The class Metapopulation
is used to centralise the information
relating to the populations that we want to simulate, as well as to define
the migration conditions between them if there are several. This class
is thus defined by a list of objects Population
and a migration
matrix.
populations
list of objects Population
nbPop
number of populations
names
names of the populations
migMat
migration matrix between population (if there is more than one)
sizes
sizes of the populations
dioecies
sexual systems of the populations (they must all be the same)
selfRates
selfing rates of the populations
demographies
demography parameter of the populations
growthRates
growth rates of the populations
initPopSizes
initial population sizes of the populations
initGenoFreqs
initial genotypic frequencies of the populations
genome
a Genome
object
genomeIDs
ID of the Genome
object
mutMat
a MutationMatrix
object
selection
a Selection
object
recMat
recombination matrix
meiosisMat
a meiosis matrix
haploCrossMat
an haplotype crossing matrix
haploCrossMatNamed
an haplotype crossing matrix with names of genotypes instead of their indices
gametogenesisMat
a gametogenesis matrix
alleleFreqMat
a matrix for calculating allelic frequencies
rawOutputSimul
raw output of the simulation function, its refinement
is done directly afterwards in the simulate
method
stopCondition
list of stop conditions for the simulation (if required)
IDstopCondition
names of stop conditions. They are given an arbitrary name if none is given by the user.
results
data.frame.
records
list.
customOutput
list.
Ehouarn Le Faou