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
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