# An Individual-Based Population Genetic Simulation Environment

## Documentation for package ‘rmetasim’ version 3.1.14

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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