check fails

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.

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.

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}

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}