), nrow(septic_patients))
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expect_true(key_antibiotics_equal("SSS", "SSS"))
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expect_false(key_antibiotics_equal("SSS", "SRS"))
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expect_true(key_antibiotics_equal("SSS", "SIS", ignore_I = TRUE))
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expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
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expect_true(key_antibiotics_equal(".SS", "SI.", ignore_I = TRUE))
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expect_false(key_antibiotics_equal(".SS", "SI.", ignore_I = FALSE))
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})
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