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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