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
Ease_0.1.2.tar.gz(r-4.7-arm64)Ease_0.1.2.tar.gz(r-4.7-x86_64)Ease_0.1.2.tar.gz(r-4.6-arm64)Ease_0.1.2.tar.gz(r-4.6-x86_64)
Ease_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Ease/json (API)

# Install 'Ease' in R:

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

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

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

cpp

2.00 score 5 scripts 321 downloads 46 exports 2 dependencies

Last updated from:fb28e39d51. Checks:6 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	147
linux-devel-x86_64	OK	130
source / vignettes	OK	208
linux-release-arm64	OK	140
linux-release-x86_64	OK	138
wasm-release	OK	112

Exports:alleleFreqMatGeneration areThereHomoz catn check.genome check.metapopulation check.mutationMatrix check.population check.selection extractAlleleComb genotyping getCustomOutput getRecords getResults haploCrossMatrix haplotyping IDgenomeGeneration IDgenotypeGeneration IDhaplotypeGeneration is.correct.transition.matrix is.default.matrix is.probability.matrix isAffected isHaploSelectFormula listing meiosisMatrix METAPOP_SIMULATION mutation mutMatFriendly mutMatRates outFunct print recombinationMatrix rowResultGen selectFormIntoVect selectInputTreatment selection.form.treatment setGenome setMetapopulation setMutationMatrix setPopulation setSelectNeutral setSelectOnGametes setSelectOnGametesProd setSelectOnInds simulate whichHomoz

Dependencies:Rcpp RcppProgress

Why and how to use the Ease package?

Rendered fromuse-the-Ease-package.Rmdusingknitr::rmarkdown

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

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

Package: Ease 0.1.2

Ease: Simulating Explicit Population Genetics Models

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