Usage
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)
Arguments
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/")