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  "Package": "Ease",
  "Type": "Package",
  "Title": "Simulating Explicit Population Genetics Models",
  "Version": "0.1.2",
  "Author": "Ehouarn Le Faou <ehouarnlefaou@orange.fr> [aut, cre]",
  "Maintainer": "Ehouarn Le Faou <ehouarnlefaou@orange.fr>",
  "Description": "Implementation in a simple and efficient way of fully\ncustomisable population genetics simulations, considering\nmultiple loci that have epistatic interactions. Specifically\nsuited to the modelling of multilocus nucleocytoplasmic systems\n(with both diploid and haploid loci), it is nevertheless\npossible to simulate purely diploid (or purely haploid) genetic\nmodels. Examples of models that can be simulated with Ease are\nnumerous, for example models of genetic incompatibilities as\npresented by Marie-Orleach et al. (2022)\n<doi:10.1101/2022.07.25.501356>. Many others are conceivable,\nalthough few are actually explored, Ease having been developed\nin particular to provide a solution so that these kinds of\nmodels can be simulated simply.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.2.1",
  "Collate": "RcppExports.R ToolFunctions.R ModelFunctions.R GenomeClass.R\nMutationMatrixClass.R SelectionClass.R PopulationClass.R\nMetapopulationClass.R UserFunctions.R",
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  "Date/Publication": "2022-11-07 13:40:08 UTC",
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    "areThereHomoz",
    "catn",
    "check.genome",
    "check.metapopulation",
    "check.mutationMatrix",
    "check.population",
    "check.selection",
    "extractAlleleComb",
    "genotyping",
    "getCustomOutput",
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    "haplotyping",
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    "IDgenotypeGeneration",
    "IDhaplotypeGeneration",
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    "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"
  ],
  "_help": [
    {
      "page": "alleleFreqMatGeneration",
      "title": "Generation of the matrix for calculating allelic frequencies",
      "topics": [
        "alleleFreqMatGeneration"
      ]
    },
    {
      "page": "areThereHomoz",
      "title": "Are there any allelic combinations including homozygosity",
      "topics": [
        "areThereHomoz"
      ]
    },
    {
      "page": "catn",
      "title": "Concatenate, print and line break",
      "topics": [
        "catn"
      ]
    },
    {
      "page": "check.genome",
      "title": "The validity check for the 'Genome' class",
      "topics": [
        "check.genome"
      ]
    },
    {
      "page": "check.metapopulation",
      "title": "The validity check for the 'Metapopulation' class",
      "topics": [
        "check.metapopulation"
      ]
    },
    {
      "page": "check.mutationMatrix",
      "title": "The validity check associated with the 'MutationMatrix' class",
      "topics": [
        "check.mutationMatrix"
      ]
    },
    {
      "page": "check.population",
      "title": "The validity check for the 'Population' class",
      "topics": [
        "check.population"
      ]
    },
    {
      "page": "check.selection",
      "title": "The validity check for the 'Selection' class",
      "topics": [
        "check.selection"
      ]
    },
    {
      "page": "extractAlleleComb",
      "title": "Extract the allele combination",
      "topics": [
        "extractAlleleComb"
      ]
    },
    {
      "page": "Genome-class",
      "title": "'Genome' class",
      "topics": [
        "Genome-class"
      ]
    },
    {
      "page": "genotyping",
      "title": "Genotyping",
      "topics": [
        "genotyping"
      ]
    },
    {
      "page": "getCustomOutput",
      "title": "Getting the custom output",
      "topics": [
        "getCustomOutput"
      ]
    },
    {
      "page": "getRecords",
      "title": "Getting the simulation results",
      "topics": [
        "getRecords"
      ]
    },
    {
      "page": "getResults",
      "title": "Getting the simulation results",
      "topics": [
        "getResults"
      ]
    },
    {
      "page": "haploCrossMatrix",
      "title": "Haplotype crossing matrix generation",
      "topics": [
        "haploCrossMatrix"
      ]
    },
    {
      "page": "haplotyping",
      "title": "Haplotyping",
      "topics": [
        "haplotyping"
      ]
    },
    {
      "page": "IDgenomeGeneration",
      "title": "Genome identifier",
      "topics": [
        "IDgenomeGeneration"
      ]
    },
    {
      "page": "IDgenotypeGeneration",
      "title": "Genotype identifier",
      "topics": [
        "IDgenotypeGeneration"
      ]
    },
    {
      "page": "IDhaplotypeGeneration",
      "title": "Haplotype identifier",
      "topics": [
        "IDhaplotypeGeneration"
      ]
    },
    {
      "page": "initialize-Genome-method",
      "title": "Initialize method for the 'Genome' class",
      "topics": [
        "initialize,Genome-method"
      ]
    },
    {
      "page": "initialize-Metapopulation-method",
      "title": "Initialize method for the 'Metapopulation' class",
      "topics": [
        "initialize,Metapopulation-method"
      ]
    },
    {
      "page": "initialize-MutationMatrix-method",
      "title": "Initialize method for the 'MutationMatrix' class",
      "topics": [
        "initialize,MutationMatrix-method"
      ]
    },
    {
      "page": "initialize-Population-method",
      "title": "Initialize method for the 'Population' class",
      "topics": [
        "initialize,Population-method"
      ]
    },
    {
      "page": "initialize-Selection-method",
      "title": "Initialize method for the 'Selection' class",
      "topics": [
        "initialize,Selection-method"
      ]
    },
    {
      "page": "is.correct.transition.matrix",
      "title": "Test if a matrix is a correct transition matrix",
      "topics": [
        "is.correct.transition.matrix"
      ]
    },
    {
      "page": "is.default.matrix",
      "title": "Test if a matrix is a default matrix",
      "topics": [
        "is.default.matrix"
      ]
    },
    {
      "page": "is.probability.matrix",
      "title": "Test if a matrix is of probability",
      "topics": [
        "is.probability.matrix"
      ]
    },
    {
      "page": "isAffected",
      "title": "Is this haplo/geno-type affected ?",
      "topics": [
        "isAffected"
      ]
    },
    {
      "page": "isHaploSelectFormula",
      "title": "Are there any allelic combinations including homozygosity",
      "topics": [
        "isHaploSelectFormula"
      ]
    },
    {
      "page": "listing",
      "title": "Listing for display",
      "topics": [
        "listing"
      ]
    },
    {
      "page": "meiosisMatrix",
      "title": "Meiosis matrix generation",
      "topics": [
        "meiosisMatrix"
      ]
    },
    {
      "page": "METAPOP_SIMULATION",
      "title": "Simulation of a metapopulation",
      "topics": [
        "METAPOP_SIMULATION"
      ]
    },
    {
      "page": "Metapopulation-class",
      "title": "Metapopulation",
      "topics": [
        "Metapopulation-class"
      ]
    },
    {
      "page": "mutation",
      "title": "Definition of a mutation",
      "topics": [
        "mutation"
      ]
    },
    {
      "page": "MutationMatrix-class",
      "title": "Mutation matrix",
      "topics": [
        "MutationMatrix-class"
      ]
    },
    {
      "page": "mutMatFriendly",
      "title": "Individual mutation definition to allelic mutation matrices",
      "topics": [
        "mutMatFriendly"
      ]
    },
    {
      "page": "mutMatRates",
      "title": "Mutation matrix from rates",
      "topics": [
        "mutMatRates"
      ]
    },
    {
      "page": "outFunct",
      "title": "Custom output function",
      "topics": [
        "outFunct"
      ]
    },
    {
      "page": "Population-class",
      "title": "Population",
      "topics": [
        "Population-class"
      ]
    },
    {
      "page": "print-Genome-method",
      "title": "Print method for the 'Genome' class",
      "topics": [
        "print,Genome-method"
      ]
    },
    {
      "page": "print-Metapopulation-method",
      "title": "Print method for the 'Metapopulation' class",
      "topics": [
        "print,Metapopulation-method"
      ]
    },
    {
      "page": "print-MutationMatrix-method",
      "title": "Print method for the 'MutationMatrix' class",
      "topics": [
        "print,MutationMatrix-method"
      ]
    },
    {
      "page": "print-Population-method",
      "title": "Print method for the 'Population' class",
      "topics": [
        "print,Population-method"
      ]
    },
    {
      "page": "print-Selection-method",
      "title": "Print method for the 'Selection' class",
      "topics": [
        "print,Selection-method"
      ]
    },
    {
      "page": "recombinationMatrix",
      "title": "Recombination matrix generation",
      "topics": [
        "recombinationMatrix"
      ]
    },
    {
      "page": "rowResultGen",
      "title": "Processing a result (or record) list",
      "topics": [
        "rowResultGen"
      ]
    },
    {
      "page": "selectFormIntoVect",
      "title": "Conversion of selection formulas",
      "topics": [
        "selectFormIntoVect"
      ]
    },
    {
      "page": "selectInputTreatment",
      "title": "Treatment of selection formulas",
      "topics": [
        "selectInputTreatment"
      ]
    },
    {
      "page": "Selection-class",
      "title": "'Selection' class",
      "topics": [
        "Selection-class"
      ]
    },
    {
      "page": "selection.form.treatment",
      "title": "Treatment of a selection formula",
      "topics": [
        "selection.form.treatment"
      ]
    },
    {
      "page": "setGenome",
      "title": "Setting the genome",
      "topics": [
        "setGenome"
      ]
    },
    {
      "page": "setMetapopulation",
      "title": "Setting a metapopulation",
      "topics": [
        "setMetapopulation"
      ]
    },
    {
      "page": "setMutationMatrix",
      "title": "Setting the mutation matrix",
      "topics": [
        "setMutationMatrix"
      ]
    },
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      "page": "setPopulation",
      "title": "Setting a population",
      "topics": [
        "setPopulation"
      ]
    },
    {
      "page": "setSelectNeutral",
      "title": "Setting the selection",
      "topics": [
        "setSelectNeutral"
      ]
    },
    {
      "page": "setSelectOnGametes",
      "title": "Setting the selection on gametes",
      "topics": [
        "setSelectOnGametes"
      ]
    },
    {
      "page": "setSelectOnGametesProd",
      "title": "Setting the selection on gamete production",
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      "page": "whichHomoz",
      "title": "Which alleles are homozygous in the input?",
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