An Individual-Based Population Genetic Simulation Environment


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Documentation for package ‘rmetasim’ version 3.1.14

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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.compress Function to resolve inconsistencies within a landscape, deprecated
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.freq.locnames Return a vector of locus IDs concatenated to Allele ids
landscape.Fst Calculates population structure statistic for the entire landscape
landscape.ind.freq Return a matrix containing genotypes in 'frequency per individual' format
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.make.genind Converts genetic marker data in a landscape into a the genind format from adegenet
landscape.make.genpop Converts genetic marker data in a landscape into a the genpop format from adegenet
landscape.mig.matrix Creates a Migration Matrix for All Life Stages
landscape.mismatchdist Calculate a mismatch distribution for a locus in 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.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.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.setallelefreq Set Allele frequencies in (a) specific stage(s)
landscape.setpopfreq Set Allele frequencies in (a) specific population(s)
landscape.simulate Run a simulation for a single landscape through time
landscape.states return a matrix containing actual genotypes for a particular locus
landscape.survive Code components to simulate a landscape
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.write.foreign Save a landscape to a file in a foreign format