An individual-based population genetic simulation environment


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Documentation for package `rmetasim' version 1.0.8

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advance.landscape Code components to simulate a landscape
allelecount.landscape Calculate allele numbers (frequency in the statistical sense) at each locus in each population
allelefreq.landscape Calculate allele frequencies at each locus in each population
carry.landscape Code components to simulate a landscape
clean.landscape Function to resolve inconsistencies within a landscape
compress.landscape Function to resolve inconsistencies within a landscape, deprecated
demography.landscape Calculate demographic parameters
exp.het.landscape Calculate expected heterozygosity
extinct.landscape Code components to simulate a landscape
Fst.landscape Calculates population structure statistic for the entire landscape
FWright.landscape Calculates Wright's Fixation index at each locus in each population
is.landscape Test whether an object is a (fairly) legitimate landscape
island rmetasim landscape containing an island migration structure
landscape.democol return a vector of population IDs from a landscape
landscape.locus return a matrix containing genotypes for a particular locus
landscape.mismatchdist Calculate a mismatch distribution for a locus in a landscape
landscape.states return a matrix containing actual genotypes for a particular locus
landscape.to.rtheta Converts genetic marker data in a landscape into a format suitable for analysis using ANOVA
locusvec Provides convenient summarys of locus characteristics
modify.landscape.epoch Modifies one of the landscape's epochs
new.epoch Create an Epoch
new.epoch.island Create an Island Model Epoch
new.example.landscape Create a Default Landscape
new.floatparam.land Create a set of floating point parameters
new.individuals Fill a landscape with individuals
new.intparam.land Create a set of integer parameters
new.landscape.empty Create a Skeletal Landscape
new.local.demo Create a Local Demography
new.locus Add a locus
new.switchparam.land Create a set of boolean parameters
obs.het.landscape Calculate observed heterozygosity
ploidy Provides convenient summarys of locus characteristics
popstruct Calculates Weir and Cokerham's theta
populations return a vector of population IDs from a landscape
read.landscape Load a landscape from a file
reproduce.landscape Code components to simulate a landscape
sim.landscape Run a simulation for a single landscape through time
states return a matrix containing actual genotypes for a particular locus
survive.landscape Code components to simulate a landscape
theta.h.landscape Calculate theta using heterozygosity
theta.k.landscape Calculate theta using the number of alleles
theta.s.landscape Calculate theta using segregating sites
write.landscape Save a landscape to a file
write.landscape.foreign Save a landscape to a file in a foreign format