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Phylodist.jl
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Phylodist.jl
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"""
This structure implements a Distribution whos likelihood is calculated
according to Felsensteins algorithm.
"""
struct PhyloDist{T<:GeneralNode,F<:Function} <: DiscreteMatrixDistribution
tree::T
base_freq::Vector{Float64}
substitution_rates::Vector{Float64}
rates::Vector{Float64}
substitution_model::F
nbase::Int64
nnodes::Int64
function PhyloDist(
tree::T,
base_freq::A,
substitution_rates::A,
rates::A,
substitution_model::F,
) where {T<:GeneralNode,A<:AbstractArray{<:Real},F<:Function}
new{T,F}(
tree,
base_freq,
substitution_rates,
rates,
substitution_model,
length(base_freq),
length(post_order(tree)),
)
end
end
function PhyloDist(
tree::T,
base_freq::S,
substitution_rates::A,
rates::B,
substitution_model::Function,
) where {
T<:TreeVariate,
S<:DenseArray{Float64},
A<:DenseArray{Float64},
B<:DenseArray{Float64},
}
PhyloDist(
tree.value,
Array(base_freq),
Array(substitution_rates),
Array(rates),
substitution_model,
)
end
function PhyloDist(
my_tree::T,
base_freq::S,
substitution_rates::R,
rates::R,
substitution_model::Function,
) where {T<:TreeVariate,S<:DenseArray{Float64},R<:Real}
PhyloDist(
my_tree.value,
Array(base_freq),
[substitution_rates],
[rates],
substitution_model,
)
end
"""
function PhyloDist(my_tree::T, base_freq::S, substitution_rates::R, rates::R, substitution_model::Function) where {T<:GeneralNode, S<:DenseArray{Float64}, R<:Real}
Convenience function which can work with MCPhylo types.
"""
function PhyloDist(
my_tree::T,
base_freq::S,
substitution_rates::R,
rates::R,
substitution_model::Function,
) where {T<:GeneralNode,S<:DenseArray{Float64},R<:Real}
PhyloDist(my_tree, Array(base_freq), [substitution_rates], [rates], substitution_model)
end
function PhyloDist(
my_tree::A,
substitution_rates::B,
rates::R,
substitution_model::K,
) where {A<:AbstractNode,B<:DenseArray{Float64},R<:DenseArray{Float64},K<:typeof(freeK)}
U, D, Uinv, _ = freeK(Float64[], Array(substitution_rates))
D[:] .= 0
D[end] = 1
eq = real.((U*diagm(D)*Uinv)[1, :])
PhyloDist(my_tree, eq, substitution_rates, rates, substitution_model)
end
minimum(d::PhyloDist) = -Inf
maximum(d::PhyloDist) = Inf
Base.size(d::PhyloDist) = (d.nbase, 1, d.nnodes)
function logpdf(d::PhyloDist{T,F}, x::AbstractArray{<:Real,3})::Float64 where {T,F}
mt = post_order(d.tree)
U, D, Uinv, mu = d.substitution_model(
d.base_freq,
d.substitution_rates,
)::Tuple{Matrix,Vector,Matrix,Float64}
blv = get_branchlength_vector(last(mt))
leaveinds = [l.num for l in get_leaves(last(mt))]
data_ext = my_repeat(x, length(d.rates), leaveinds)
Down = deepcopy(data_ext)
trans_probs = parallel_transition_prob(U, D, Uinv, d.rates, mu, blv)
FelsensteinFunction(mt, data_ext, Down, d.base_freq, trans_probs)
end
function gradlogpdf(d::PhyloDist{T,F}, x::AbstractArray) where {T,F}
mt = post_order(d.tree)
U, D, Uinv, mu = d.substitution_model(d.base_freq, d.substitution_rates)#::Tuple{Matrix{Float64},Vector{Float64},Matrix{Float64},Float64}
blv = get_branchlength_vector(d.tree)
data_ext = my_repeat(x, length(d.rates), [l.num for l in get_leaves(d.tree)])
Down = deepcopy(data_ext)
trans_probs = parallel_transition_prob(U, D, Uinv, d.rates, mu, blv)
ptg = zeros(size(trans_probs))
out2 = similar(ptg)
R_gemmturbo_large_ptg!(out2, U, mu, blv, D, d.rates)
L_gemmturbo_large!(ptg, out2, Uinv)
ll, gr = FelsensteinFunction(mt, data_ext, Down, d.base_freq, trans_probs, ptg)
ll, gr
end
mutable struct MultiplePhyloDist <: DiscreteMatrixDistribution
DistCollector::Array{PhyloDist}
size_array::Array{Int64}
function MultiplePhyloDist(
tree_array::Array{T},
base_freq::Array{Float64,2},
substitution_rates::Array{Float64,2},
rates::Array{Float64,2},
substitution_model::Function,
) where {T<:GeneralNode}
size_array::Array{Int64,1} = Array{Int64,1}(undef, length(tree_array))
pd_array = PhyloDist[]
for (ind, tree) in enumerate(tree_array)
pd = PhyloDist(
tree,
base_freq[:, ind],
substitution_rates[:, ind],
rates[:, ind],
substitution_model,
)
push!(pd_array, pd)
size_array[ind] = length(post_order(tree))
end
new(pd_array, size_array)
end
end
function MultiplePhyloDist(
tree_array::Array{T},
base_freq::S,
substitution_rates::R,
rates::U,
substitution_model::Function,
) where {
T<:GeneralNode,
S<:DenseArray{Float64},
R<:DenseArray{Float64},
U<:DenseArray{Float64},
}
n_t = length(tree_array)
base_freq_l = Array{Float64,2}(undef, size(base_freq, 1), n_t)
substitution_rates_l = Array{Float64,2}(undef, size(substitution_rates, 1), n_t)
rates_l = Array{Float64,2}(undef, size(rates, 1), n_t)
if size(base_freq, 2) == n_t
base_freq_l .= base_freq
elseif size(base_freq, 2) == 1
for i = 1:n_t
base_freq_l[:, i] .= base_freq
end
else
throw(DimensionMismatch("Size of base_freq and tree_array are incompatible"))
end
if size(substitution_rates, 2) == n_t
substitution_rates_l .= substitution_rates
elseif size(substitution_rates, 2) == 1
for i = 1:n_t
substitution_rates_l[:, i] .= substitution_rates
end
else
throw(
DimensionMismatch("Size of substitution_rates and tree_array are incompatible"),
)
end
if size(rates, 2) == n_t
rates_l .= rates
elseif size(rates, 2) == 1
for i = 1:n_t
rates_l[:, i] .= rates
end
else
throw(DimensionMismatch("Size of rates and tree_array are incompatible"))
end
MultiplePhyloDist(
tree_array,
base_freq_l,
substitution_rates_l,
rates_l,
substitution_model,
)
end
function MultiplePhyloDist(
tree_array::Array{T},
substitution_rates::R,
rates::S,
substitution_model::K,
) where {T<:GeneralNode,S<:DenseArray{Float64},R<:DenseArray{Float64},K<:typeof(freeK)}
n = size(substitution_rates, 1)
s = Int(round((sqrt(8n + 1) - 1) / 2))
n_t = length(tree_array)
base_freq_l = Array{Float64,2}(undef, s, n_t)
substitution_rates_l = Array{Float64,2}(undef, size(substitution_rates, 1), n_t)
if size(substitution_rates, 2) == n_t
for i = 1:n_t
U, D, Uinv, _ = freeK(Float64[], Array(substitution_rates[:, i]))
D[:] .= 0
D[end] = 1
eq = real.((U*diagm(D)*Uinv)[1, :])
substitution_rates_l[:, i] .= substitution_rates[:, i]
base_freq_l[:, i] .= eq
end
elseif size(substitution_rates, 2) == 1
U, D, Uinv, _ = freeK(Float64[], Array(substitution_rates))
D[:] .= 0
D[end] = 1
eq = real.((U*diagm(D)*Uinv)[1, :])
for i = 1:n_t
substitution_rates_l[:, i] .= substitution_rates
base_freq_l[:, i] .= eq
end
else
throw(
DimensionMismatch("Size of substitution_rates and tree_array are incompatible"),
)
end
MultiplePhyloDist(
tree_array,
base_freq_l,
substitution_rates_l,
rates,
substitution_model,
)
end
minimum(d::MultiplePhyloDist) = -Inf
maximum(d::MultiplePhyloDist) = Inf
Base.size(d::MultiplePhyloDist) =
(size(d.DistCollector[1].base_freq, 1), 1, maximum(d.size_array), length(d.size_array))
function logpdf(d::MultiplePhyloDist, x::AbstractArray{<:Real,4})::Float64
res = zero(Float64)
@inbounds for (ind, s) in enumerate(d.size_array)
xt = x[:, :, 1:s, ind]
res += logpdf(d.DistCollector[ind], xt)
end
res
end
function __logpdf(d::MultiplePhyloDist, x::AbstractArray)
res = Tuple[]
@inbounds for (ind, s) in enumerate(d.size_array)
xt = x[:, :, 1:s, ind]
push!(res, gradlogpdf(d.DistCollector[ind], xt))
end
res
end
const PhylogeneticDistribution = Union{PhyloDist,MultiplePhyloDist}