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Ease (version 0.1.2)

Simulating Explicit Population Genetics Models

Description

Implementation in a simple and efficient way of fully customisable population genetics simulations, considering multiple loci that have epistatic interactions. Specifically suited to the modelling of multilocus nucleocytoplasmic systems (with both diploid and haploid loci), it is nevertheless possible to simulate purely diploid (or purely haploid) genetic models. Examples of models that can be simulated with Ease are numerous, for example models of genetic incompatibilities as presented by Marie-Orleach et al. (2022) . Many others are conceivable, although few are actually explored, Ease having been developed in particular to provide a solution so that these kinds of models can be simulated simply.

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Version

Install

install.packages('Ease')

Version

0.1.2

License

MIT + file LICENSE

Maintainer

Last Published

November 7th, 2022

Functions in Ease (0.1.2)

alleleFreqMatGeneration

Generation of the matrix for calculating allelic frequencies
IDhaplotypeGeneration

Haplotype identifier
MutationMatrix-class

Mutation matrix
Metapopulation-class

Metapopulation
Population-class

Population
IDgenomeGeneration

Genome identifier
Genome-class

Genome class
Selection-class

Selection class
METAPOP_SIMULATION

Simulation of a metapopulation
IDgenotypeGeneration

Genotype identifier
check.selection

The validity check for the Selection class
extractAlleleComb

Extract the allele combination
haploCrossMatrix

Haplotype crossing matrix generation
genotyping

Genotyping
getCustomOutput

Getting the custom output
haplotyping

Haplotyping
initialize,Metapopulation-method

Initialize method for the Metapopulation class
initialize,Genome-method

Initialize method for the Genome class
check.mutationMatrix

The validity check associated with the MutationMatrix class
meiosisMatrix

Meiosis matrix generation
check.population

The validity check for the Population class
listing

Listing for display
catn

Concatenate, print and line break
areThereHomoz

Are there any allelic combinations including homozygosity
rowResultGen

Processing a result (or record) list
selectFormIntoVect

Conversion of selection formulas
initialize,Selection-method

Initialize method for the Selection class
check.genome

The validity check for the Genome class
setMutationMatrix

Setting the mutation matrix
setSelectOnInds

Setting the selection on individuals
isAffected

Is this haplo/geno-type affected ?
setSelectOnGametesProd

Setting the selection on gamete production
is.default.matrix

Test if a matrix is a default matrix
is.correct.transition.matrix

Test if a matrix is a correct transition matrix
check.metapopulation

The validity check for the Metapopulation class
selection.form.treatment

Treatment of a selection formula
initialize,MutationMatrix-method

Initialize method for the MutationMatrix class
setPopulation

Setting a population
isHaploSelectFormula

Are there any allelic combinations including homozygosity
is.probability.matrix

Test if a matrix is of probability
selectInputTreatment

Treatment of selection formulas
getRecords

Getting the simulation results
initialize,Population-method

Initialize method for the Population class
mutation

Definition of a mutation
print,MutationMatrix-method

Print method for the MutationMatrix class
getResults

Getting the simulation results
print,Population-method

Print method for the Population class
show,Population-method

Show method for the Population class
show,MutationMatrix-method

Show method for the MutationMatrix class
whichHomoz

Which alleles are homozygous in the input?
mutMatFriendly

Individual mutation definition to allelic mutation matrices
recombinationMatrix

Recombination matrix generation
setSelectOnGametes

Setting the selection on gametes
print,Selection-method

Print method for the Selection class
setSelectNeutral

Setting the selection
mutMatRates

Mutation matrix from rates
print,Genome-method

Print method for the Genome class
setGenome

Setting the genome
show,Selection-method

Show method for the Selection class
simulate,Metapopulation-method

Simulate method for the Metapopulation class
outFunct

Custom output function
show,Genome-method

Show method for the Genome class
show,Metapopulation-method

Show method for the Metapopulation class
print,Metapopulation-method

Print method for the Metapopulation class
setMetapopulation

Setting a metapopulation