[R-gregmisc-users] SF.net SVN: r-gregmisc:[1774] trunk/gtools

[<wa...@us...>]

Revision: 1774
          http://sourceforge.net/p/r-gregmisc/code/1774
Author:   warnes
Date:     2014-03-01 20:02:08 +0000 (Sat, 01 Mar 2014)
Log Message:
-----------
Fix bug in gtools::mixedorder regular expression for regognizing numbers. (Periods weren't escaped).

Modified Paths:
--------------
    trunk/gtools/R/mixedsort.R

Added Paths:
-----------
    trunk/gtools/tests/test_mixedorder.R

Modified: trunk/gtools/R/mixedsort.R
===================================================================
--- trunk/gtools/R/mixedsort.R	2014-02-11 17:44:04 UTC (rev 1773)
+++ trunk/gtools/R/mixedsort.R	2014-03-01 20:02:08 UTC (rev 1774)
@@ -17,7 +17,7 @@
     if( is.numeric(x) )
         return( order(x) )
 
-    
+
     delim="\\$\\@\\$"
 
     numeric <- function(x)
@@ -37,7 +37,7 @@
 
     if(length(which.blanks) >0)
         x[ which.blanks ] <- -Inf
-    
+
     if(length(which.nas) >0)
         x[ which.nas ] <- Inf
 
@@ -47,7 +47,7 @@
     ####
 
     # find and mark numbers in the form of +1.23e+45.67
-    delimited <- gsub("([+-]{0,1}[0-9]+.{0,1}[0-9]*([eE][\\+\\-]{0,1}[0-9]+.{0,1}[0-9]*){0,1})",
+    delimited <- gsub("([+-]{0,1}[0-9]+\\.{0,1}[0-9]*([eE][\\+\\-]{0,1}[0-9]+\\.{0,1}[0-9]*){0,1})",
                       paste(delim,"\\1",delim,sep=""), x)
 
     # separate out numbers
@@ -90,7 +90,7 @@
                         t(rank.character) +
                         apply(matrix(rank.numeric),2,max,na.rm=TRUE)
                         )
-    
+
     rank.overall <- ifelse(is.na(rank.character),rank.numeric,rank.character)
 
     order.frame <- as.data.frame(rank.overall)

Added: trunk/gtools/tests/test_mixedorder.R
===================================================================
--- trunk/gtools/tests/test_mixedorder.R	                        (rev 0)
+++ trunk/gtools/tests/test_mixedorder.R	2014-03-01 20:02:08 UTC (rev 1774)
@@ -0,0 +1,27 @@
+library(gtools)
+
+## Examples from man page
+Treatment <- c("Control", "Asprin 10mg/day", "Asprin 50mg/day",
+               "Asprin 100mg/day", "Acetomycin 100mg/day",
+               "Acetomycin 1000mg/day")
+
+stopifnot( mixedorder(tmp)==c(4, 5, 1, 2, 3 ))
+
+
+x <- rev(c("AA 0.50 ml", "AA 1.5 ml", "AA 500 ml", "AA 1500 ml",
+           "EXP 1", "AA 1e3 ml", "A A A", "1 2 3 A", "NA", NA, "1e2",
+           "", "-", "1A", "1 A", "100", "100A", "Inf"))
+
+stopifnot( mixedorder(x)==c(7, 11, 4, 5, 3, 8, 2, 1, 6, 12, 18, 17, 16, 13, 15, 14, 10, 9) )
+
+## Bug reported by Aaron Taudt on 2014-03-01
+
+tmp <- c("uniresult_simulated_H3k27ac_binsize_200_chr1.RData",
+         "uniresult_simulated_H3k27me3_binsize_200_chr1.RData",
+         "uniresult_simulated_H3k36me3_binsize_200_chr1.RData",
+         "uniresult_simulated_H3k4me3_binsize_200_chr1.RData",
+         "uniresult_simulated_H3k9me3_binsize_200_chr1.RData")
+
+stopifnot( mixedorder(tmp)==c(4, 5, 1, 2, 3) )
+
+

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