Package: Ease 0.1.2

Ehouarn Le Faou

Ease: Simulating Explicit Population Genetics Models

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) <doi:10.1101/2022.07.25.501356>. 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.

Authors:Ehouarn Le Faou <[email protected]> [aut, cre]

Ease_0.1.2.tar.gz
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Ease_0.1.2.tgz(r-4.4-emscripten)Ease_0.1.2.tgz(r-4.3-emscripten)
Ease.pdf |Ease.html✨
Ease/json (API)
NEWS

# Install 'Ease' in R:
install.packages('Ease', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

2.00 score 4 scripts 212 downloads 46 exports 2 dependencies

Last updated 2 years agofrom:fb28e39d51. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 02 2024
R-4.5-linux-x86_64OKDec 02 2024

Exports:alleleFreqMatGenerationareThereHomozcatncheck.genomecheck.metapopulationcheck.mutationMatrixcheck.populationcheck.selectionextractAlleleCombgenotypinggetCustomOutputgetRecordsgetResultshaploCrossMatrixhaplotypingIDgenomeGenerationIDgenotypeGenerationIDhaplotypeGenerationis.correct.transition.matrixis.default.matrixis.probability.matrixisAffectedisHaploSelectFormulalistingmeiosisMatrixMETAPOP_SIMULATIONmutationmutMatFriendlymutMatRatesoutFunctprintrecombinationMatrixrowResultGenselectFormIntoVectselectInputTreatmentselection.form.treatmentsetGenomesetMetapopulationsetMutationMatrixsetPopulationsetSelectNeutralsetSelectOnGametessetSelectOnGametesProdsetSelectOnIndssimulatewhichHomoz

Dependencies:RcppRcppProgress

Why and how to use the Ease package?

Ehouarn Le Faou

Rendered fromuse-the-Ease-package.Rmdusingknitr::rmarkdownon Dec 02 2024.

Last update: 2022-10-18
Started: 2022-09-19

Readme and manuals

Help Manual

Help pageTopics
Generation of the matrix for calculating allelic frequenciesalleleFreqMatGeneration
Are there any allelic combinations including homozygosityareThereHomoz
Concatenate, print and line breakcatn
The validity check for the 'Genome' classcheck.genome
The validity check for the 'Metapopulation' classcheck.metapopulation
The validity check associated with the 'MutationMatrix' classcheck.mutationMatrix
The validity check for the 'Population' classcheck.population
The validity check for the 'Selection' classcheck.selection
Extract the allele combinationextractAlleleComb
'Genome' classGenome-class
Genotypinggenotyping
Getting the custom outputgetCustomOutput
Getting the simulation resultsgetRecords
Getting the simulation resultsgetResults
Haplotype crossing matrix generationhaploCrossMatrix
Haplotypinghaplotyping
Genome identifierIDgenomeGeneration
Genotype identifierIDgenotypeGeneration
Haplotype identifierIDhaplotypeGeneration
Initialize method for the 'Genome' classinitialize,Genome-method
Initialize method for the 'Metapopulation' classinitialize,Metapopulation-method
Initialize method for the 'MutationMatrix' classinitialize,MutationMatrix-method
Initialize method for the 'Population' classinitialize,Population-method
Initialize method for the 'Selection' classinitialize,Selection-method
Test if a matrix is a correct transition matrixis.correct.transition.matrix
Test if a matrix is a default matrixis.default.matrix
Test if a matrix is of probabilityis.probability.matrix
Is this haplo/geno-type affected ?isAffected
Are there any allelic combinations including homozygosityisHaploSelectFormula
Listing for displaylisting
Meiosis matrix generationmeiosisMatrix
Simulation of a metapopulationMETAPOP_SIMULATION
MetapopulationMetapopulation-class
Definition of a mutationmutation
Mutation matrixMutationMatrix-class
Individual mutation definition to allelic mutation matricesmutMatFriendly
Mutation matrix from ratesmutMatRates
Custom output functionoutFunct
PopulationPopulation-class
Print method for the 'Genome' classprint,Genome-method
Print method for the 'Metapopulation' classprint,Metapopulation-method
Print method for the 'MutationMatrix' classprint,MutationMatrix-method
Print method for the 'Population' classprint,Population-method
Print method for the 'Selection' classprint,Selection-method
Recombination matrix generationrecombinationMatrix
Processing a result (or record) listrowResultGen
Conversion of selection formulasselectFormIntoVect
Treatment of selection formulasselectInputTreatment
'Selection' classSelection-class
Treatment of a selection formulaselection.form.treatment
Setting the genomesetGenome
Setting a metapopulationsetMetapopulation
Setting the mutation matrixsetMutationMatrix
Setting a populationsetPopulation
Setting the selectionsetSelectNeutral
Setting the selection on gametessetSelectOnGametes
Setting the selection on gamete productionsetSelectOnGametesProd
Setting the selection on individualssetSelectOnInds
Show method for the 'Genome' classshow,Genome-method
Show method for the 'Metapopulation' classshow,Metapopulation-method
Show method for the 'MutationMatrix' classshow,MutationMatrix-method
Show method for the 'Population' classshow,Population-method
Show method for the 'Selection' classshow,Selection-method
Simulate method for the 'Metapopulation' classsimulate,Metapopulation-method
Which alleles are homozygous in the input?whichHomoz