# Simulating Explicit Population Genetics Models

## Documentation for package ‘Ease’ version 0.1.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

alleleFreqMatGeneration | Generation of the matrix for calculating allelic frequencies
areThereHomoz | Are there any allelic combinations including homozygosity
catn | Concatenate, print and line break
check.genome | The validity check for the 'Genome' class
check.metapopulation | The validity check for the 'Metapopulation' class
check.mutationMatrix | The validity check associated with the 'MutationMatrix' class
check.population | The validity check for the 'Population' class
check.selection | The validity check for the 'Selection' class
extractAlleleComb | Extract the allele combination
Genome-class | 'Genome' class
genotyping | Genotyping
getCustomOutput | Getting the custom output
getRecords | Getting the simulation results
getResults | Getting the simulation results
haploCrossMatrix | Haplotype crossing matrix generation
haplotyping | Haplotyping
IDgenomeGeneration | Genome identifier
IDgenotypeGeneration | Genotype identifier
IDhaplotypeGeneration | Haplotype identifier
initialize-method | Initialize method for the 'Genome' class
initialize-method | Initialize method for the 'Metapopulation' class
initialize-method | Initialize method for the 'MutationMatrix' class
initialize-method | Initialize method for the 'Population' class
initialize-method | Initialize method for the 'Selection' class
is.correct.transition.matrix | Test if a matrix is a correct transition matrix
is.default.matrix | Test if a matrix is a default matrix
is.probability.matrix | Test if a matrix is of probability
isAffected | Is this haplo/geno-type affected ?
isHaploSelectFormula | Are there any allelic combinations including homozygosity
listing | Listing for display
meiosisMatrix | Meiosis matrix generation
Metapopulation-class | Metapopulation
METAPOP_SIMULATION | Simulation of a metapopulation
mutation | Definition of a mutation
MutationMatrix-class | Mutation matrix
mutMatFriendly | Individual mutation definition to allelic mutation matrices
mutMatRates | Mutation matrix from rates
outFunct | Custom output function
Population-class | Population
print-method | Print method for the 'Genome' class
print-method | Print method for the 'Metapopulation' class
print-method | Print method for the 'MutationMatrix' class
print-method | Print method for the 'Population' class
print-method | Print method for the 'Selection' class
recombinationMatrix | Recombination matrix generation
rowResultGen | Processing a result (or record) list
selectFormIntoVect | Conversion of selection formulas
selectInputTreatment | Treatment of selection formulas
Selection-class | 'Selection' class
selection.form.treatment | Treatment of a selection formula
setGenome | Setting the genome
setMetapopulation | Setting a metapopulation
setMutationMatrix | Setting the mutation matrix
setPopulation | Setting a population
setSelectNeutral | Setting the selection
setSelectOnGametes | Setting the selection on gametes
setSelectOnGametesProd | Setting the selection on gamete production
setSelectOnInds | Setting the selection on individuals
show-method | Show method for the 'Genome' class
show-method | Show method for the 'Metapopulation' class
show-method | Show method for the 'MutationMatrix' class
show-method | Show method for the 'Population' class
show-method | Show method for the 'Selection' class
simulate-method | Simulate method for the 'Metapopulation' class
whichHomoz | Which alleles are homozygous in the input?