Sample

struct Sample <: AbstractVector{Sequence}

Contain a sample of haplotypes and informations about them.

Implements the iteration interface and the array interface.

Fields

• H::Vector{Sequence}: Vector of haplotypes

• μ::Float64: Unscaled (per-locus) mutation rate

• ρ::Float64: Unscaled (per-locus) recombination rate

• Ne::Float64: Effective population size

• sequence_length::Float64: Sequence length

• positions::Vector{Float64}: Marker's positions

• coefs::Tuple{Float64, Float64}: Coefficients for positions' line

Constructors

Sample(H, μ, ρ, Ne, sequence_length, positions, coefs)
Sample(H, μ, ρ, Ne, sequence_length, positions, coefs)

defined at /home/pfournier/Documents/Softwares/Moonshine.jl/src/Sample.jl:38.

Sample(H; μ, ρ, Ne, positions, sequence_length)

defined at /home/pfournier/Documents/Softwares/Moonshine.jl/src/Sample.jl:54.

Sample(treesequence)

defined at /home/pfournier/Documents/Softwares/Moonshine.jl/src/Sample.jl:69.

Sample(rng, n, μ, ρ, Ne, sequence_length)

defined at /home/pfournier/Documents/Softwares/Moonshine.jl/src/Sample.jl:136.

Sample(mat, positions; μ, ρ, Ne)

defined at /home/pfournier/Documents/Softwares/Moonshine.jl/src/Sample.jl:139.

where:

• H: haplotypes
• μ (-1): mutation rate
• ρ (-1): recombination rate
• Ne (1): effective population size
• positions: position of markers
• sequence_length (maximum(positions)): sequence length
• n: number of sequences
• rng: random number generator
• ts: Tree Sequence
• mat: matrix of haplotypes (haplotypes -> columns)

effective_pop_size(sample, haploid=true)

Effective population size. If haploid=true, it is multiplied by 2; the resulting value is the haploid effective population size (assuming the stored value is for diploids).

mut_rate(sample, haploid=true)

Mutation rate. If haploid=true, it is multiplied by 2; the resulting value is the haploid mutation rate (assuming the stored value is for diploids).

rec_rate(sample, haploid=true)

Recombination rate. If haploid=true, it is multiplied by 2; the resulting value is the haploid recombination rate (assuming the stored value is for diploids).