HZ: HZ

In gilles-guillot/Geneland: Clustering of living organisms from geo-referenced genetic and/or morphometrics data

Description

Estimate parameters of a hybrid zone model by MCMC simulation. The function does not currently accept more than one genotype matrix. @param coordinates Spatial coordinates of individuals. A matrix with 2

@param geno.dip.codom Genotypes for diploid data with codominant markers. A matrix with one line per individual and two columns per locus.

@param 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.

@param 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.

@param 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.

@param 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.

@param 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

@param cluster.indiv Cluster membership of individuals. A numeric vector with integer values (maximum values being the total number of clusters)

@param 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/")

@param a.init A numerical value to use as fixed or initial value for the a parameter

@param b.init A numerical value to use as fixed or initial value for the b parameter

@param c.init A numerical value to use as fixed or initial value for the c parameter

@param a.max Maximum value allowed along MCMC simulation for parameter a (default is 1)

@param b.max Maximum value allowed along MCMC simulation for parameter b (default is a small fraction of the study area diameter)

@param c.max Maximum value allowed along MCMC simulation for parameter c (default is 1

@param estimate.a Logical. If TRUE, parameter a is estimated, if FALSE it is left at the initial value.

@param estimate.b Logical. If TRUE, parameter b is estimated, if FALSE it is left at the initial value.

@param estimate.c Logical. If TRUE, parameter c is estimated, if FALSE it is left at the initial value.

@param common.param If TRUE, parameters a, b and c are common to all clusters. If FALSE, the program attemps to estimate cluster-specific values.

@param nit Number of MCMC iteration.

@param 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)

@param 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/")

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
)

Value

No object is returned. All outputs are stored in ascii file located in the path.mcmc directory

gilles-guillot/Geneland documentation built on Feb. 24, 2020, 11:44 a.m.