Simulating Explicit Population Genetics Models

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Documentation for package ‘Ease’ version 0.1.2

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

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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?