[Rflptools-commits] r5 - in pkg/RFLPtools: . R inst/doc man

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

Author: stamats
Date: 2010-06-14 10:24:30 +0200 (Mon, 14 Jun 2010)
New Revision: 5

Added:
   pkg/RFLPtools/R/diffDist.R
   pkg/RFLPtools/man/diffDist.Rd
Modified:
   pkg/RFLPtools/DESCRIPTION
   pkg/RFLPtools/NAMESPACE
   pkg/RFLPtools/NEWS
   pkg/RFLPtools/inst/doc/RFLPtools.pdf
   pkg/RFLPtools/man/0RFLP-package.Rd
Log:
added function diffDist, increased version number to 1.3

Modified: pkg/RFLPtools/DESCRIPTION
===================================================================
--- pkg/RFLPtools/DESCRIPTION	2010-06-09 08:41:28 UTC (rev 4)
+++ pkg/RFLPtools/DESCRIPTION	2010-06-14 08:24:30 UTC (rev 5)
@@ -1,8 +1,8 @@
 Package: RFLPtools
 Type: Package
 Title: Tools to analyse RFLP data
-Version: 1.2
-Date: 2010-06-09
+Version: 1.3
+Date: 2010-06-14
 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	2010-06-09 08:41:28 UTC (rev 4)
+++ pkg/RFLPtools/NAMESPACE	2010-06-14 08:24:30 UTC (rev 5)
@@ -1,4 +1,5 @@
 export(read.rflp,
+       diffDist,
        RFLPqc,
        RFLPdist,
        RFLPdist2,

Modified: pkg/RFLPtools/NEWS
===================================================================
--- pkg/RFLPtools/NEWS	2010-06-09 08:41:28 UTC (rev 4)
+++ pkg/RFLPtools/NEWS	2010-06-14 08:24:30 UTC (rev 5)
@@ -24,3 +24,8 @@
 - added reference to recent article
 - in examples now use of simPlot instead of corPlot, hence requires package
   MKmisc version 0.8
+
+###########################################################
+## Version 1.3
+###########################################################
+- added function diffDist
\ No newline at end of file

Added: pkg/RFLPtools/R/diffDist.R
===================================================================
--- pkg/RFLPtools/R/diffDist.R	                        (rev 0)
+++ pkg/RFLPtools/R/diffDist.R	2010-06-14 08:24:30 UTC (rev 5)
@@ -0,0 +1,4 @@
+diffDist <- function(x, method = "euclidean", diag = FALSE, upper = FALSE, p = 2){ 
+    x.diff <- t(diff(t(x))) 
+    dist(x.diff, method = method, diag = diag, upper = upper, p = p) 
+}

Modified: pkg/RFLPtools/inst/doc/RFLPtools.pdf
===================================================================
(Binary files differ)

Modified: pkg/RFLPtools/man/0RFLP-package.Rd
===================================================================
--- pkg/RFLPtools/man/0RFLP-package.Rd	2010-06-09 08:41:28 UTC (rev 4)
+++ pkg/RFLPtools/man/0RFLP-package.Rd	2010-06-14 08:24:30 UTC (rev 5)
@@ -14,8 +14,8 @@
 \details{
 \tabular{ll}{
 Package: \tab RFLPtools\cr
-Version: \tab 1.2 \cr
-Date: \tab 2010-06-09 \cr
+Version: \tab 1.3 \cr
+Date: \tab 2010-06-14 \cr
 Depends: \tab R(>= 2.10.0), stats, utils, grDevices, RColorBrewer\cr
 Suggests: \tab lattice, MKmisc(>= 0.8)\cr
 License: \tab LGPL-3\cr

Added: pkg/RFLPtools/man/diffDist.Rd
===================================================================
--- pkg/RFLPtools/man/diffDist.Rd	                        (rev 0)
+++ pkg/RFLPtools/man/diffDist.Rd	2010-06-14 08:24:30 UTC (rev 5)
@@ -0,0 +1,52 @@
+\name{diffDist}
+\alias{diffDist}
+\title{ Distance Matrix Computation }
+\description{
+  This function computes and returns the distance matrix computed by
+  using the specified distance measure to compute the distances between
+  the rows of a data matrix. Instead of the row values as in the case of 
+  \code{\link[stats]{dist}}, the successive differences of the row values
+  are used.
+}
+\usage{
+diffDist(x, method = "euclidean", diag = FALSE, upper = FALSE, p = 2)
+}
+\arguments{
+  \item{x}{a numeric matrix, data frame or \code{"dist"} object.}
+  \item{method}{the distance measure to be used. This must be one of
+    \code{"euclidean"}, \code{"maximum"}, \code{"manhattan"},
+    \code{"canberra"}, \code{"binary"} or \code{"minkowski"}.
+    Any unambiguous substring can be given.}
+  \item{diag}{logical value indicating whether the diagonal of the
+    distance matrix should be printed by \code{print.dist}.}
+  \item{upper}{logical value indicating whether the upper triangle of the
+    distance matrix should be printed by \code{print.dist}.}
+  \item{p}{The power of the Minkowski distance.}
+}
+\details{
+  This function computes and returns the distance matrix computed by
+  using the specified distance measure to compute the distances between
+  the rows of a data matrix. Instead of the row values as in the case of 
+  \code{\link[stats]{dist}}, the successive differences of the row values
+  are used.
+  
+  It's a simple wrapper function arround \code{\link[stats]{dist}}. For
+  more details about the distances we refer to \code{\link[stats]{dist}}.
+  
+  The function may be helpful, if there is a shift w.r.t.\ the measured
+  bands; e.g.\ \code{c(550, 500, 300, 250)} vs.\ \code{c(510, 460, 260, 210)}.
+}
+\value{
+  \code{diffDist} returns an object of class \code{"dist"}; cf. \code{\link[stats]{dist}}.
+}
+%\references{}
+\author{ Matthias Kohl \email{Matthias.Kohl at stamats.de}}
+%\note{}
+\examples{
+## assume a shift in the measured bands
+M <- rbind(c(550, 500, 300, 250), c(510, 460, 260, 210),
+           c(550, 500, 300, 200))
+dist(M)
+diffDist(M)
+}
+\keyword{multivariate}