[Rflptools-commits] r13 - in pkg/RFLPtools: . R man

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

Author: stamats
Date: 2013-01-03 06:51:10 +0100 (Thu, 03 Jan 2013)
New Revision: 13

Modified:
   pkg/RFLPtools/DESCRIPTION
   pkg/RFLPtools/NAMESPACE
   pkg/RFLPtools/NEWS
   pkg/RFLPtools/R/RFLPdist2.R
   pkg/RFLPtools/R/RFLPplot.R
   pkg/RFLPtools/man/0RFLP-package.Rd
   pkg/RFLPtools/man/RFLPqc.Rd
Log:
added new function RFLPcombine to combine RFLP data sets

Modified: pkg/RFLPtools/DESCRIPTION
===================================================================
--- pkg/RFLPtools/DESCRIPTION	2012-10-26 02:36:17 UTC (rev 12)
+++ pkg/RFLPtools/DESCRIPTION	2013-01-03 05:51:10 UTC (rev 13)
@@ -1,8 +1,8 @@
 Package: RFLPtools
 Type: Package
 Title: Tools to analyse RFLP data
-Version: 1.4
-Date: 2012-10-23
+Version: 1.5
+Date: 2013-01-03
 Author: Fabienne Flessa, Alexandra Kehl, Matthias Kohl
 Maintainer: Matthias Kohl <Matthias.Kohl at stamats.de>
 Description: RFLPtools provides functions to analyse DNA fragment samples 

Modified: pkg/RFLPtools/NAMESPACE
===================================================================
--- pkg/RFLPtools/NAMESPACE	2012-10-26 02:36:17 UTC (rev 12)
+++ pkg/RFLPtools/NAMESPACE	2013-01-03 05:51:10 UTC (rev 13)
@@ -7,6 +7,7 @@
        RFLPplot,
        RFLPdist2ref,
        RFLPrefplot,
+       RFLPcombine,
        nrBands,
        read.blast,
        simMatrix,

Modified: pkg/RFLPtools/NEWS
===================================================================
--- pkg/RFLPtools/NEWS	2012-10-26 02:36:17 UTC (rev 12)
+++ pkg/RFLPtools/NEWS	2013-01-03 05:51:10 UTC (rev 13)
@@ -3,6 +3,12 @@
 ###############################################################################
 
 ###########################################################
+## Version 1.5
+###########################################################
+- new function RFLPcombine to combine RFLP datasets
+
+
+###########################################################
 ## Version 1.4
 ###########################################################
 - correction of some minor bugs
@@ -11,12 +17,14 @@
 - updated affiliations in vignette and added some explanations regarding the 
   use of NCBI BLAST
 - added option "sep" to function "read.blast".
-  
+
+
 ###########################################################
 ## Version 1.3
 ###########################################################
 - added function diffDist for distance matrix computation based on
   successive differences
+
   
 ###########################################################
 ## Version 1.2
@@ -27,6 +35,7 @@
 - in examples now use of simPlot instead of corPlot, hence requires package
   MKmisc version 0.8
 
+  
 ###########################################################
 ## Version 1.1
 ###########################################################
@@ -36,6 +45,7 @@
   which do not occur as query.ids
 - extended vignette and package Rd-file by RFLPplot and RFLPrefplot examples
 
+
 ###########################################################
 ## Version 1.0
 ###########################################################

Modified: pkg/RFLPtools/R/RFLPdist2.R
===================================================================
--- pkg/RFLPtools/R/RFLPdist2.R	2012-10-26 02:36:17 UTC (rev 12)
+++ pkg/RFLPtools/R/RFLPdist2.R	2013-01-03 05:51:10 UTC (rev 13)
@@ -19,7 +19,6 @@
     stopifnot(is.function(distfun))
 
     x1 <- split(x, x$Sample)
-    nrbands <- sort(unique(sapply(x1, nrow)))
     x1.bands <- sapply(x1, nrow)
 
     temp <- do.call("rbind", x1[x1.bands %in% c(nrBands:(nrBands+nrMissing))])

Modified: pkg/RFLPtools/R/RFLPplot.R
===================================================================
--- pkg/RFLPtools/R/RFLPplot.R	2012-10-26 02:36:17 UTC (rev 12)
+++ pkg/RFLPtools/R/RFLPplot.R	2013-01-03 05:51:10 UTC (rev 13)
@@ -15,7 +15,6 @@
         stop("Number of Bands 'nrBands' is missing.")
         
     x1 <- split(x, x$Sample)
-    nrbands <- sort(unique(sapply(x1, nrow)))
     x1.bands <- sapply(x1, nrow)
 
     if(missing(nrMissing)){

Modified: pkg/RFLPtools/man/0RFLP-package.Rd
===================================================================
--- pkg/RFLPtools/man/0RFLP-package.Rd	2012-10-26 02:36:17 UTC (rev 12)
+++ pkg/RFLPtools/man/0RFLP-package.Rd	2013-01-03 05:51:10 UTC (rev 13)
@@ -14,8 +14,8 @@
 \details{
 \tabular{ll}{
 Package: \tab RFLPtools\cr
-Version: \tab 1.4 \cr
-Date: \tab 2012-10-23 \cr
+Version: \tab 1.5 \cr
+Date: \tab 2013-01-03 \cr
 Depends: \tab R(>= 2.10.0), stats, utils, grDevices, RColorBrewer\cr
 Suggests: \tab lattice, MKmisc(>= 0.8)\cr
 License: \tab LGPL-3\cr

Modified: pkg/RFLPtools/man/RFLPqc.Rd
===================================================================
--- pkg/RFLPtools/man/RFLPqc.Rd	2012-10-26 02:36:17 UTC (rev 12)
+++ pkg/RFLPtools/man/RFLPqc.Rd	2013-01-03 05:51:10 UTC (rev 13)
@@ -34,7 +34,7 @@
   If \code{rm.band1 = TRUE} band 1 of all samples is removed and the remaining band 
   numbers are reduced by 1. 
   
-  If \code{QC.rm = TRUE} samples with insufficient quality are entirely removed from the 
+  If \code{QC.rm = TRUE} samples of insufficient quality are entirely removed from the 
   given data and the resulting \code{data.frame} is returned.
 }
 \value{