rmetasim: An Individual-Based Population Genetic Simulation Environment
Version 3.0.5

An interface between R and the metasim simulation engine. The simulation environment is documented in: "Strand, A.(2002) 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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rmetasim")

Getting started

README.md
Creating rmetasim landscapes
rmetasim overview
Setting up simulations in rmetasim

Popular man pages

landscape.amova.locus: uses functions in ade4 to calcuate phi-st for a particular...
landscape.demography: Calculate demographic 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.states: return a matrix containing actual genotypes for a particular...
landscape.theta.h: Calculate theta using heterozygosity
See all...

All man pages Function index File listing

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

assignmentTest Source code
basediff Source code
coal2rmet Source code
countPopulation Source code
geneseq Source code
getMyAlleleIndex Source code
indxfreqNormal Source code
indxfreqWithout Source code
internalrelate Source code
is.landscape Man page Source code
is.nsquare Source code
lambda.demomat Source code
landscape.FWright Source code
landscape.Fst Man page Source code
landscape.advance Man page Source code
landscape.allelecount Man page Source code
landscape.allelefreq Man page Source code
landscape.allelefreq.old Source code
landscape.amova Man page Source code
landscape.amova.locus Man page Source code
landscape.amova.pairwise Man page Source code
landscape.amova.pairwise.old Source code
landscape.carry Man page Source code
landscape.clean Man page Source code
landscape.coalinput Man page Source code
landscape.coerce Source code
landscape.compress Man page Source code
landscape.democol Man page Source code
landscape.demography Man page Source code
landscape.exp.het Man page Source code
landscape.extinct Man page Source code
landscape.freq.locnames Man page Source code
landscape.ind.freq Man page Source code
landscape.locus Man page Source code
landscape.locus.states Man page Source code
landscape.locusvec Man page Source code
landscape.make.genind Man page Source code
landscape.make.genpop Man page Source code
landscape.mig.matrix Man page Source code
landscape.mismatchdist Man page Source code
landscape.modify.epoch Man page Source code
landscape.new.default Source code
landscape.new.empty Man page Source code
landscape.new.epoch Man page Source code
landscape.new.example Man page Source code
landscape.new.floatparam Man page Source code
landscape.new.individuals Man page Source code
landscape.new.intparam Man page Source code
landscape.new.local.demo Man page Source code
landscape.new.locus Man page Source code
landscape.new.switchparam Man page Source code
landscape.obs.het Man page Source code
landscape.ploidy Man page Source code
landscape.populations Man page Source code
landscape.relate Source code
landscape.reproduce Man page Source code
landscape.sample Man page Source code
landscape.sample.pops Source code
landscape.sample.stages Source code
landscape.simulate Man page Source code
landscape.states Man page Source code
landscape.survive Man page Source code
landscape.tajima.d Source code
landscape.theta.h Man page Source code
landscape.theta.k Man page Source code
landscape.theta.s Man page Source code
landscape.write.foreign Man page Source code
landscape.write.genepop Source code
lociAIndex Source code
makealleles Source code
parse.arlequin Source code
popsizedist.plot.landscape Source code
rm.lambda Source code
sampleFromSubPopulations Source code
stgsizedist.plot.landscape Source code
test.landscape.function Source code
typelookup Source code

Files

inst
inst/doc
inst/doc/rmetasim.html
inst/doc/CreatingLandscapes.html
inst/doc/Simulating.html
inst/doc/rmetasim.Rmd
inst/doc/CreatingLandscapes.R
inst/doc/Simulating.R
inst/doc/island.R
inst/doc/CreatingLandscapes.Rmd
inst/doc/Simulating.Rmd
src
src/Makevars
src/metasim.h
src/RandLib.cc
src/AlleleObj.h
src/FastSeqAllele.h
src/utilities.h
src/Landscape.cc
src/AlleleObj.cc
src/rmetasim.h
src/Eigen.cc
src/SiteObj.cc
src/TransMat.h
src/AlleleTbl.h
src/TransMat.cc
src/BaseObj.cc
src/Genotype.cc
src/FastAllele.cc
src/rmetasim.cc
src/Genotype.h
src/Landscape.h
src/FastAllele.h
src/Democlass.cc
src/const.h
src/RandLib.h
src/PackedIndividual.h
src/BaseObj.h
src/SiteObj.h
src/PackedIndividual.cc
src/Eigen.h
src/FastSeqAllele.cc
src/Democlass.h
src/AlleleTbl.cc
NAMESPACE
CHANGELOG
R
R/landscape.make.genpop.R
R/landscape.freq.locnames.R
R/landscape.write.genepop.R
R/landscape.ind.freq.R
R/demography.R
R/popstruct.R
R/graphics.R
R/create_landscape.R
R/pegas_interface.R
R/amova.R
R/dnadiversity.R
R/landscape.mig.matrix.R
R/landscape.sample.R
R/landscape.coalinput.R
R/lambda.R
R/landscape.allelefreq.R
R/individuals.R
R/test.R
R/landscape.write.foreign.R
R/update_landscape.R
R/assign.R
R/landscapeIO.R
R/diversity.R
R/relatedness.R
R/runsimulation.R
R/loci.R
R/is_landscape.R
R/landscape.make.genind.R
vignettes
vignettes/rmetasim.Rmd
vignettes/CreatingLandscapes.Rmd
vignettes/Simulating.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/landscape.mismatchdist.Rd
man/landscape.coalinput.Rd
man/landscape.new.locus.Rd
man/landscape.make.genind.Rd
man/landscape.obs.het.Rd
man/landscape.new.intparam.Rd
man/landscape.allelefreq.Rd
man/landscape.new.switchparam.Rd
man/landscape.compress.Rd
man/landscape.simulate.Rd
man/landscape.new.floatparam.Rd
man/landscape.states.Rd
man/landscape.amova.Rd
man/landscape.new.individuals.Rd
man/landscape.demography.Rd
man/landscape.sample.Rd
man/landscape.new.empty.Rd
man/landscape.new.local.demo.Rd
man/landscape.Fst.Rd
man/SimulationComponents.Rd
man/landscape.clean.Rd
man/landscape.amova.locus.Rd
man/landscape.theta.k.Rd
man/landscape.amova.pairwise.Rd
man/landscape.allelecount.Rd
man/landscape.locus.states.Rd
man/landscape.locus.Rd
man/landscape.ind.freq.Rd
man/landscape.freq.locnames.Rd
man/landscape.modify.epoch.Rd
man/is.landscape.Rd
man/landscape.exp.het.Rd
man/landscape.new.example.Rd
man/landscape.mig.matrix.Rd
man/landscape.democol.Rd
man/landscape.write.foreign.Rd
man/landscape.new.epoch.Rd
man/landscape.theta.s.Rd
man/landscape.ploidy.Rd
man/landscape.make.genpop.Rd
man/landscape.populations.Rd
man/landscape.locusvec.Rd
man/landscape.theta.h.Rd
rmetasim documentation built on May 20, 2017, 12:20 a.m.

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