problem whit Geneland

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

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.