HZ: Estimate parameters of the hybrid zone model by MCMC...
In Geneland: Detection of Structure from Multilocus Genetic Data

Description Usage Arguments Value Author(s) References

Estimate parameters of a hybrid zone model by MCMC simulation. The function does not currently accept more than one genotype matrix.

            HZ(coordinates,
               geno.dip.codom=NULL,
               geno.dip.dom=NULL,
               geno.hap=NULL,
               dist.IC=NULL,
               allele.freq=NULL,
               ncluster=NULL,
               cluster.indiv=NULL,
               path.mcmc.noadm=NULL,
               a.init=NULL,
               b.init=NULL,
               c.init=1,
               a.max=10,
               b.max=NULL,
               c.max=1,
               estimate.a=TRUE,
               estimate.b=TRUE,
               estimate.c=FALSE,
               common.param=TRUE,
               nit,
               thinning,
               path.mcmc.adm=NULL)

`coordinates`	Spatial coordinates of individuals. A matrix with 2
`geno.dip.codom`	Genotypes for diploid data with codominant markers. A matrix with one line per individual and two columns per locus.
`geno.dip.dom`	Genotypes for diploid data with dominant markers. A matrix with one line per individual and one column per locus. Presence/absence of a band should be coded as 0/1 (0 for absence / 1 for presence). Dominant and codominant markers can be analyzed jointly by passing variables to arguments geno.dip.codom and geno.dip.dom. Haploid data and diploid dominant data can not be analyzed jointly in the current version.
`geno.hap`	Genotypes of haploid data. A matrix with one line per individual and one column per locus. Dominant diploid data and haploid data can be analyzed jointly (e.g. to analyse microsatelite data or SNP data together with mtDNA. Haploid data and diploid dominant data can not be analyzed jointly in the current version.
`dist.IC`	A matrix with `nindiv` lines and `ncluster` column. The parameter `ncluster` being the number of clusters, most often 2 when there is a single hybrid zone. If `dist.IC` is missing, the user has to provide instead the path to a directory storing results from a no-admixture MCMC run.
`allele.freq`	An array with `ncluster` x `nloc` x `nalmax` If missing, it will be estimated from the output from the MCMC run to estimate clusters.
`ncluster`	Number of clusters. If missing, the user has to provide instead the path to a directory storing results from a no-admixture MCMC run
`cluster.indiv`	Cluster membership of individuals. A numeric vector with integer values (maximum values being the total number of clusters)
`path.mcmc.noadm`	Path to output files directory of the previous Geneland no-admixture run. It seems that the path should be given in the Unix style even under Windows (use \/ instead of \). This path has to end with a slash (\/) (e.g. path.mcmc="/home/me/Geneland-noadmixture/")
`a.init`	A numerical value to use as fixed or initial value for the `a` parameter
`b.init`	A numerical value to use as fixed or initial value for the `b` parameter
`c.init`	A numerical value to use as fixed or initial value for the `c` parameter
`a.max`	Maximum value allowed along MCMC simulation for parameter `a` (default is 1)
`b.max`	Maximum value allowed along MCMC simulation for parameter `b` (default is a small fraction of the study area diameter)
`c.max`	Maximum value allowed along MCMC simulation for parameter `c` (default is 1)
`estimate.a`	Logical. If TRUE, parameter `a` is estimated, if FALSE it is left at the initial value.
`estimate.b`	Logical. If TRUE, parameter `b` is estimated, if FALSE it is left at the initial value.
`estimate.c`	Logical. If TRUE, parameter `c` is estimated, if FALSE it is left at the initial value.
`common.param`	If TRUE, parameters `a`, `b` and `c` are common to all clusters. If FALSE, the program attemps to estimate cluster-specific values.
`nit`	Number of MCMC iteration.
`thinning`	Number of MCMC iterations between two writing steps (if `thinning`=1, all states are saved whereas if e.g. `thinning`=10 only each 10 iteration is saved)
`path.mcmc.adm`	Path to output files directory for the admixture model. It seems that the path should be given in the Unix style even under Windows (use \/ instead of \). This path has to end with a slash (\/) (e.g. path.mcmc="/home/me/Geneland-admixture/")