diff --git a/DESCRIPTION b/DESCRIPTION index 2b574620..bb6c14b9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 0.6.1.9035 +Version: 0.6.1.9036 Date: 2019-05-23 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/R/globals.R b/R/globals.R index 2bf59970..41bf5b06 100755 --- a/R/globals.R +++ b/R/globals.R @@ -23,6 +23,10 @@ globalVariables(c(".", "..property", "ab", "abbreviations", + "mdr", + "mono_count", + "second", + "xdr", "antibiotic", "Antibiotic", "antibiotics", diff --git a/R/key_antibiotics.R b/R/key_antibiotics.R index d6dd5b6a..04e5d7dc 100755 --- a/R/key_antibiotics.R +++ b/R/key_antibiotics.R @@ -23,7 +23,7 @@ #' #' 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. #' @param x table with antibiotics coloms, like \code{AMX} or \code{amox} -#' @param x,y characters to compare +#' @param y,z characters to compare #' @inheritParams first_isolate #' @param universal_1,universal_2,universal_3,universal_4,universal_5,universal_6 column names of \strong{broad-spectrum} antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}. #' @param GramPos_1,GramPos_2,GramPos_3,GramPos_4,GramPos_5,GramPos_6 column names of antibiotics for \strong{Gram positives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}. @@ -218,13 +218,15 @@ key_antibiotics <- function(x, #' @importFrom dplyr progress_estimated %>% #' @rdname key_antibiotics #' @export -key_antibiotics_equal <- function(x, - y, +key_antibiotics_equal <- function(y, + z, type = c("keyantibiotics", "points"), ignore_I = TRUE, points_threshold = 2, info = FALSE) { - # x is active row, y is lag + # y is active row, z is lag + x <- y + y <- z type <- type[1] diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index fe103ca0..c15316ee 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -78,7 +78,7 @@ AMR (for R) - 0.6.1.9035 + 0.6.1.9036 diff --git a/docs/articles/index.html b/docs/articles/index.html index d552f329..8dfd7c23 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.6.1.9035 + 0.6.1.9036 diff --git a/docs/authors.html b/docs/authors.html index 76a5d06d..2e522f8d 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -78,7 +78,7 @@ AMR (for R) - 0.6.1.9035 + 0.6.1.9036 diff --git a/docs/index.html b/docs/index.html index 912a3c59..a10d4e13 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 0.6.1.9035 + 0.6.1.9036 diff --git a/docs/news/index.html b/docs/news/index.html index 744bdd2d..bb653856 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.6.1.9035 + 0.6.1.9036 diff --git a/docs/reference/index.html b/docs/reference/index.html index da61e4ea..18f7aba4 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.6.1.9035 + 0.6.1.9036 diff --git a/docs/reference/key_antibiotics.html b/docs/reference/key_antibiotics.html index 9414cb98..38563408 100644 --- a/docs/reference/key_antibiotics.html +++ b/docs/reference/key_antibiotics.html @@ -80,7 +80,7 @@ AMR (for R) - 0.6.1.9035 + 0.6.1.9036 @@ -262,7 +262,7 @@ GramNeg_5 = guess_ab_col(x, "CAZ"), GramNeg_6 = guess_ab_col(x, "MEM"), warnings = TRUE, ...) -key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"), +key_antibiotics_equal(y, z, type = c("keyantibiotics", "points"), ignore_I = TRUE, points_threshold = 2, info = FALSE)

Arguments

@@ -296,6 +296,10 @@ ...

other parameters passed on to function

+ + y, z +

characters to compare

+ type

type to determine weighed isolates; can be "keyantibiotics" or "points", see Details

@@ -312,10 +316,6 @@ info

print progress

- - x, y -

characters to compare

-

Details

diff --git a/man/key_antibiotics.Rd b/man/key_antibiotics.Rd index 85173932..7356d9b0 100755 --- a/man/key_antibiotics.Rd +++ b/man/key_antibiotics.Rd @@ -19,7 +19,7 @@ key_antibiotics(x, col_mo = NULL, universal_1 = guess_ab_col(x, "AMX"), GramNeg_5 = guess_ab_col(x, "CAZ"), GramNeg_6 = guess_ab_col(x, "MEM"), warnings = TRUE, ...) -key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"), +key_antibiotics_equal(y, z, type = c("keyantibiotics", "points"), ignore_I = TRUE, points_threshold = 2, info = FALSE) } \arguments{ @@ -37,6 +37,8 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"), \item{...}{other parameters passed on to function} +\item{y, z}{characters to compare} + \item{type}{type to determine weighed isolates; can be \code{"keyantibiotics"} or \code{"points"}, see Details} \item{ignore_I}{logical to determine whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantibiotics"}, see Details} @@ -44,8 +46,6 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"), \item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see Details} \item{info}{print progress} - -\item{x, y}{characters to compare} } \description{ 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.