
I am trying to use the function 'filter.NA=TRUE' in Geneland. The function 
appears to be set on TRUE by default, as it appears as TRUE in the 
'parameter.txt'  file output and hence I do not need to enter the function 
per se (as it is an 'Unused argument otherwise') . Hence all my missing 
data (individuals that I have not yet scored at that specific loci) are 
scored as double null  alleles, this even though I use the default setting 
NA in my 'score matrix'.  I am therefore trying to enter a matrix of  103 
x 9 (103 individual x 9loci) with 0 for real alleles (null or not) and 1 
for non scored alleles called upon using the miss.loc function in MCMC, in 
addition to the 'genotype' and 'coordinate' matrices.  However when 
starting the MCMC, after initialisation of all functions I get this 
message:


list (object) can not be coerced into integer


And the MCMC is stopped. I only get this message when entering the 'null 
allele' matrix and using the miss.loc function in the MCMC.

Any idea what this is about? Here is the command I enter:


library(Geneland)
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 


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