Hi,

I am trying to estimate the parameters of a ODE model with N equations. The model’s output are probabilities, ie, a vector of N probabilities each time step. Each coordinate of the vector defines the probability that patch i is occupied at time t. The observed data is 0/1 which means empty/occupied, this data is yearly. So I am using a Bernoulli distribution for the likelihood.

I have the output of the model which is “continuous” and I compare it with the 0/1 of the observed data. To do that I take t = 15 August year X from the output of the model and compare to the 0/1 of this year X. Also the model is non autonomous so it has a parameter that depends on time, which I interpolate and after in the model ODE it calls this interpolation to compute the value of the parameter. So I have some issues:

- There is no multivariate Bernouilli. So I do it in two loops as it can be seen in the code.
- This is an example with fake data when I run it with the real data i get many warnings from the SciMLBase:

I am using rtil = 1e-20 and the DP8() for solving the ODE. - The size of the system is big and it takes ages. Just to solve the ODE it takes minutes. Is there a way to make it faster?

I do not know if there is something that I am doing wrong and this is why it never finish or its just slow due to the cost of the integration method.

This is how I code this using fake input data:

```
# Code that integrates the Hanski model to obtain the solutions
# With input: (from code input_Hanski.R)
# . Distance matrix
# . Flow matrix
# . Area vector
# . R_M vector
# And estimate the parameters of the model from the presence absence data
# Load pkgs and remove data -----------------------------------------------------
import Pkg
using DifferentialEquations
using DataFrames
using CSV
using Plots
using Shapefile
import GeoDataFrames as GDF
using LinearAlgebra
using ODE
using Interpolations
using DiffEqParamEstim
using SparseArrays
using ParameterizedFunctions
#using RecursiveArrayTools
using Optimization
using Distributions
# Constants
m_c = 0.001 # probability of mosquito in a car
alp = 1/200 # average natural dispersal distance
# Create fake data
end_ind = 5
eta = rand(Uniform(0, 1000),end_ind, end_ind)
eta[diagind(eta)] .= 0
# Set to zero random entraces
eta[1,4] = 0
eta[2,3] = 0
eta[5,1:end] .= 0
N = size(eta, 1) # Number of patches
d_1 = rand(Uniform(0, 100),end_ind, end_ind)
d_1[5,:] .= rand(Uniform(900, 1000),end_ind,1)
typeof(d_1[1,1])
mat = exp.(-alp*d_1)
mat[diagind(mat)] .= 0 # Set to zero diagonal of distance
# Choose number of patches and IC
pop_init = zeros(N)
pop_init[1] = 1
# Fake time series
num_years = 6
num_days = 365*num_years
days = 1:num_days
days_per_year = 365
dates = collect(1:num_days)
# Fake seasonal
R_Ms = zeros(num_days,end_ind)
R_Ms[1:end,1] .= (30 .+ 10 * sin.(2 * π * days / days_per_year) + 2. * randn(num_days))./10
R_Ms[1:end,2] .= (30 .+ 10 * sin.(2 * π * days / days_per_year) + 2. * randn(num_days))./30
R_Ms[1:end,3] .= (30 .+ 10 * sin.(2 * π * days / days_per_year) + 2. * randn(num_days))./40
R_Ms[1:end,4] .= (30 .+ 10 * sin.(2 * π * days / days_per_year) + 2. * randn(num_days))./10
R_Ms[1:end,5] .= (30 .+ 10 * sin.(2 * π * days / days_per_year) + 2. * randn(num_days))./100
plot(days, R_Ms[1:end,1], title="Positive Seasonal Pattern with Random Variation", xlabel="Days", ylabel="Value")
# Create an array to store interpolated functions
interpolated_functions = []
# Perform interpolation for each location
for i in 1:end_ind
# Extract temperature values for the current location
R_Ms_val = R_Ms[:, i]
dates_num = 1:size(dates, 1)
# Perform linear interpolation
itp = LinearInterpolation(dates_num, R_Ms_val,extrapolation_bc=Flat())
# Store the interpolated function
push!(interpolated_functions, itp)
end
plot(interpolated_functions[1:N])
# Integration non autonomous
function fun_na!(du, u, p, t)
R_M_vec = [interpolated_functions[i](t) for i in 1:N]
eta1 = 1.0./(1.0 .+ exp.(-p[4].*eta.+p[5]))
Cd = p[1].*mat*u # Natural dispersal
Ch = p[2].*(m_c*eta1)*u # Human mobility
du.= R_M_vec.*(Cd .+ Ch) .* (1 .- u) - p[3] .* u
nothing
end
# Set parameters
t0=0.0
tf=2000.0
tspan = (t0, tf)
t_vect=1:tf
u0 = pop_init
p = [0.001,0.001,0.001,0.5,500]
# Create the ode model
prob = DifferentialEquations.ODEProblem(fun_na!, u0, tspan, p)
rtol=1e-14
alg= DP8() #For low tolerances, Rodas4()
# Test Integrate ODE
@time sol = DifferentialEquations.solve(prob,alg,reltol = rtol)
plot(sol)
# Create the vector of times of the observation. Assuming we observe in August 15 (or 16 depending onn leap years)
t_obs = zeros(num_years)
t_obs[1] = 227
for i = 2:length(t_obs)
t_obs[i] = t_obs[i-1] + 365
end
# Create fake obs if p(t)>0.5 then 1
matrix_obs = zeros(end_ind,num_years)
# Loop through unique id_mitma values
for i in 1:end_ind
# Get years for the current id_mitma
for j in 1:num_years
prob = sol(t_obs[j])[i]
# Convert years to indices in the matrix
if (prob > 0.5)
matrix_obs[i,j:end] .= 1
end
end
end
# Load packages
using Turing
using StatsPlots
# Estimation Bayesian --------------------------------
@model function fitlv(data, prob)
# Prior distributions.
c_d_dist ~ Uniform(0.1e-4, 0.1)
c_h_dist ~ Uniform(0.1e-4, 0.1)
e_dist ~ Uniform(0.1e-7, 0.1)
a_dist ~ Uniform(0.1, 0.8)
b_dist ~ Uniform(450,550)
# Simulate Hanski model.
p = [c_d_dist, c_h_dist, e_dist,a_dist,b_dist]
#print("p:\n")
#print(p)
predicted = DifferentialEquations.solve(prob,alg,reltol = rtol) # Observations.
#if length(predicted) > 0
for i in 1:length(t_obs)
predicted_value = predicted(t_obs[i])
for j in 1:length(predicted_value)
data[j, i] ~ Bernoulli(clamp(predicted_value[j],0,1)) # Ensure it's a probability it goes to -7.e-10 which is zero
end
end
return nothing
end
# Save the Bayesian model to fit with the observed data and the ode model
prob = DifferentialEquations.ODEProblem(fun_na!, u0, tspan, p)
model = fitlv(matrix_obs, prob)
# Sample 3 independent chains with forward-mode automatic differentiation (the default).
iterations = 1000
print("Before MCMC")
chain = sample(model, NUTS(), MCMCSerial(),1000, 3,
init_params = [0.01, 0.01, 0.001,0.45,490] ; progress=false, verbose = false)
```