Displaying 4 results from an estimated 4 matches for "varnpop".
2009 Jan 13
3
problem whit Geneland
...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
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VincenzoLandi
AnimalScience Phd student
...
2010 May 20
1
Geneland error on unix: Error in MCMC(........ :, unused argument(s) (ploidy = 2, genotypes = geno)
...te(read.table(GENO.TABLE))
+ coord<-read.table(XY.TABLE)
+
+ ## Loop for multiple runs
+
+ for(irun in 1:nrun)
+ {
+ ## define path to MCMC directory
+
+ path.mcmc <- paste(path.sp,irun,"/",sep="")
+ dir.create(path.mcmc)
+ MCMC(coordinates=coord, ploidy=2, genotypes=geno, varnpop=T,
npopmax=MAXPOP, npopinit=MINPOP, spatial=T, freq.model="Correlated",
nit=NITS, thinning=500, rate.max=nrow(geno), delta.coord=100,
path.mcmc=path.mcmc)
+ ## MCMC postprocessing
+ PostProcessChain(coordinates=coord,path.mcmc=path.mcmc,genotypes=geno,
nxdom=50,nydom=50,burnin=burnin)...
2010 May 31
0
miss.loc function in MCMC Geneland: can't make it work
...coord<-read.table("path.txt")
geno<-read.table("path.txt")
nullal<-read.table("path.txt")
dim(nullal)
dim(coord)
dim(geno)
plot(coord,xlab="east",ylab="north",asp=1)
MCMC(coordinates=coord,geno.dip.codom=geno,miss.loc=nullal,delta.coord=0,varnpop=TRUE,npopmax=40,spatial=TRUE,freq.model="Uncorrelated",nit=100000,thinning=10,path.mcmc="path_whichever
it is/")
Olivier BAGGIANO
PhD Candidate
Australian Rivers Institute
Griffith School of Environment
Griffith University, Nathan Qld 4111
Work: (07) 3735 5359
--
View th...
2011 Apr 04
0
Multithreading of Geneland
Hi all,
I would like to multithread that script, to detect structure from multilocus genetic data :
>library(Geneland)
>
>geno = read.table("cot966gen_test.txt") #the file is show after
>MCMC(geno.dip.codom = geno, varnpop=T, npopmax=20, spatial = F, nit=100000, thinnin=100, path.mcmc="./")
>PostProcessChain(path.mcmc="./", nxdom=100, nydom=100, burnin=200)
I have an 8 cores computer, and since I have to compute that bit on a thousand of line like that :
209 209 217 217 180 180 154 154 181 18...