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doc fix

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dr. M.S. (Matthijs) Berends
2019-05-23 17:35:58 +02:00
parent 60983a1640
commit bbf8b611e3
11 changed files with 26 additions and 20 deletions
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6
man/key_antibiotics.Rd
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@ -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.