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dr. M.S. (Matthijs) Berends 2018-07-17 14:48:11 +02:00
parent 5cb9c541f8
commit 2a4d759fbc
4 changed files with 5 additions and 2 deletions
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2
R/first_isolates.R
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@ -49,7 +49,7 @@
#' \strong{2. Using} \code{type = "points"} \strong{and parameter} \code{points_threshold} \cr #' \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. #' 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 #' @keywords isolate isolates first
#' @seealso \code{\link{keyantibiotics}} #' @seealso \code{\link{key_antibiotics}}
#' @export #' @export
#' @importFrom dplyr arrange_at lag between row_number filter mutate arrange #' @importFrom dplyr arrange_at lag between row_number filter mutate arrange
#' @return A vector to add to table, see Examples. #' @return A vector to add to table, see Examples.

1
R/key_antibiotics.R
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@ -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. #' 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 tbl table with antibiotics coloms, like \code{amox} and \code{amcl}.
#' @param x,y characters to compare
#' @inheritParams first_isolate #' @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 #' @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. #' @details The function \code{key_antibiotics} returns a character vector with antibiotic results.

2
man/first_isolate.Rd
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@ -126,7 +126,7 @@ tbl$first_resp_isolate_weighed <-
} }
} }
\seealso{ \seealso{
\code{\link{keyantibiotics}} \code{\link{key_antibiotics}}
} }
\keyword{first} \keyword{first}
\keyword{isolate} \keyword{isolate}

2
man/key_antibiotics.Rd
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@ -24,6 +24,8 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
\item{info}{print progress} \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{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} \item{ignore_I}{logical to determine whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantibiotics"}, see Details}