Man pages for Ease
Simulating Explicit Population Genetics Models
| 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-Genome-method | Initialize method for the 'Genome' class |
| initialize-Metapopulation-method | Initialize method for the 'Metapopulation' class |
| initialize-MutationMatrix-method | Initialize method for the 'MutationMatrix' class |
| initialize-Population-method | Initialize method for the 'Population' class |
| initialize-Selection-method | Initialize method for the 'Selection' class |
| isAffected | Is this haplo/geno-type affected ? |
| is.correct.transition.matrix | Test if a matrix is a correct transition matrix |
| is.default.matrix | Test if a matrix is a default matrix |
| isHaploSelectFormula | Are there any allelic combinations including homozygosity |
| is.probability.matrix | Test if a matrix is of probability |
| listing | Listing for display |
| meiosisMatrix | Meiosis matrix generation |
| METAPOP_SIMULATION | Simulation of a metapopulation |
| Metapopulation-class | 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-Genome-method | Print method for the 'Genome' class |
| print-Metapopulation-method | Print method for the 'Metapopulation' class |
| print-MutationMatrix-method | Print method for the 'MutationMatrix' class |
| print-Population-method | Print method for the 'Population' class |
| print-Selection-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-Genome-method | Show method for the 'Genome' class |
| show-Metapopulation-method | Show method for the 'Metapopulation' class |
| show-MutationMatrix-method | Show method for the 'MutationMatrix' class |
| show-Population-method | Show method for the 'Population' class |
| show-Selection-method | Show method for the 'Selection' class |
| simulate-Metapopulation-method | Simulate method for the 'Metapopulation' class |
| whichHomoz | Which alleles are homozygous in the input? |
