[adegenet-commits] r938 - in pkg: . R inst/doc man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jul 4 16:54:20 CEST 2011
Author: jombart
Date: 2011-07-04 16:54:20 +0200 (Mon, 04 Jul 2011)
New Revision: 938
Removed:
pkg/inst/doc/.RData
Modified:
pkg/DESCRIPTION
pkg/R/haploGen.R
pkg/R/zzz.R
pkg/man/adegenet.package.Rd
pkg/man/haploGen.Rd
pkg/man/seqTrack.Rd
Log:
Moved to 1.3-1
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2011-06-29 16:03:22 UTC (rev 937)
+++ pkg/DESCRIPTION 2011-07-04 14:54:20 UTC (rev 938)
@@ -1,6 +1,6 @@
Package: adegenet
-Version: 1.3-0
-Date: 2011/06/22
+Version: 1.3-1
+Date: 2011/06/30
Title: adegenet: a R package for the multivariate analysis of genetic markers.
Author: Thibaut Jombart <t.jombart at imperial.ac.uk>
with contributions of: Ismail Ahmed, Peter Solymos
Modified: pkg/R/haploGen.R
===================================================================
--- pkg/R/haploGen.R 2011-06-29 16:03:22 UTC (rev 937)
+++ pkg/R/haploGen.R 2011-07-04 14:54:20 UTC (rev 938)
@@ -567,28 +567,28 @@
##########################
## as("haploGen", "graphNEL")
##########################
-if(require(graph)){
- setOldClass("haploGen")
+## if(require(graph)){
+## setOldClass("haploGen")
- setAs("haploGen", "graphNEL", def=function(from){
- if(!require(ape)) stop("package ape is required")
- if(!require(graph)) stop("package graph is required")
+## setAs("haploGen", "graphNEL", def=function(from){
+## if(!require(ape)) stop("package ape is required")
+## if(!require(graph)) stop("package graph is required")
- N <- length(from$ances)
- areNA <- is.na(from$ances)
+## N <- length(from$ances)
+## areNA <- is.na(from$ances)
- ## EXTRACT WEIGHTS (nb of mutations)
- M <- as.matrix(dist.dna(from$seq, model="raw")*ncol(from$seq))
- rownames(M) <- colnames(M) <- from$id
- w <- mapply(function(i,j) {M[i, j]}, i=from$ances[!areNA], j=from$id[!areNA])
+## ## EXTRACT WEIGHTS (nb of mutations)
+## M <- as.matrix(dist.dna(from$seq, model="raw")*ncol(from$seq))
+## rownames(M) <- colnames(M) <- from$id
+## w <- mapply(function(i,j) {M[i, j]}, i=from$ances[!areNA], j=from$id[!areNA])
- ## CONVERT TO GRAPH
- res <- ftM2graphNEL(ft=cbind(from$ances[!areNA], from$id[!areNA]), W=w, edgemode = "directed", V=from$id)
- return(res)
- })
+## ## CONVERT TO GRAPH
+## res <- ftM2graphNEL(ft=cbind(from$ances[!areNA], from$id[!areNA]), W=w, edgemode = "directed", V=from$id)
+## return(res)
+## })
-}
+## }
Modified: pkg/R/zzz.R
===================================================================
--- pkg/R/zzz.R 2011-06-29 16:03:22 UTC (rev 937)
+++ pkg/R/zzz.R 2011-07-04 14:54:20 UTC (rev 938)
@@ -2,7 +2,7 @@
#.initAdegenetClasses()
#.initAdegenetUtils()
library.dynam("adegenet", pkg, lib)
- startup.txt <- " ==========================\n adegenet 1.3-0 is loaded\n ==========================\n\n - to start, type '?adegenet'\n - to browse adegenet website, type 'adegenetWeb()'\n - to post questions/comments: adegenet-forum at lists.r-forge.r-project.org\n\n"
+ startup.txt <- " ==========================\n adegenet 1.3-1 is loaded\n ==========================\n\n - to start, type '?adegenet'\n - to browse adegenet website, type 'adegenetWeb()'\n - to post questions/comments: adegenet-forum at lists.r-forge.r-project.org\n\n"
packageStartupMessage(startup.txt)
}
Deleted: pkg/inst/doc/.RData
===================================================================
(Binary files differ)
Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd 2011-06-29 16:03:22 UTC (rev 937)
+++ pkg/man/adegenet.package.Rd 2011-07-04 14:54:20 UTC (rev 938)
@@ -187,8 +187,8 @@
\tabular{ll}{
Package: \tab adegenet\cr
Type: \tab Package\cr
- Version: \tab 1.3-0\cr
- Date: \tab 2011-06-22 \cr
+ Version: \tab 1.3-1\cr
+ Date: \tab 2011-06-30 \cr
License: \tab GPL (>=2)
}
}
Modified: pkg/man/haploGen.Rd
===================================================================
--- pkg/man/haploGen.Rd 2011-06-29 16:03:22 UTC (rev 937)
+++ pkg/man/haploGen.Rd 2011-07-04 14:54:20 UTC (rev 938)
@@ -12,8 +12,8 @@
\alias{plotHaploGen}
\alias{sample.haploGen}
%\alias{as,haploGen,graphNEL-method}
-\alias{coerce,haploGen,graphNEL-method}
-\alias{as,haploGen,graphNEL-method}
+%\alias{coerce,haploGen,graphNEL-method}
+%\alias{as,haploGen,graphNEL-method}
\title{Simulation of genealogies of haplotypes}
\description{
The function \code{haploGen} implements simulations of genealogies of
@@ -48,7 +48,7 @@
as.seqTrack.haploGen(x)
plotHaploGen(x, annot=FALSE, date.range=NULL, col=NULL, bg="grey", add=FALSE, \dots)
sample.haploGen(x, n)
-\S4method{coerce}{haploGen,graphNEL}(from, to, strict=TRUE)
+%\S4method{coerce}{haploGen,graphNEL}(from, to, strict=TRUE)
}
\arguments{
\item{seq.length}{an integer indicating the length of the simulated
@@ -100,14 +100,14 @@
\item{annot,date.range,col,bg,add}{arguments to be passed to \code{\link{plotSeqTrack}}.}
\item{n}{an integer indicating the number of haplotypes to be retained
in the sample}
- \item{from, to}{arguments of the conversion function, for converting a
- \code{haploGen} object into a \code{graphNEL-class}.}
+ % \item{from, to}{arguments of the conversion function, for converting a
+ % \code{haploGen} object into a \code{graphNEL-class}.}
\item{tz, origin}{ aguments to be passed to \code{\link{as.POSIXct}}
(see ?as.POSIXct)}
\item{\dots}{further arguments to be passed to other methods}
- \item{strict}{a logical used for compatibility with \code{as} generic
- function, but not used in the conversion. See \code{\link{setAs}} for
- more information.}
+ % \item{strict}{a logical used for compatibility with \code{as} generic
+ % function, but not used in the conversion. See \code{\link{setAs}} for
+ % more information.}
}
\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
\references{
@@ -152,14 +152,15 @@
See the respective vignettes for more information on using these packages.
- === Converting haploGen objects to graphs ===\cr
- \code{haploGen} objects can be converted to \code{graphNEL-class}
- objects, which can in turn be plotted and manipulated using classical
- graph tools. Simply use 'as(x, "graphNEL")' where 'x' is a
- \code{haploGen} object. This functionality requires the \code{graph}
- package (see 'details').
+ % === Converting haploGen objects to graphs ===\cr
+ % \code{haploGen} objects can be converted to \code{graphNEL-class}
+ % objects, which can in turn be plotted and manipulated using classical
+ % graph tools. Simply use 'as(x, "graphNEL")' where 'x' is a
+ % \code{haploGen} object. This functionality requires the \code{graph}
+ % package (see 'details').
}
\examples{
+\dontrun{
if(require(ape)){
## PERFORM SIMULATIONS
x <- haploGen(repro=2)
@@ -169,17 +170,17 @@
plotHaploGen(x, bg="white")
title("Spatial dispersion of the haplotypes")
-## PLOT GENEALOGY
-if(require(graph) & require(Rgraphviz)){
-g=as(x, "graphNEL")
-g
-renderGraph(layoutGraph(g))
-}
+% ## PLOT GENEALOGY
+% if(require(graph) & require(Rgraphviz)){
+% g=as(x, "graphNEL")
+% g
+% renderGraph(layoutGraph(g))
+% }
## USE SEQTRACK RECONSTRUCTION
x.recons <- seqTrack(x)
mean(x.recons$ances==x$ances, na.rm=TRUE) # proportion of correct reconstructions
-
}
}
+}
Modified: pkg/man/seqTrack.Rd
===================================================================
--- pkg/man/seqTrack.Rd 2011-06-29 16:03:22 UTC (rev 937)
+++ pkg/man/seqTrack.Rd 2011-07-04 14:54:20 UTC (rev 938)
@@ -6,8 +6,8 @@
\alias{get.likelihood}
\alias{get.likelihood.seqTrack}
\alias{seqTrack-class}
-\alias{as,seqTrack,graphNEL-method}
-\alias{coerce,seqTrack,graphNEL-method}
+%\alias{as,seqTrack,graphNEL-method}
+%\alias{coerce,seqTrack,graphNEL-method}
\title{SeqTrack algorithm for reconstructing genealogies}
\description{
The SeqTrack algorithm [1] aims at reconstructing genealogies of sampled
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