[Rcolony-commits] r93 - in pkg: . R man

[noreply at r-forge.r-project.org]

Author: jonesor
Date: 2013-01-21 15:06:49 +0100 (Mon, 21 Jan 2013)
New Revision: 93

Modified:
   pkg/DESCRIPTION
   pkg/R/build.colony.input.R
   pkg/man/get.colony.data.Rd
Log:
Various minor fixes after running CMD R check

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2013-01-21 13:45:53 UTC (rev 92)
+++ pkg/DESCRIPTION	2013-01-21 14:06:49 UTC (rev 93)
@@ -2,9 +2,9 @@
 Type: Package
 Title: Tools for implementation and visualisation of Colony2 and its outputs.
 Version: 1.3
-Date: 2012-12-12
+Date: 2013-01-21
 Author: Owen R. Jones
 Maintainer: Owen R. Jones <jones at demogr.mpg.de>
 Description: The RColony package provides tools for the implementation of the Colony pedigree analysis software. In addition it provides tools for visualising, and summarising the results of the Colony analyses. 
-License: GNU General Public License (GPL)
+License: GPL
 LazyLoad: yes

Modified: pkg/R/build.colony.input.R
===================================================================
--- pkg/R/build.colony.input.R	2013-01-21 13:45:53 UTC (rev 92)
+++ pkg/R/build.colony.input.R	2013-01-21 14:06:49 UTC (rev 93)
@@ -162,7 +162,7 @@
       Sys.sleep(.2)
       flush.console()
       colonyfile$AlleleFreqPATH = file.choose()
-      colonyfile$allele.frequency = read.table(colonyfile$AlleleFreqPATH, header = FALSE, colClasses = c("character"), sep = delim, fill = TRUE, flush = TRUE, na.string = "", col.names = 1:max(count.fields(colonyfile$AlleleFreqPATH)))
+      colonyfile$allele.frequency = read.table(colonyfile$AlleleFreqPATH, header = FALSE, colClasses = c("character"), sep = delim, fill = TRUE, flush = TRUE, na.strings = "", col.names = 1:max(count.fields(colonyfile$AlleleFreqPATH)))
       flush.console()
     }
     
@@ -463,7 +463,7 @@
       cat("Provide the path to the PATERNAL sibships file.\n\n\n")
       flush.console()
       colonyfile$paternities.and.sibships.PATH = file.choose()
-      colonyfile$paternities.and.sibships = read.table(colonyfile$paternities.and.sibships.PATH, header = FALSE, colClasses = c("character"), sep = delim, fill = TRUE, flush = TRUE, na.string = "", col.names = 1:max(count.fields(colonyfile$paternities.and.sibships.PATH)))
+      colonyfile$paternities.and.sibships = read.table(colonyfile$paternities.and.sibships.PATH, header = FALSE, colClasses = c("character"), sep = delim, fill = TRUE, flush = TRUE, na.strings = "", col.names = 1:max(count.fields(colonyfile$paternities.and.sibships.PATH)))
       flush.console()
       
       #split the file up
@@ -548,7 +548,7 @@
       colonyfile$maternities.and.sibships.PATH = file.choose()
       
       #Read in the data...
-      colonyfile$maternities.and.sibships = read.table(colonyfile$maternities.and.sibships.PATH, header = FALSE, colClasses = c("character"), sep = delim, fill = TRUE, flush = TRUE, na.string = "", col.names = 1:max(count.fields(colonyfile$maternities.and.sibships.PATH)))
+      colonyfile$maternities.and.sibships = read.table(colonyfile$maternities.and.sibships.PATH, header = FALSE, colClasses = c("character"), sep = delim, fill = TRUE, flush = TRUE, na.strings = "", col.names = 1:max(count.fields(colonyfile$maternities.and.sibships.PATH)))
       flush.console()
       
       #split the file up

Modified: pkg/man/get.colony.data.Rd
===================================================================
--- pkg/man/get.colony.data.Rd	2013-01-21 13:45:53 UTC (rev 92)
+++ pkg/man/get.colony.data.Rd	2013-01-21 14:06:49 UTC (rev 93)
@@ -5,12 +5,13 @@
 
 \description{When provided with the directory name, and the name of the *.DAT colony input file, this function creates a list object containing pertinent information from the Colony output files.}
 
-\usage{get.colony.data(datadir, filename)}
+\usage{get.colony.data(datadir, filename, colonyVersion)}
 
 \arguments{
   \item{datadir}{The path to the directory that contains the Colony output files and the *.DAT Colony input file.}
   \item{filename}{Optional. The name of the Colony input file. If this argument is omitted, the command will search for a *.DAT file in the data directory (datadir) and use that as the input file.}
-  \item{colonyVersion}{The version of Colony that was used (default is 2.0, other option is 2.0.3).}}
+  \item{colonyVersion}{The version of Colony that was used (default is 2.0, other option is 2.0.3).}
+  }
 \details{}
 \value{A list, containing data extracted from the Colony output files}