This function simulates a population with an approximate level of population substructure. This is achieved by subdividing a population into equal sized subpopulations and allowing them to breed within themselves for $$t = $$$$ \lceil{\frac{\log_e(1-\theta)}{\log\left(1-\frac{1}{2N_s}\right)}}\rceil$$ generations, where \(N_s\) is the number of individuals in each subpopulation. This will produce a population with an estimated coancestry coefficient approximately equal to \(\theta\)
breedFst(Freqs, theta = 0.01, N = 10000, ns = 10, DNAtools = FALSE)An object of class 'population' which is a list with the following elements
profiles - a vector of profiles where the
level of inbreeding is approximately equal to \(\theta\)
nProfiles - the total number of individuals in the population
nSubpops - the number of sub-populations in the population
nLoci - the number of loci each individual is typed at
theta - the desired level of substructure in the population. The
actual value will be near to this.
Freqs - a Freq object
representing the ancestral frequencies of the population
A list with an element, freqs which contains a list of
vectors, where each vector is a set of allele frequencies for a locus
A desired level of inbreeding, where \(0 < \theta < 0.5\)
Total population size
The number of subpopulations. \(N/n_s\) needs to be greater than 100
If TRUE then the profiles in the return population
will be formatted as a data frame with an id column and two columns per
locus.
James M. Curran
data(USCaucs)
pop = breedFst(USCaucs)
Run the code above in your browser using DataLab