From 40de1b4ac265b1d4676f7dd8384498b37e253cd3 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Mon, 23 Jul 2018 10:37:49 +0200 Subject: [PATCH] man --- man/key_antibiotics.Rd | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/man/key_antibiotics.Rd b/man/key_antibiotics.Rd index 2e782e09..4e222c2b 100755 --- a/man/key_antibiotics.Rd +++ b/man/key_antibiotics.Rd @@ -11,7 +11,7 @@ key_antibiotics(tbl, col_bactid = "bactid", universal_1 = "amox", GramPos_2 = "teic", GramPos_3 = "tetr", GramPos_4 = "eryt", GramPos_5 = "oxac", GramPos_6 = "rifa", GramNeg_1 = "gent", GramNeg_2 = "tobr", GramNeg_3 = "coli", GramNeg_4 = "cfot", - GramNeg_5 = "cfta", GramNeg_6 = "mero", info = TRUE) + GramNeg_5 = "cfta", GramNeg_6 = "mero", warnings = TRUE) key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"), ignore_I = TRUE, points_threshold = 2, info = FALSE) @@ -27,7 +27,7 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"), \item{GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6}{column names of antibiotics for \strong{Gram negatives}, case-insensitive} -\item{info}{print progress} +\item{warnings}{give warning about missing antibiotic columns, they will anyway be ignored} \item{x, y}{characters to compare} @@ -36,6 +36,8 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"), \item{ignore_I}{logical to determine whether antibiotic interpretations with \code{"I"} will be ignored when \code{type = "keyantibiotics"}, see Details} \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} } \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.