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.

AuthorAllan Strand <stranda@cofc.edu>, James Niehaus
Date of publication2016-04-09 09:39:14
MaintainerAllan Strand <stranda@cofc.edu>
LicenseGPL
Version3.0.5

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

Functions

is.landscape Man page
landscape.advance Man page
landscape.allelecount Man page
landscape.allelefreq Man page
landscape.amova Man page
landscape.amova.locus Man page
landscape.amova.pairwise Man page
landscape.carry Man page
landscape.clean Man page
landscape.coalinput Man page
landscape.compress Man page
landscape.democol Man page
landscape.demography Man page
landscape.exp.het Man page
landscape.extinct Man page
landscape.freq.locnames Man page
landscape.Fst Man page
landscape.ind.freq Man page
landscape.locus Man page
landscape.locus.states Man page
landscape.locusvec Man page
landscape.make.genind Man page
landscape.make.genpop Man page
landscape.mig.matrix Man page
landscape.mismatchdist Man page
landscape.modify.epoch Man page
landscape.new.empty Man page
landscape.new.epoch Man page
landscape.new.example Man page
landscape.new.floatparam Man page
landscape.new.individuals Man page
landscape.new.intparam Man page
landscape.new.local.demo Man page
landscape.new.locus Man page
landscape.new.switchparam Man page
landscape.obs.het Man page
landscape.ploidy Man page
landscape.populations Man page
landscape.reproduce Man page
landscape.sample Man page
landscape.simulate Man page
landscape.states Man page
landscape.survive Man page
landscape.theta.h Man page
landscape.theta.k Man page
landscape.theta.s Man page
landscape.write.foreign Man page

Files

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

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