I do the these passages:
library(Geneland)
set.seed(1)
data <- simdata(nindiv=200,
coord.lim=c(0,1,0,1) ,
number.nuclei=5 ,
allele.numbers=rep(10,20),
IBD=FALSE,
npop=2,
give.tess.grid=FALSE)
geno <- data$genotypes
coord <- t(data$coord.indiv)
path.mcmc <- paste(tempdir(),"/",sep="")
set.seed(1)
mcmcFmodel(coordinates=coord,
genotypes=geno,
path.mcmc=path.mcmc,
rate.max=10,
delta.coord=0,
npopmin=1,
npopinit=5,
npopmax=5,
nb.nuclei.max=50,
nit=500,
thinning=1,
freq.model="Dirichlet",
varnpop=FALSE,
spatial=TRUE)
But at the end R say to me that do had found the function
"mcmcFmodel".
Any sugestion?
thanks
**********************************************************
**********************************************************
VincenzoLandi
AnimalScience Phd student
Faculty of Agricolture
Universityof Perugia (Italy).
Departamentof Genetica
Campus deRabanales
Universidadde Cordoba
Cordoba(Spain)
Contacts:
cell phone: +39 3395388713
Skype: vincenzozoot
Italy: +39 0755857109
Spain:+34 957218706
[[alternative HTML version deleted]]
Vincenzo, there is no function 'mcmcFmodel' in Geneland. Perhaps you intend to use 'MCMC'? See ?MCMC for a proper use. Additionally you might profit from reading the Geneland Manual on http://folk.uio.no/gillesg/Geneland/Geneland.html HTH Christoph ________________________________________________________ Christoph Heibl Systematic Botany Ludwig-Maximilians-Universit?t M?nchen Menzinger Str. 67 D-80638 M?nchen GERMANY phone: +49-(0)89-17861-251 e-mail: heibl at lmu.de http://www.christophheibl.de/ch-home.html SAVE PAPER - THINK BEFORE YOU PRINT On Jan 13, 2009, at 11:20 AM, Vincenzo Landi wrote:> I do the these passages: > library(Geneland) > > set.seed(1) > > data <- simdata(nindiv=200, > coord.lim=c(0,1,0,1) , > number.nuclei=5 , > allele.numbers=rep(10,20), > IBD=FALSE, > npop=2, > give.tess.grid=FALSE) > > geno <- data$genotypes > coord <- t(data$coord.indiv) > > path.mcmc <- paste(tempdir(),"/",sep="") > > set.seed(1) > mcmcFmodel(coordinates=coord, > genotypes=geno, > path.mcmc=path.mcmc, > rate.max=10, > delta.coord=0, > npopmin=1, > npopinit=5, > npopmax=5, > nb.nuclei.max=50, > nit=500, > thinning=1, > freq.model="Dirichlet", > varnpop=FALSE, > > spatial=TRUE) > But at the end R say to me that do had found the function > "mcmcFmodel". > Any sugestion? > thanks > > ********************************************************** > ********************************************************** > VincenzoLandi > AnimalScience Phd student > > Faculty of Agricolture > Universityof Perugia (Italy). > > Departamentof Genetica > Campus deRabanales > Universidadde Cordoba > Cordoba(Spain) > > Contacts: > > cell phone: +39 3395388713 > Skype: vincenzozoot > Italy: +39 0755857109 > Spain:+34 957218706 > > > > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code.
help.search did not offer any clues. Using Baron's search page, I got reference to r-help entries from 2004, but looking at the current documentation , I see no such function. I am wondering if the name of the function was changed in later versions of the package and you are mixing old documentation or examples with a newer installation of that package? Here is a 2005 version of the package documentation and it does have that function: http://phase.hpcc.jp/mirrors/stat/R/CRAN/doc/packages/Geneland.pdf Perhaps you want the MCMC function? Description Markov Chain Monte-Carlo inference under various models Usage MCMC( coordinates=NULL, genotypes,## ploidy=2, dominance="Codominant", allele.numbers, path.mcmc, # path to output directory # hyper-prior parameters rate.max,delta.coord=0,shape1=2,shape2=20, npopmin=1,npopinit,npopmax, # dimensions nb.nuclei.max, # options in mcmc computations nit,thinning=1,freq.model="Uncorrelated", varnpop=TRUE, spatial=TRUE, jcf=TRUE, filter.null.alleles=TRUE, prop.update.cell=0.1, write.rate.Poisson.process=FALSE, write.number.nuclei=TRUE, write.number.pop=TRUE, write.coord.nuclei=TRUE, write.color.nuclei=TRUE, write.freq=TRUE, write.ancestral.freq=TRUE, write.drifts=TRUE, write.logposterior=TRUE, write.loglikelihood=TRUE, write.true.coord=TRUE, write.size.pop=FALSE, miss.loc) -- David Winsemius On Jan 13, 2009, at 5:20 AM, Vincenzo Landi wrote:> I do the these passages: > library(Geneland) > > set.seed(1) > > data <- simdata(nindiv=200, > coord.lim=c(0,1,0,1) , > number.nuclei=5 , > allele.numbers=rep(10,20), > IBD=FALSE, > npop=2, > give.tess.grid=FALSE) > > geno <- data$genotypes > coord <- t(data$coord.indiv) > > path.mcmc <- paste(tempdir(),"/",sep="") > > set.seed(1) > mcmcFmodel(coordinates=coord, > genotypes=geno, > path.mcmc=path.mcmc, > rate.max=10, > delta.coord=0, > npopmin=1, > npopinit=5, > npopmax=5, > nb.nuclei.max=50, > nit=500, > thinning=1, > freq.model="Dirichlet", > varnpop=FALSE, > > spatial=TRUE) > But at the end R say to me that do had found the function > "mcmcFmodel". > Any sugestion? > thanks > > ********************************************************** > ********************************************************** > VincenzoLandi > AnimalScience Phd student > > Faculty of Agricolture > Universityof Perugia (Italy). > > Departamentof Genetica > Campus deRabanales > Universidadde Cordoba > Cordoba(Spain) > > Contacts: > > cell phone: +39 3395388713 > Skype: vincenzozoot > Italy: +39 0755857109 > Spain:+34 957218706 > > > > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
David Winsemius wrote:> help.search did not offer any clues. Using Baron's search page, I got reference to r-help entries from 2004, but looking at the current documentation , I see no such function. I am wondering if the name of the function was changed in later versions of the package and you are mixing old documentation or examples with a newer installation of that package? > > Here is a 2005 version of the package documentation and it does have that function: > http://phase.hpcc.jp/mirrors/stat/R/CRAN/doc/packages/Geneland.pdf > > Perhaps you want the MCMC function? > > Description > Markov Chain Monte-Carlo inference under various models > > Usage > MCMC( coordinates=NULL, genotypes,## ploidy=2, dominance="Codominant", > allele.numbers, > path.mcmc, # path to output directory > # hyper-prior parameters > rate.max,delta.coord=0,shape1=2,shape2=20, npopmin=1,npopinit,npopmax, > # dimensions > nb.nuclei.max, > # options in mcmc computations > nit,thinning=1,freq.model="Uncorrelated", varnpop=TRUE, spatial=TRUE, jcf=TRUE, filter.null.alleles=TRUE, prop.update.cell=0.1, write.rate.Poisson.process=FALSE, write.number.nuclei=TRUE, write.number.pop=TRUE, write.coord.nuclei=TRUE, write.color.nuclei=TRUE, write.freq=TRUE, write.ancestral.freq=TRUE, write.drifts=TRUE, write.logposterior=TRUE, write.loglikelihood=TRUE, write.true.coord=TRUE, write.size.pop=FALSE, miss.loc)Hello, You might reach a broader range of Geneland users by sending your post to R-sig-genetics: https://stat.ethz.ch/mailman/listinfo/r-sig-genetics Cheers, Thibaut. -- ###################################### Dr Thibaut JOMBART MRC Centre for Outbreak Analysis and Modelling Department of Infectious Disease Epidemiology Imperial College - Faculty of Medicine St Mary’s Campus Norfolk Place London W2 1PG United Kingdom Tel. : 0044 (0)20 7594 3658 jombart@biomserv.univ-lyon1.fr http://biomserv.univ-lyon1.fr/%7Ejombart/ http://adegenet.r-forge.r-project.org/ [[alternative HTML version deleted]]
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