fix for keyab, more examples

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.2.0.9014
+Version: 0.2.0.9015
-Date: 2018-07-19
+Date: 2018-07-23
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(

R/g.test.R

@@ -254,3 +254,4 @@ ratio <- function(x, ratio) {
   }
   base::sum(x, na.rm = TRUE) * (ratio / base::sum(ratio, na.rm = TRUE))
 }
+

R/key_antibiotics.R

@@ -25,7 +25,8 @@
 #' @param universal_1,universal_2,universal_3,universal_4,universal_5,universal_6 column names of \strong{broad-spectrum} antibiotics, case-insensitive
 #' @param GramPos_1,GramPos_2,GramPos_3,GramPos_4,GramPos_5,GramPos_6 column names of antibiotics for \strong{Gram positives}, case-insensitive
 #' @param GramNeg_1,GramNeg_2,GramNeg_3,GramNeg_4,GramNeg_5,GramNeg_6 column names of antibiotics for \strong{Gram negatives}, case-insensitive
-#' @details The function \code{key_antibiotics} returns a character vector with antibiotic results.
+#' @param warnings give warning about missing antibiotic columns, they will anyway be ignored
+#' @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.
 #'
 #'   At default, the antibiotics that are used for \strong{Gram positive bacteria} are (colum names): \cr
 #'   \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"}.
@@ -34,7 +35,7 @@
 #'   \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"}.
 #'
 #'
-#'   The function \code{key_antibiotics_equal} checks the characters returned by \code{key_antibiotics} for equality, and returns a logical value.
+#'   The function \code{key_antibiotics_equal} checks the characters returned by \code{key_antibiotics} for equality, and returns a logical vector.
 #' @inheritSection first_isolate Key antibiotics
 #' @rdname key_antibiotics
 #' @export
@@ -54,6 +55,16 @@
 #'   first_isolate(tbl,
 #'                 col_keyantibiotics = 'keyab')
 #' }
+#'
+#' # output of the `key_antibiotics` function could be like this:
+#' strainA <- "SSSRR.S.R..S"
+#' strainB <- "SSSIRSSSRSSS"
+#'
+#' key_antibiotics_equal(strainA, strainB)
+#' # TRUE, because I is ignored (as are missing values)
+#'
+#' key_antibiotics_equal(strainA, strainB, ignore_I = FALSE)
+#' # FALSE, because I is not ignored and so the 4th value differs
 key_antibiotics <- function(tbl,
                             col_bactid = "bactid",
                             universal_1 = "amox",
@@ -74,7 +85,7 @@ key_antibiotics <- function(tbl,
                             GramNeg_4 = "cfot",
                             GramNeg_5 = "cfta",
                             GramNeg_6 = "mero",
-                            info = TRUE) {
+                            warnings = TRUE) {
 
   if (!col_bactid %in% colnames(tbl)) {
     stop('Column ', col_bactid, ' not found.', call. = FALSE)
@@ -84,7 +95,7 @@ key_antibiotics <- function(tbl,
   col.list <- c(universal_1, universal_2, universal_3, universal_4, universal_5, universal_6,
                 GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6,
                 GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6)
-  col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info)
+  col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = warnings)
   universal_1 <- col.list[universal_1]
   universal_2 <- col.list[universal_2]
   universal_3 <- col.list[universal_3]
@@ -173,10 +184,17 @@ key_antibiotics_equal <- function(x,
       x <- gsub('I', '.', x, ignore.case = TRUE)
       y <- gsub('I', '.', y, ignore.case = TRUE)
     }
+
     for (i in 1:length(x)) {
+      x_split <- strsplit(x[i], "")[[1]]
+      y_split <- strsplit(y[i], "")[[1]]
+      y_split[x_split == "."] <- "."
+      x_split[y_split == "."] <- "."
+      x_checkfor <- paste(x_split, collapse = "")
+      y_checkfor <- paste(y_split, collapse = "")
       result[i] <- nchar(x[i]) == nchar(y[i]) &
-        (x[i] %like% paste0("^", y[i], "$") |
+        (x_checkfor %like% y_checkfor |
-           y[i] %like% paste0("^", x[i], "$"))
+           y_checkfor %like% x_checkfor)
     }
     return(result)
 

man/key_antibiotics.Rd

@@ -41,7 +41,7 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
 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.
 }
 \details{
-The function \code{key_antibiotics} returns a character vector with antibiotic results.
+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.
 
   At default, the antibiotics that are used for \strong{Gram positive bacteria} are (colum names): \cr
   \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"}.
@@ -50,7 +50,7 @@ The function \code{key_antibiotics} returns a character vector with antibiotic r
   \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"}.
 
 
-  The function \code{key_antibiotics_equal} checks the characters returned by \code{key_antibiotics} for equality, and returns a logical value.
+  The function \code{key_antibiotics_equal} checks the characters returned by \code{key_antibiotics} for equality, and returns a logical vector.
 }
 \section{Key antibiotics}{
 
@@ -77,6 +77,16 @@ tbl$first_isolate_weighed <-
   first_isolate(tbl,
                 col_keyantibiotics = 'keyab')
 }
+
+# output of the `key_antibiotics` function could be like this:
+strainA <- "SSSRR.S.R..S"
+strainB <- "SSSIRSSSRSSS"
+
+key_antibiotics_equal(strainA, strainB)
+# TRUE, because I is ignored (as are missing values)
+
+key_antibiotics_equal(strainA, strainB, ignore_I = FALSE)
+# FALSE, because I is not ignored and so the 4th value differs
 }
 \seealso{
 \code{\link{first_isolate}}

tests/testthat/test-first_isolates.R

@@ -1,13 +1,5 @@
 context("first_isolates.R")
 
-test_that("keyantibiotics work", {
-  expect_equal(length(key_antibiotics(septic_patients, info = FALSE)), nrow(septic_patients))
-  expect_true(key_antibiotics_equal("SSS", "SSS"))
-  expect_false(key_antibiotics_equal("SSS", "SRS"))
-  expect_true(key_antibiotics_equal("SSS", "SIS", ignore_I = TRUE))
-  expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
-})
-
 test_that("first isolates work", {
   # septic_patients contains 1959 out of 2000 first isolates
   expect_equal(

tests/testthat/test-key_antibiotics.R

@@ -0,0 +1,11 @@
+context("key_antibiotics.R")
+
+test_that("keyantibiotics work", {
+  expect_equal(length(key_antibiotics(septic_patients, warnings = FALSE)), nrow(septic_patients))
+  expect_true(key_antibiotics_equal("SSS", "SSS"))
+  expect_false(key_antibiotics_equal("SSS", "SRS"))
+  expect_true(key_antibiotics_equal("SSS", "SIS", ignore_I = TRUE))
+  expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
+  expect_true(key_antibiotics_equal(".SS", "SI.", ignore_I = TRUE))
+  expect_false(key_antibiotics_equal(".SS", "SI.", ignore_I = FALSE))
+})