Temporal matrices are identical and ignore extinctions when there is no rewiring

[SimmonsBI]

Elements of output[:p][:tmpA] are all identical when rewire_method = :none in simulate().

Elements of :tmpA should be updated to remove extinct species. e.g. by updating the A matrix as in the below code after each extinction:

extinct = out[:p][:extinctions] 
tokeep = trues(S)
tokeep[extinct] .= false 
A_i = out[:p][:A]
A_eq = A_i[tokeep, tokeep]

Example:

# Load packages
using BioEnergeticFoodWebs
using EcologicalNetworks

import Random.seed!
seed!(123)

siz = 10
con = 0.2
zed = 10.0
A_bool = EcologicalNetworks.nichemodel(siz, con) #use the niche model from Ecological Network to generate food webs
A = Int.(A_bool.A) #convert the UnipartiteNetwork object to Matrix of 1s and 0s
bm = ones(size(A, 1)) # assign biomasses of 1
p = model_parameters(A, Z = zed, rewire_method = :none)
out = simulate(p, bm, start=0, stop=500) 
out[:p][:tmpA][1] == out[:p][:tmpA][4] # true