From 5593aee19e44a76da46096a4f446ce8fcba765ca Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Wed, 30 May 2018 23:02:16 +0200
Subject: [PATCH] edit as.rsi algor.

---
 DESCRIPTION | 5 ++---
 R/classes.R | 4 ++--
 R/freq.R    | 2 +-
 man/freq.Rd | 2 +-
 4 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3f40d08a..8b6e9edc 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 0.2.0.9000
-Date: 2018-05-22
+Version: 0.2.0.9001
+Date: 2018-05-30
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(
@@ -38,7 +38,6 @@ Imports:
 Suggests:
     testthat (>= 1.0.2),
     covr (>= 3.0.1),
-    knitr,
     rmarkdown
 VignetteBuilder: knitr
 URL: https://github.com/msberends/AMR
diff --git a/R/classes.R b/R/classes.R
index 20c7db64..56f915ce 100755
--- a/R/classes.R
+++ b/R/classes.R
@@ -43,8 +43,8 @@ as.rsi <- function(x) {
     na_before <- x[is.na(x) | x == ''] %>% length()
     # remove all spaces
     x <- gsub(' {2,55}', '', x)
-    # disallow more than 3 characters
-    x[nchar(x) > 3] <- NA
+    # disallow more than 10 characters to start with
+    x[nchar(x) > 10] <- NA
     # remove all invalid characters
     x <- gsub('[^RSI]+', '', x %>% toupper())
     # needed for UMCG in cases of "S;S" but also "S;I"; the latter will be NA:
diff --git a/R/freq.R b/R/freq.R
index dbbc1e7b..6aacc2b2 100755
--- a/R/freq.R
+++ b/R/freq.R
@@ -20,7 +20,7 @@
 #'
 #' Create a frequency table of a vector of data, a single column or a maximum of 9 columns of a data frame. Supports markdown for reports.
 #' @param x data
-#' @param sort.count Sort on count. Use \code{FALSE} to sort alphabetically on item.
+#' @param sort.count sort on count. Use \code{FALSE} to sort alphabetically on item.
 #' @param nmax number of row to print. The default, \code{15}, uses \code{\link{getOption}("max.print.freq")}. Use \code{nmax = 0} or \code{nmax = NA} to print all rows.
 #' @param na.rm a logical value indicating whether NA values should be removed from the frequency table. The header will always print the amount of \code{NA}s.
 #' @param markdown print table in markdown format (this forces \code{nmax = NA})
diff --git a/man/freq.Rd b/man/freq.Rd
index 32f30029..51f9f748 100755
--- a/man/freq.Rd
+++ b/man/freq.Rd
@@ -16,7 +16,7 @@ frequency_tbl(x, sort.count = TRUE, nmax = getOption("max.print.freq"),
 \arguments{
 \item{x}{data}
 
-\item{sort.count}{Sort on count. Use \code{FALSE} to sort alphabetically on item.}
+\item{sort.count}{sort on count. Use \code{FALSE} to sort alphabetically on item.}
 
 \item{nmax}{number of row to print. The default, \code{15}, uses \code{\link{getOption}("max.print.freq")}. Use \code{nmax = 0} or \code{nmax = NA} to print all rows.}