Spatially explicit population genetic simulations


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Documentation for package ‘kernelPop’ version 0.9.09

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is.landscape Test whether an object is a (fairly) legitimate landscape
landscape.advance Code components to simulate a landscape
landscape.allelecount Calculate allele numbers (frequency in the statistical sense) at each locus in each population
landscape.allelefreq Calculate allele frequencies at each locus in each population
landscape.amova calcuates phi-st for every locus in the landscape
landscape.amova.locus uses functions in ade4 to calcuate phi-st for a particular locus
landscape.amova.pairwise calculates pairwise phi-ST for a landscape
landscape.carry Code components to simulate a landscape
landscape.clean Function to resolve inconsistencies within a landscape
landscape.coalinput Add loci and individuals based upon output from SimCoal 2.0
landscape.democol return largest demographic column from a landscape
landscape.demography Calculate demographic parameters
landscape.exp.het Calculate expected heterozygosity
landscape.extinct Code components to simulate a landscape
landscape.Fst Calculates population structure statistic for the entire landscape
landscape.FWright Calculates Wright's Fixation index at each locus in each population
landscape.genepop.output writes genepop files based on the genotypes of individuals in a landscape
landscape.generate.locations generates randomly located and sized, non-overlapping habitat patches on the landscape
landscape.locus return a matrix containing genotypes for a particular locus
landscape.locus.states return a matrix containing actual allelic states and their indices
landscape.locusvec return a vector with the locus ids for each column in the individuals component of a landscape
landscape.modify.epoch Modifies one of the landscape's epochs
landscape.new.empty Create a Skeletal Landscape
landscape.new.epoch Create an Epoch
landscape.new.example Create a Default Landscape
landscape.new.expression don't use
landscape.new.floatparam Create a set of floating point parameters
landscape.new.individuals Fill a landscape with individuals
landscape.new.intparam Create a set of integer parameters
landscape.new.local.demo Create a Local Demography
landscape.new.locus Add a locus
landscape.new.switchparam Create a set of boolean parameters
landscape.obs.het Calculate observed heterozygosity
landscape.ploidy return a vector with the ploidy of each locus
landscape.plot.locations plots the locations of all habitats and individuals
landscape.pollen.kernel.demo takes parameters that define a pollen kernel and plots the results of simulating that kernel
landscape.populations return a vector of population IDs from a landscape
landscape.reproduce Code components to simulate a landscape
landscape.sample simulates sampling for genetics on the landscape
landscape.simulate Run a simulation for a single landscape through time
landscape.states return a list object containing actual allele states and their associated indices for a particular locus
landscape.survive Code components to simulate a landscape
landscape.test.function tests whatever c code is compiled in
landscape.theta.h Calculate theta using heterozygosity
landscape.theta.k Calculate theta using the number of alleles
landscape.theta.s Calculate theta using segregating sites
landscape.to.rtheta Converts genetic marker data in a landscape into a format suitable for analysis using ANOVA
landscape.write.fdist writes a landscapes allele frequencies to an FDIST file
landscape.write.foreign Save a landscape to a file in a foreign format