An individual-based population genetic simulation environment


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Documentation for package `rmetasim' version 1.1.02

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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.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.Fst Calculates population structure statistic for the entire 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.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.read Load a landscape from a file
landscape.reproduce Code components to simulate a landscape
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.to.rtheta Converts genetic marker data in a landscape into a format suitable for analysis using ANOVA
landscape.write Save a landscape to a file
landscape.write.foreign Save a landscape to a file in a foreign format