rmetasim: An Individual-Based Population Genetic Simulation Environment

An interface between R and the metasim simulation engine. The simulation environment is documented in: "Strand, A.(2002) <DOI:10.1046/j.1471-8286.2002.00208.x> Metasim 1.0: an individual-based environment for simulating population genetics of complex population dynamics. Mol. Ecol. Notes. Please see the vignettes CreatingLandscapes and Simulating to get some ideas on how to use the packages. See the rmetasim vignette to get an overview and to see important changes to the code in the most recent version.

Author
Allan Strand <stranda@cofc.edu>, James Niehaus
Date of publication
2016-04-09 09:39:14
Maintainer
Allan Strand <stranda@cofc.edu>
License
GPL
Version
3.0.5

View on CRAN

Man pages

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.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

Files in this package

rmetasim
rmetasim/inst
rmetasim/inst/doc
rmetasim/inst/doc/rmetasim.html
rmetasim/inst/doc/CreatingLandscapes.html
rmetasim/inst/doc/Simulating.html
rmetasim/inst/doc/rmetasim.Rmd
rmetasim/inst/doc/CreatingLandscapes.R
rmetasim/inst/doc/Simulating.R
rmetasim/inst/doc/island.R
rmetasim/inst/doc/CreatingLandscapes.Rmd
rmetasim/inst/doc/Simulating.Rmd
rmetasim/src
rmetasim/src/Makevars
rmetasim/src/metasim.h
rmetasim/src/RandLib.cc
rmetasim/src/AlleleObj.h
rmetasim/src/FastSeqAllele.h
rmetasim/src/utilities.h
rmetasim/src/Landscape.cc
rmetasim/src/AlleleObj.cc
rmetasim/src/rmetasim.h
rmetasim/src/Eigen.cc
rmetasim/src/SiteObj.cc
rmetasim/src/TransMat.h
rmetasim/src/AlleleTbl.h
rmetasim/src/TransMat.cc
rmetasim/src/BaseObj.cc
rmetasim/src/Genotype.cc
rmetasim/src/FastAllele.cc
rmetasim/src/rmetasim.cc
rmetasim/src/Genotype.h
rmetasim/src/Landscape.h
rmetasim/src/FastAllele.h
rmetasim/src/Democlass.cc
rmetasim/src/const.h
rmetasim/src/RandLib.h
rmetasim/src/PackedIndividual.h
rmetasim/src/BaseObj.h
rmetasim/src/SiteObj.h
rmetasim/src/PackedIndividual.cc
rmetasim/src/Eigen.h
rmetasim/src/FastSeqAllele.cc
rmetasim/src/Democlass.h
rmetasim/src/AlleleTbl.cc
rmetasim/NAMESPACE
rmetasim/CHANGELOG
rmetasim/R
rmetasim/R/landscape.make.genpop.R
rmetasim/R/landscape.freq.locnames.R
rmetasim/R/landscape.write.genepop.R
rmetasim/R/landscape.ind.freq.R
rmetasim/R/demography.R
rmetasim/R/popstruct.R
rmetasim/R/graphics.R
rmetasim/R/create_landscape.R
rmetasim/R/pegas_interface.R
rmetasim/R/amova.R
rmetasim/R/dnadiversity.R
rmetasim/R/landscape.mig.matrix.R
rmetasim/R/landscape.sample.R
rmetasim/R/landscape.coalinput.R
rmetasim/R/lambda.R
rmetasim/R/landscape.allelefreq.R
rmetasim/R/individuals.R
rmetasim/R/test.R
rmetasim/R/landscape.write.foreign.R
rmetasim/R/update_landscape.R
rmetasim/R/assign.R
rmetasim/R/landscapeIO.R
rmetasim/R/diversity.R
rmetasim/R/relatedness.R
rmetasim/R/runsimulation.R
rmetasim/R/loci.R
rmetasim/R/is_landscape.R
rmetasim/R/landscape.make.genind.R
rmetasim/vignettes
rmetasim/vignettes/rmetasim.Rmd
rmetasim/vignettes/CreatingLandscapes.Rmd
rmetasim/vignettes/Simulating.Rmd
rmetasim/README.md
rmetasim/MD5
rmetasim/build
rmetasim/build/vignette.rds
rmetasim/DESCRIPTION
rmetasim/man
rmetasim/man/landscape.mismatchdist.Rd
rmetasim/man/landscape.coalinput.Rd
rmetasim/man/landscape.new.locus.Rd
rmetasim/man/landscape.make.genind.Rd
rmetasim/man/landscape.obs.het.Rd
rmetasim/man/landscape.new.intparam.Rd
rmetasim/man/landscape.allelefreq.Rd
rmetasim/man/landscape.new.switchparam.Rd
rmetasim/man/landscape.compress.Rd
rmetasim/man/landscape.simulate.Rd
rmetasim/man/landscape.new.floatparam.Rd
rmetasim/man/landscape.states.Rd
rmetasim/man/landscape.amova.Rd
rmetasim/man/landscape.new.individuals.Rd
rmetasim/man/landscape.demography.Rd
rmetasim/man/landscape.sample.Rd
rmetasim/man/landscape.new.empty.Rd
rmetasim/man/landscape.new.local.demo.Rd
rmetasim/man/landscape.Fst.Rd
rmetasim/man/SimulationComponents.Rd
rmetasim/man/landscape.clean.Rd
rmetasim/man/landscape.amova.locus.Rd
rmetasim/man/landscape.theta.k.Rd
rmetasim/man/landscape.amova.pairwise.Rd
rmetasim/man/landscape.allelecount.Rd
rmetasim/man/landscape.locus.states.Rd
rmetasim/man/landscape.locus.Rd
rmetasim/man/landscape.ind.freq.Rd
rmetasim/man/landscape.freq.locnames.Rd
rmetasim/man/landscape.modify.epoch.Rd
rmetasim/man/is.landscape.Rd
rmetasim/man/landscape.exp.het.Rd
rmetasim/man/landscape.new.example.Rd
rmetasim/man/landscape.mig.matrix.Rd
rmetasim/man/landscape.democol.Rd
rmetasim/man/landscape.write.foreign.Rd
rmetasim/man/landscape.new.epoch.Rd
rmetasim/man/landscape.theta.s.Rd
rmetasim/man/landscape.ploidy.Rd
rmetasim/man/landscape.make.genpop.Rd
rmetasim/man/landscape.populations.Rd
rmetasim/man/landscape.locusvec.Rd
rmetasim/man/landscape.theta.h.Rd