Man pages for rmetasim
An Individual-Based Population Genetic Simulation Environment
| is.landscape | Test whether an object is a (fairly) legitimate landscape |
| landscape.allelecount | Calculate allele numbers (frequency in the statistical sense)... |
| 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... |
| landscape.amova.pairwise | calculates pairwise phi-ST for 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,... |
| landscape.democol | return largest demographic column from a landscape |
| landscape.demography | Calculate demographic parameters |
| landscape.exp.het | Calculate expected heterozygosity |
| landscape.freq.locnames | Return a vector of locus IDs concatenated to Allele ids |
| landscape.Fst | Calculates population structure statistic for the entire... |
| landscape.ind.freq | Return a matrix containing genotypes in 'frequency per... |
| landscape.locus | return a matrix containing genotypes for a particular locus |
| landscape.locus.states | return a matrix containing actual allelic states and their... |
| landscape.locusvec | return a vector with the locus ids for each column in the... |
| landscape.make.genind | Converts genetic marker data in a landscape into a the genind... |
| landscape.make.genpop | Converts genetic marker data in a landscape into a the genpop... |
| 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.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... |
| 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 |
| SimulationComponents | Code components to simulate a landscape |
