[adegenet-commits] r290 - pkg pkg/R pkg/man pkg/src www/files
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Apr 1 21:15:13 CEST 2009
Author: jombart
Date: 2009-04-01 21:15:13 +0200 (Wed, 01 Apr 2009)
New Revision: 290
Modified:
pkg/ChangeLog
pkg/DESCRIPTION
pkg/R/classes.R
pkg/R/dist.genpop.R
pkg/R/export.R
pkg/R/import.R
pkg/R/monmonier.R
pkg/R/spca.R
pkg/R/spca.rtests.R
pkg/man/HWE.Rd
pkg/man/accessors.Rd
pkg/man/adegenet.package.Rd
pkg/man/as-methods.Rd
pkg/man/as.genind.Rd
pkg/man/as.genpop.Rd
pkg/man/auxil.Rd
pkg/man/chooseCN.Rd
pkg/man/colorplot.Rd
pkg/man/df2genind.Rd
pkg/man/dist.genpop.Rd
pkg/man/export.Rd
pkg/man/fstat.Rd
pkg/man/genind.Rd
pkg/man/genind2genpop.Rd
pkg/man/genpop.Rd
pkg/man/gstat.randtest.Rd
pkg/man/hybridize.Rd
pkg/man/import.Rd
pkg/man/isPoly.Rd
pkg/man/loadingplot.Rd
pkg/man/makefreq.Rd
pkg/man/monmonier.Rd
pkg/man/na.replace.Rd
pkg/man/old2new.Rd
pkg/man/propShared.Rd
pkg/man/propTyped.Rd
pkg/man/read.fstat.Rd
pkg/man/read.genepop.Rd
pkg/man/read.genetix.Rd
pkg/man/read.structure.Rd
pkg/man/repool.Rd
pkg/man/scale.Rd
pkg/man/selpopsize.Rd
pkg/man/seploc.Rd
pkg/man/seppop.Rd
pkg/man/sequences.Rd
pkg/man/sim2pop.Rd
pkg/man/spca.Rd
pkg/man/spca.rtests.Rd
pkg/man/spcaIllus.Rd
pkg/man/truenames.Rd
pkg/man/virClasses.Rd
pkg/src/monmonier-utils.c
pkg/src/sharedAll.c
www/files/worksOnlyInDiploids.txt
Log:
changed to my imperial college email.
Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/ChangeLog 2009-04-01 19:15:13 UTC (rev 290)
@@ -16,6 +16,9 @@
o 'hybridize' can now be used for genotypes having any even degree
of ploidy (e.g. tetraploid genotypes).
+ o the new function 'isPoly' checks which loci are polymorphic, or
+ which alleles contribute to polymorphism.
+
o the new function 'pop' can be used to retrieve and set the pop
slot of genind object.
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/DESCRIPTION 2009-04-01 19:15:13 UTC (rev 290)
@@ -2,8 +2,8 @@
Version: 1.2-3
Date: 2009/04/01
Title: adegenet: a R package for the multivariate analysis of genetic markers.
-Author: Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>, with contributions from Peter Solymos
-Maintainer: Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>
+Author: Thibaut Jombart <t.jombart at imperial.ac.uk>, with contributions from Peter Solymos
+Maintainer: Thibaut Jombart <t.jombart at imperial.ac.uk>
Suggests: ade4, genetics, hierfstat, spdep, tripack, ape
Depends: methods
Description: Classes and functions for genetic data analysis within the multivariate framework.
Modified: pkg/R/classes.R
===================================================================
--- pkg/R/classes.R 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/R/classes.R 2009-04-01 19:15:13 UTC (rev 290)
@@ -2,7 +2,7 @@
# adegenet classes definitions. All classes are S4.
#
# Thibaut Jombart, November 2007
-# jombart at biomserv.univ-lyon1.fr
+# t.jombart at imperial.ac.uk
########################################################################
###############################
Modified: pkg/R/dist.genpop.R
===================================================================
--- pkg/R/dist.genpop.R 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/R/dist.genpop.R 2009-04-01 19:15:13 UTC (rev 290)
@@ -5,7 +5,7 @@
# by Daniel Chessel
#
# Thibaut Jombart
-# jombart at biomserv.univ-lyon1.fr
+# t.jombart at imperial.ac.uk
###################################
Modified: pkg/R/export.R
===================================================================
--- pkg/R/export.R 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/R/export.R 2009-04-01 19:15:13 UTC (rev 290)
@@ -4,7 +4,7 @@
# into other R classes
#
# Thibaut Jombart
-# jombart at biomserv.univ-lyon1.fr
+# t.jombart at imperial.ac.uk
#
############################################
Modified: pkg/R/import.R
===================================================================
--- pkg/R/import.R 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/R/import.R 2009-04-01 19:15:13 UTC (rev 290)
@@ -9,7 +9,7 @@
## .stru (STRUCTURE)
##
## Thibaut Jombart, avril 2006
-## jombart at biomserv.univ-lyon1.fr
+## t.jombart at imperial.ac.uk
##
##################################################################
Modified: pkg/R/monmonier.R
===================================================================
--- pkg/R/monmonier.R 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/R/monmonier.R 2009-04-01 19:15:13 UTC (rev 290)
@@ -1,6 +1,6 @@
# Algorithm to detect boundaries, based on Monmonier's algorithm
# Extended to any connection network
-# Thibaut Jombart 2006-2008 (jombart at biomserv.univ-lyon1.fr)
+# Thibaut Jombart 2006-2008 (t.jombart at imperial.ac.uk)
Modified: pkg/R/spca.R
===================================================================
--- pkg/R/spca.R 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/R/spca.R 2009-04-01 19:15:13 UTC (rev 290)
@@ -7,7 +7,7 @@
# generic functions were derived from
# those of multispati class (ade4)
#
-# T. Jombart (jombart at biomserv.univ-lyon1.fr)
+# T. Jombart (t.jombart at imperial.ac.uk)
# 31 may 2007
##############################################
Modified: pkg/R/spca.rtests.R
===================================================================
--- pkg/R/spca.rtests.R 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/R/spca.rtests.R 2009-04-01 19:15:13 UTC (rev 290)
@@ -3,7 +3,7 @@
# Tests for global and local structures
#
# Thibaut Jombart 2007
-# jombart at biomserv.univ-lyon1.fr
+# t.jombart at imperial.ac.uk
#
########################################
Modified: pkg/man/HWE.Rd
===================================================================
--- pkg/man/HWE.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/HWE.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -50,7 +50,7 @@
}
\seealso{\code{\link[pkg:genetics]{HWE.test}},\code{\link[pkg:stats]{chisq.test}}
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
data(nancycats)
obj <- nancycats
Modified: pkg/man/accessors.Rd
===================================================================
--- pkg/man/accessors.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/accessors.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -60,8 +60,9 @@
\usage{
nLoc(x, \dots)
pop(x)
-locNames(x)
-\S4method{locNames}{genind,genpop}(x, withAlleles=FALSE, \dots)
+locNames(x, \dots)
+\S4method{locNames}{genind}(x, withAlleles=FALSE, \dots)
+\S4method{locNames}{genpop}(x, withAlleles=FALSE, \dots)
}
\arguments{
\item{x}{a \linkS4class{genind} or a \linkS4class{genpop} object.}
@@ -73,7 +74,7 @@
\value{
A \linkS4class{genind} or \linkS4class{genpop} object.
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\details{
The "[" operator can treat elements in the \code{@other} slot as
well. For instance, if \code{obj at other$xy} contains spatial
Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/adegenet.package.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -119,7 +119,7 @@
License: \tab GPL (>=2)
}
}
-\author{Thibaut Jombart <jombart at biomserv.univ-lyon1.fr>\cr
+\author{Thibaut Jombart <t.jombart at imperial.ac.uk>\cr
with contributions of Peter Solymos}
\references{
Jombart T. (2008) adegenet: a R package for the multivariate analysis of genetic markers
Modified: pkg/man/as-methods.Rd
===================================================================
--- pkg/man/as-methods.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/as-methods.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -49,7 +49,7 @@
class and the returned object is of the new class \code{"Class"}.}
}
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr}}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
\examples{
data(microbov)
x <- na.replace(microbov,method="0")
Modified: pkg/man/as.genind.Rd
===================================================================
--- pkg/man/as.genind.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/as.genind.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -46,7 +46,7 @@
\value{
For \code{genind} and \code{as.genind}, a genind object. For \code{is.genind}, a logical.
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr}}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
\seealso{
\code{"\linkS4class{genind}"}, and \code{\link{import2genind}} for
importing from various types of file.
Modified: pkg/man/as.genpop.Rd
===================================================================
--- pkg/man/as.genpop.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/as.genpop.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -37,7 +37,7 @@
\value{
For \code{genpop} and \code{as.genpop}, a genpop object. For \code{is.genpop}, a logical.
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr}}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
\seealso{
\code{"\linkS4class{genpop}"}, and \code{\link{genind2genpop}} for
conversion from a genind to a genpop object.
Modified: pkg/man/auxil.Rd
===================================================================
--- pkg/man/auxil.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/auxil.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -36,7 +36,7 @@
\value{
For \code{.genlab}, a character vector of size "n".
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
\dontrun{
## this opens the adegenet website
Modified: pkg/man/chooseCN.Rd
===================================================================
--- pkg/man/chooseCN.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/chooseCN.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -61,7 +61,7 @@
}
\seealso{\code{\link{spca}}
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
data(nancycats)
if(require(spdep) & require(ade4)){
Modified: pkg/man/colorplot.Rd
===================================================================
--- pkg/man/colorplot.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/colorplot.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -37,7 +37,7 @@
\value{
Invisibly returns the matched call.
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr}}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
\examples{
# a toy example
xy <- expand.grid(1:10,1:10)
Modified: pkg/man/df2genind.Rd
===================================================================
--- pkg/man/df2genind.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/df2genind.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -64,7 +64,7 @@
a matrix of biallelic genotypes for \code{genind2df}}
\seealso{\code{\link{import2genind}}, \code{\link{read.genetix}},
\code{\link{read.fstat}}, \code{\link{read.structure}}}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
df <- data.frame(loc1=c("11","11","12","32"),
loc2=c(NA,"34","55","15"),loc3=c("22","22","21","22"))
Modified: pkg/man/dist.genpop.Rd
===================================================================
--- pkg/man/dist.genpop.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/dist.genpop.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -98,7 +98,7 @@
Legendre P. and Legendre L. (1998) \emph{Numerical Ecology}, Elsevier
Science B.V. 20, pp274--288.\cr
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr}\cr
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}\cr
Former dist.genet code by Daniel Chessel \email{chessel at biomserv.univ-lyon1.fr}\cr
and documentation by Anne B. Dufour \email{dufour at biomserv.univ-lyon1.fr}
}
Modified: pkg/man/export.Rd
===================================================================
--- pkg/man/export.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/export.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -48,7 +48,7 @@
Goudet. http://www2.unil.ch/popgen/softwares/fstat.htm\cr
}
\seealso{\code{\link{import2genind}}}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
if(require(hierfstat)){
Modified: pkg/man/fstat.Rd
===================================================================
--- pkg/man/fstat.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/fstat.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -21,7 +21,7 @@
\seealso{\code{\link[pkg:hierfstat]{varcomp.glob}},
\code{\link{gstat.randtest}}
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
if(require(hierfstat)){
data(nancycats)
Modified: pkg/man/genind.Rd
===================================================================
--- pkg/man/genind.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/genind.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -66,7 +66,7 @@
\code{\link{read.fstat}}, \code{\link{na.replace}}
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
showClass("genind")
Modified: pkg/man/genind2genpop.Rd
===================================================================
--- pkg/man/genind2genpop.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/genind2genpop.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -50,7 +50,7 @@
A genpop object. The component @other in 'x' is passed to the created
genpop object.
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr}}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
\seealso{
\linkS4class{genind}, \linkS4class{genpop}, \code{\link{na.replace}}
}
Modified: pkg/man/genpop.Rd
===================================================================
--- pkg/man/genpop.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/genpop.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -52,7 +52,7 @@
\references{}
\seealso{\code{\link{as.genpop}}, \code{\link{is.genpop}},\code{\link{makefreq}}, \code{\link{genind}}, \code{\link{import2genind}}, \code{\link{read.genetix}}, \code{\link{read.genepop}}, \code{\link{read.fstat}}, \code{\link{na.replace}}
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
obj1 <- import2genind(system.file("files/nancycats.gen",
package="adegenet"))
Modified: pkg/man/gstat.randtest.Rd
===================================================================
--- pkg/man/gstat.randtest.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/gstat.randtest.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -49,7 +49,7 @@
\code{\link[pkg:hierfstat]{test.between}},\code{\link[pkg:ade4]{as.randtest}},
\code{\link{genind2hierfstat}}
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
if(require(hierfstat)){
# here the example of g.stats.glob is taken using gstat.randtest
Modified: pkg/man/hybridize.Rd
===================================================================
--- pkg/man/hybridize.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/hybridize.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -53,7 +53,7 @@
- one row = one genotype (onerowperind will be true)\cr
- missing values coded by "-9" (the software's default)\cr
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
## Let's make some cattle hybrids
##
Modified: pkg/man/import.Rd
===================================================================
--- pkg/man/import.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/import.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -69,7 +69,7 @@
\seealso{\code{\link{import2genind}}, \code{\link{read.genetix}},
\code{\link{read.fstat}}, \code{\link{read.structure}}, \code{\link{read.genepop}}
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
import2genind(system.file("files/nancycats.gtx",
package="adegenet"))
Modified: pkg/man/isPoly.Rd
===================================================================
--- pkg/man/isPoly.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/isPoly.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -24,7 +24,7 @@
\value{
A vector of logicals.
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
data(nancycats)
isPoly(nancycats,by="loc", thres=0.1)
Modified: pkg/man/loadingplot.Rd
===================================================================
--- pkg/man/loadingplot.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/loadingplot.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -50,7 +50,7 @@
- var.idx: the indices of observations above the threshold\cr
- var.values: the values above the threshold\cr
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr}}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
\examples{
x <- runif(20)
names(x) <- letters[1:20]
Modified: pkg/man/makefreq.Rd
===================================================================
--- pkg/man/makefreq.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/makefreq.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -31,7 +31,7 @@
}
\seealso{\code{\link{genpop}}
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
data(microbov)
obj1 <- microbov
Modified: pkg/man/monmonier.Rd
===================================================================
--- pkg/man/monmonier.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/monmonier.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -118,7 +118,7 @@
Manni, F., Guerard, E. and Heyer, E. (2004) Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by "Monmonier's algorithm". \emph{Human Biology}, \bold{76}, 173--190
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr}}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
\seealso{\code{\link{spca}},\code{\link[pkg:spdep]{nb}}}
Modified: pkg/man/na.replace.Rd
===================================================================
--- pkg/man/na.replace.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/na.replace.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -41,7 +41,7 @@
Chi-squared test. This is obtained by the product of the sums of
both margins divided by the total number of alleles.
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
data(nancycats)
Modified: pkg/man/old2new.Rd
===================================================================
--- pkg/man/old2new.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/old2new.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -24,7 +24,7 @@
converted. These are to be coerced into a list and set in the
\code{@other} slot of the new object.
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\keyword{methods}
\keyword{classes}
\keyword{manip}
\ No newline at end of file
Modified: pkg/man/propShared.Rd
===================================================================
--- pkg/man/propShared.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/propShared.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -21,7 +21,7 @@
\value{Returns a matrix of proportions}
\seealso{\code{\link{dist.genpop}}
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
## make a small object
data(microbov)
Modified: pkg/man/propTyped.Rd
===================================================================
--- pkg/man/propTyped.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/propTyped.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -36,7 +36,7 @@
with entities in rows (individuals or populations) and markers in
columns. The values of the matrix are 1 for typed data, and 0 for NA.
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
data(nancycats)
propTyped(nancycats,by="loc")
Modified: pkg/man/read.fstat.Rd
===================================================================
--- pkg/man/read.fstat.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/read.fstat.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -37,7 +37,7 @@
\code{\link{read.genetix}}, \code{\link{read.structure}}, \code{\link{read.genepop}}
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
obj <- read.fstat(system.file("files/nancycats.dat",package="adegenet"))
obj
Modified: pkg/man/read.genepop.Rd
===================================================================
--- pkg/man/read.genepop.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/read.genepop.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -37,7 +37,7 @@
\code{\link{read.fstat}}, \code{\link{read.structure}},
\code{\link{read.genetix}}
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
obj <- read.genepop(system.file("files/nancycats.gen",package="adegenet"))
obj
Modified: pkg/man/read.genetix.Rd
===================================================================
--- pkg/man/read.genetix.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/read.genetix.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -38,7 +38,7 @@
\code{\link{import2genind}}, \code{\link{df2genind}},
\code{\link{read.fstat}}, \code{\link{read.structure}}, \code{\link{read.genepop}}
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
obj <- read.genetix(system.file("files/nancycats.gtx",package="adegenet"))
obj
Modified: pkg/man/read.structure.Rd
===================================================================
--- pkg/man/read.structure.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/read.structure.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -61,7 +61,7 @@
\code{\link{import2genind}}, \code{\link{df2genind}},
\code{\link{read.fstat}}, \code{\link{read.genetix}}, \code{\link{read.genepop}}
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
obj <- read.structure(system.file("files/nancycats.str",package="adegenet"),
onerowperind=FALSE, n.ind=237, n.loc=9, col.lab=1, col.pop=2, ask=FALSE)
Modified: pkg/man/repool.Rd
===================================================================
--- pkg/man/repool.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/repool.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -24,7 +24,7 @@
\value{
A \linkS4class{genind} object.
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\seealso{\code{\link{seploc}}, \code{\link{seppop}}}
\examples{
## use the cattle breeds dataset
Modified: pkg/man/scale.Rd
===================================================================
--- pkg/man/scale.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/scale.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -47,7 +47,7 @@
allele frequency. This can be used to avoid that frequencies close to
0.5 have a stronger variance that those close to 0 or 1.
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
## load data
data(microbov)
Modified: pkg/man/selpopsize.Rd
===================================================================
--- pkg/man/selpopsize.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/selpopsize.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -25,7 +25,7 @@
\value{
A \linkS4class{genind} object.
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\seealso{\code{\link{seploc}}, \code{\link{repool}}}
\examples{
data(microbov)
Modified: pkg/man/seploc.Rd
===================================================================
--- pkg/man/seploc.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/seploc.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -28,7 +28,7 @@
same class as the initial object, or a list of matrices similar to
x\$tab.\cr
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\seealso{\code{\link{seppop}}, \code{\link{repool}}}
\examples{
data(microbov)
Modified: pkg/man/seppop.Rd
===================================================================
--- pkg/man/seppop.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/seppop.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -36,7 +36,7 @@
According to 'rse.type': a list of \linkS4class{genind} object
(default) or a matrix of data corresponding to the 'tab' slots.
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\seealso{\code{\link{seploc}}, \code{\link{repool}}}
\examples{
data(microbov)
Modified: pkg/man/sequences.Rd
===================================================================
--- pkg/man/sequences.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/sequences.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -31,7 +31,7 @@
\code{\link{read.fstat}}, \code{\link{read.structure}},
\code{\link{read.genepop}}, \code{\link[pkg:ape]{DNAbin}}.
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
if(require(ape)){
data(woodmouse)
Modified: pkg/man/sim2pop.Rd
===================================================================
--- pkg/man/sim2pop.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/sim2pop.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -27,7 +27,7 @@
}
\author{
- Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr}
+ Thibaut Jombart \email{t.jombart at imperial.ac.uk}
}
\references{
Balloux F (2001) Easypop (version 1.7): a computer program for oppulation
Modified: pkg/man/spca.Rd
===================================================================
--- pkg/man/spca.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/spca.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -180,7 +180,7 @@
\code{\link[pkg:PBSmapping]{convUL}} to convert longitude/latitude to
UTM coordinates.
}
-\author{ Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
## data(spcaIllus) illustrates the sPCA
## see ?spcaIllus
Modified: pkg/man/spca.rtests.Rd
===================================================================
--- pkg/man/spca.rtests.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/spca.rtests.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -43,7 +43,7 @@
Revealing cryptic spatial patterns in genetic variability by a new
multivariate method. \emph{Heredity}, \bold{101}, 92--103.
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr}}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
\seealso{ \code{\link{chooseCN}}, \code{\link{spca}}, \code{\link{monmonier}}}
\examples{
\dontrun{
Modified: pkg/man/spcaIllus.Rd
===================================================================
--- pkg/man/spcaIllus.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/spcaIllus.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -28,7 +28,7 @@
multivariate method. \emph{Heredity}, \bold{101}, 92--103.
}
\author{
- Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr}
+ Thibaut Jombart \email{t.jombart at imperial.ac.uk}
}
\seealso{ \code{\link{spca}} }
\references{
Modified: pkg/man/truenames.Rd
===================================================================
--- pkg/man/truenames.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/truenames.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -27,7 +27,7 @@
vector with true names (\$pop).\cr
}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\examples{
data(microbov)
microbov
Modified: pkg/man/virClasses.Rd
===================================================================
--- pkg/man/virClasses.Rd 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/man/virClasses.Rd 2009-04-01 19:15:13 UTC (rev 290)
@@ -11,5 +11,5 @@
\title{Virtual classes for adegenet}
\description{These virtual classes are only for internal use in adegenet}
\section{Objects from the Class}{A virtual Class: No objects may be created from it.}
-\author{Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr} }
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
\keyword{classes}
Modified: pkg/src/monmonier-utils.c
===================================================================
--- pkg/src/monmonier-utils.c 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/src/monmonier-utils.c 2009-04-01 19:15:13 UTC (rev 290)
@@ -4,7 +4,7 @@
A part of the code is new and devoted to some monmonier algorithm computations
To compile : R CMD SHLIB monmonier-utils.c
-Thibaut Jombart (jombart at biomserv.univ-lyon1.fr), 2006, to fit his egocentric needs.
+Thibaut Jombart (t.jombart at imperial.ac.uk), 2006, to fit his egocentric needs.
The original copyright follows.
*/
Modified: pkg/src/sharedAll.c
===================================================================
--- pkg/src/sharedAll.c 2009-04-01 18:39:46 UTC (rev 289)
+++ pkg/src/sharedAll.c 2009-04-01 19:15:13 UTC (rev 290)
@@ -8,7 +8,7 @@
- nCol: the number of columns of matAll, i.e. twice the number of loci
- resVec: a vector of length (n(n-1)/2) storing the proportion of shared alleles for each couple of genotypes.
-Thibaut Jombart (jombart at biomserv.univ-lyon1.fr), 2008.
+Thibaut Jombart (t.jombart at imperial.ac.uk), 2008.
*/
#include <stdio.h>
Modified: www/files/worksOnlyInDiploids.txt
===================================================================
--- www/files/worksOnlyInDiploids.txt 2009-04-01 18:39:46 UTC (rev 289)
+++ www/files/worksOnlyInDiploids.txt 2009-04-01 19:15:13 UTC (rev 290)
@@ -2,7 +2,6 @@
- fstat (d)
- gstat.randtest (d)
- HWE.test.genind (d)
-- hybridize (+)
- read.genetix (d)
- read.fstat (d)
- read.genpop (d)
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