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dynamic_model_network.jl
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dynamic_model_network.jl
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"""
population_model_network(du, u, (network, inputs), t)
Solve network implementation of dynamic population model.
"""
function population_model_network(du, u, (network, inputs), t)
##################
# Parameters #
##################
n_nodes = count_nodes(network)
for (index_node, node_pair) in enumerate(network.nodes)
key_nodename, node = node_pair
for (index_organism, key_species) in enumerate(keys(node.organisms))
genetics = get_genetics(network, key_nodename, key_species)
gN = count_genotypes(genetics)
likelihood = genetics.likelihood
S = genetics.S
Τ = genetics.Τ
Φ = genetics.Φ
Ξ_m = genetics.Ξ_m
Ξ_f = genetics.Ξ_f
Ω = genetics.Ω
Β = genetics.Β
Η = genetics.Η
n_substages = count_substages(network, key_nodename, key_species)
nE = n_substages[1]
nL = n_substages[2]
nP = n_substages[3]
nJuv = nE + nL + nP
nM = n_substages[4]
nF = n_substages[5] * gN + nM + nJuv
Q = get_migration(network, key_species)
##################
# State space #
##################
# TODO: fix
E = u.x[index_node].x[index_organism][1:nE, :]
dE = @view du.x[index_node].x[index_organism][1:nE, :]
L = u.x[index_node].x[index_organism][(1 + nE):(nE + nL), :]
dL = @view du.x[index_node].x[index_organism][(1 + nE):(nE + nL), :]
P = u.x[index_node].x[index_organism][(1 + nE + nL):(nE + nL + nP), :]
dP = @view du.x[index_node].x[index_organism][(1 + nE + nL):(nE + nL + nP), :]
M = u.x[index_node].x[index_organism][1 + nJuv, :]
dM = @view du.x[index_node].x[index_organism][1 + nJuv, :]
F = u.x[index_node].x[index_organism][(1 + nM + nJuv):nF, :]
dF = @view du.x[index_node].x[index_organism][(1 + nM + nJuv):nF, :]
for gene_index in 1:gN
eggsnew = oviposit(F, node, key_species, genetics, gene_index, inputs, t)
create_egg!(dE, E, node, key_species, eggsnew, gene_index, inputs, t)
create_larva!(dL, L, E, node, key_species, gene_index, inputs, t)
create_pupa!(dP, P, L, node, key_species, gene_index, inputs, t)
create_male!(dM, M, P, Φ, Ξ_m, Ω, node, key_species, gene_index, inputs, t)
matematrix = mate(P, M, Φ, Ξ_f, Η, node, key_species, gene_index, inputs, t)
create_female!(
dF,
F,
Ω,
Ξ_f,
node,
key_species,
matematrix,
gene_index,
inputs,
t,
)
##################
# Migration #
##################
for n in 1:nE
dE[n, gene_index] =
dE[n, gene_index] +
Q[n, gene_index][index_node, :]' *
[u.x[i].x[index_organism][n, gene_index] for i in 1:n_nodes]
end
for n in 1:nL
dL[n, gene_index] =
dL[n, gene_index] +
Q[n + nE, gene_index][index_node, :]' *
[u.x[i].x[index_organism][n + nE, gene_index] for i in 1:n_nodes]
end
for n in 1:nP
dP[n, gene_index] =
dP[n, gene_index] +
Q[n + nE + nL, gene_index][index_node, :]' * [
u.x[i].x[index_organism][n + nE + nL, gene_index] for
i in 1:n_nodes
]
end
dM[gene_index] =
dM[gene_index] +
Q[nM + nE + nL + nP, gene_index][index_node, :]' * [
u.x[i].x[index_organism][nM + nE + nL + nP, gene_index] for
i in 1:n_nodes
]
for n in 1:gN
dF[n, gene_index] =
dF[n, gene_index] +
Q[n + nE + nL + nP + nM, gene_index][index_node, :]' * [
u.x[i].x[index_organism][n + nE + nL + nP + nM, gene_index] for
i in 1:n_nodes
]
end
end
end
end
end