diff --git a/R/first_isolates.R b/R/first_isolates.R index 56e5fe20..7ebd9465 100755 --- a/R/first_isolates.R +++ b/R/first_isolates.R @@ -49,7 +49,7 @@ #' \strong{2. Using} \code{type = "points"} \strong{and parameter} \code{points_threshold} \cr #' A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds \code{points_threshold}, an isolate will be (re)selected as a first weighted isolate. #' @keywords isolate isolates first -#' @seealso \code{\link{keyantibiotics}} +#' @seealso \code{\link{key_antibiotics}} #' @export #' @importFrom dplyr arrange_at lag between row_number filter mutate arrange #' @return A vector to add to table, see Examples. diff --git a/R/key_antibiotics.R b/R/key_antibiotics.R index 40186c4f..ad1edf98 100644 --- a/R/key_antibiotics.R +++ b/R/key_antibiotics.R @@ -20,6 +20,7 @@ #' #' 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 tbl table with antibiotics coloms, like \code{amox} and \code{amcl}. +#' @param x,y characters to compare #' @inheritParams first_isolate #' @param amcl,amox,cfot,cfta,cfur,cipr,coli,eryt,gent,mero,oxac,pita,rifa,teic,tetr,tobr,trsu,vanc column names of antibiotics, case-insensitive #' @details The function \code{key_antibiotics} returns a character vector with antibiotic results. diff --git a/man/first_isolate.Rd b/man/first_isolate.Rd index 253b4667..f9e8e457 100755 --- a/man/first_isolate.Rd +++ b/man/first_isolate.Rd @@ -126,7 +126,7 @@ tbl$first_resp_isolate_weighed <- } } \seealso{ -\code{\link{keyantibiotics}} +\code{\link{key_antibiotics}} } \keyword{first} \keyword{isolate} diff --git a/man/key_antibiotics.Rd b/man/key_antibiotics.Rd index b9ce8f53..0f672756 100755 --- a/man/key_antibiotics.Rd +++ b/man/key_antibiotics.Rd @@ -24,6 +24,8 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"), \item{info}{print progress} +\item{x, y}{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}