Contributions towards Arma/Arima models (#531)

* Patch: Switch to fork of benchmarkCI (#520)

* patch to fork of benchmarkCI

* put fork version of BenchmarkCI in [sources]

* swap order

* add EpiAware [source]

* fix path

* rm benchmarkCI from project

* Patch fix: add `Manifest.toml` to benchmarking (#524)

* trigger

* Update benchmark.yaml

* Update benchmark.yaml

* commit benchmark Manifest

* try alternate approach

* Update benchmark.yaml

* Update EpiMethod.jl

* Update benchmark.yaml

* change baseline to origin/main

* remove trigger

* rm other trigger

* Issue 465: Add an infection generating model for ODE problems (#510)

* CompatHelper: bump compat for Turing to 0.35 for package EpiAware, (drop existing compat) (#516)

* CompatHelper: bump compat for Turing to 0.35 for package EpiAware, (drop existing compat)

* Update Project.toml

* fix Project.toml

---------

Co-authored-by: CompatHelper Julia <[email protected]>
Co-authored-by: Sam Abbott <[email protected]>
Co-authored-by: Samuel Brand <[email protected]>
Co-authored-by: Samuel Brand <[email protected]>

* CompatHelper: bump compat for DynamicPPL to 0.30 for package EpiAware, (drop existing compat) (#528)

Co-authored-by: CompatHelper Julia <[email protected]>

* rename IDD -> IID

* rename test file

* Issue 529: Create null Latent model (#530)

* Null Latent model

* Null Latent model

* fix doctest

* fix generate_epiaware unit tests

New usage of RW

* fix turing method test

underlying std of step size changed name

* fix broadcast test

Underlying std param changed name

* fix HN unit test

Default std prior had changed

* fix AR unit tests

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: CompatHelper Julia <[email protected]>
Co-authored-by: Sam Abbott <[email protected]>

.github/workflows/benchmark.yaml

@@ -21,10 +21,7 @@ jobs:
       - name: Install dependencies
         run: |
           julia --project=benchmark -e 'using Pkg;
-          Pkg.rm("EpiAware");
-          Pkg.resolve();
-          Pkg.instantiate();
-          Pkg.develop(path = "./EpiAware")'
+          Pkg.instantiate()'
       - name: Run benchmarks
         run: julia --project=benchmark -e 'using BenchmarkCI; BenchmarkCI.judge(; baseline = "origin/main", retune = true)'
       - name: Post results

.gitignore

@@ -391,3 +391,5 @@ EpiAware/docs/src/examples/*.md
 EpiAware/docs/src/getting-started/tutorials/censored-obs.md
 */Manifest*.toml
 EpiAware/docs/Manifest*.toml
+
+!benchmark/Manifest.toml

EpiAware/Project.toml

@@ -17,6 +17,7 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
 MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
 ManifoldDiff = "af67fdf4-a580-4b9f-bbec-742ef357defd"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Pathfinder = "b1d3bc72-d0e7-4279-b92f-7fa5d6d2d454"
 QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -33,19 +34,20 @@ AdvancedHMC = "0.6"
 DataFramesMeta = "0.15"
 Distributions = "0.25"
 DocStringExtensions = "0.9"
-DynamicPPL = "0.27, 0.28, 0.29, 0.30"
+DynamicPPL = "0.30"
 FillArrays = "1.11"
 HybridArrays = "0.4.16"
 LinearAlgebra = ">= 1.9"
 LogExpFunctions = "0.3"
 MCMCChains = "6.0"
 ManifoldDiff = "0.3.10"
-Pathfinder = "0.8"
+OrdinaryDiffEq = "6.89.0"
+Pathfinder = "0.9"
 QuadGK = "2.9"
-Random = ">= 1.9"
+Random = "1.11"
 Reexport = "1.2"
-SparseArrays = "1.10"
-Statistics = "1.10"
+SparseArrays = "1.11"
+Statistics = "1.11"
 Tables = "1.11"
-Turing = "0.32, 0.33, 0.34"
-julia = ">= 1.9"
+Turing = "0.35"
+julia = "1.11"

EpiAware/src/EpiAwareUtils/prefix_submodel.jl

@@ -20,7 +20,7 @@ submodel = prefix_submodel(FixedIntercept(0.1), generate_latent, string(1), 2)
 
 We can now draw a sample from the submodel.
 
-```julia
+```@example
 rand(submodel)
 ```
 "

EpiAware/src/EpiInfModels/EpiInfModels.jl

@@ -6,10 +6,15 @@ module EpiInfModels
 using ..EpiAwareBase
 using ..EpiAwareUtils
 
-using Turing, Distributions, DocStringExtensions, LinearAlgebra, LogExpFunctions
+using LogExpFunctions: xexpy
+
+using Turing, Distributions, DocStringExtensions, LinearAlgebra, OrdinaryDiffEq
+
+#Export parameter helpers
+export EpiData
 
 #Export models
-export EpiData, DirectInfections, ExpGrowthRate, Renewal
+export DirectInfections, ExpGrowthRate, Renewal, ODEProcess
 
 #Export functions
 export R_to_r, r_to_R, expected_Rt
@@ -20,6 +25,7 @@ include("DirectInfections.jl")
 include("ExpGrowthRate.jl")
 include("RenewalSteps.jl")
 include("Renewal.jl")
+include("ODEProcess.jl")
 include("utils.jl")
 
 end

EpiAware/src/EpiInfModels/ODEProcess.jl

@@ -0,0 +1,306 @@
+@doc raw"""
+A structure representing an infection process modeled by an Ordinary Differential Equation (ODE).
+At a high level, an `ODEProcess` struct object combines:
+
+- An `AbstractTuringParamModel` which defines the ODE model in terms of `OrdinaryDiffEq` types,
+     the parameters of the ODE model and a method to generate the parameters.
+- A technique for solving and interpreting the ODE model using the `SciML` ecosystem. This includes
+    the solver used in the ODE solution, keyword arguments to send to the solver and a function
+    to map the `ODESolution` solution object to latent infections.
+
+# Constructors
+- `ODEProcess(prob::ODEProblem; ts, solver, sol2infs)`: Create an `ODEProcess`
+object with the ODE problem `prob`, time points `ts`, solver `solver`, and function `sol2infs`.
+
+# Predefined ODE models
+Two basic ODE models are provided in the `EpiAware` package: `SIRParams` and `SEIRParams`.
+In both cases these are defined in terms of the proportions of the population in each compartment
+of the SIR and SEIR models respectively.
+
+## SIR model
+
+```math
+\begin{aligned}
+\frac{dS}{dt} &= -\beta SI \\
+\frac{dI}{dt} &= \beta SI - \gamma I \\
+\frac{dR}{dt} &= \gamma I
+\end{aligned}
+```
+Where `S` is the proportion of the population that is susceptible, `I` is the proportion of the
+population that is infected and `R` is the proportion of the population that is recovered. The
+parameters are the infectiousness `β` and the recovery rate `γ`.
+
+```jldoctest sirexample; output = false
+using EpiAware, OrdinaryDiffEq, Distributions
+
+# Create an instance of SIRParams
+sirparams = SIRParams(
+    tspan = (0.0, 100.0),
+    infectiousness = LogNormal(log(0.3), 0.05),
+    recovery_rate = LogNormal(log(0.1), 0.05),
+    initial_prop_infected = Beta(1, 99)
+)
+nothing
+
+# output
+
+```
+
+## SEIR model
+
+```math
+\begin{aligned}
+\frac{dS}{dt} &= -\beta SI \\
+\frac{dE}{dt} &= \beta SI - \alpha E \\
+\frac{dI}{dt} &= \alpha E - \gamma I \\
+\frac{dR}{dt} &= \gamma I
+\end{aligned}
+```
+Where `S` is the proportion of the population that is susceptible, `E` is the proportion of the
+population that is exposed, `I` is the proportion of the population that is infected and `R` is
+the proportion of the population that is recovered. The parameters are the infectiousness `β`,
+the incubation rate `α` and the recovery rate `γ`.
+
+```jldoctest; output = false
+using EpiAware, OrdinaryDiffEq, Distributions, Random
+Random.seed!(1234)
+
+# Create an instance of SIRParams
+seirparams = SEIRParams(
+    tspan = (0.0, 100.0),
+    infectiousness = LogNormal(log(0.3), 0.05),
+    incubation_rate = LogNormal(log(0.1), 0.05),
+    recovery_rate = LogNormal(log(0.1), 0.05),
+    initial_prop_infected = Beta(1, 99)
+)
+nothing
+
+# output
+
+```
+
+# Usage example with `ODEProcess` and predefined SIR model
+
+In this example we define an `ODEProcess` object using the predefined `SIRParams` model from
+above. We then generate latent infections using the `generate_latent_infs` function, and refit
+the model using a `Turing` model.
+
+We assume that the latent infections are observed with a Poisson likelihood around their
+ODE model prediction. The population size is `N = 1000`, which we put into the `sol2infs` function,
+which maps the ODE solution to the number of infections. Recall that the `EpiAware` default SIR
+implementation assumes the model is in density/proportion form. Also, note that since the `sol2infs`
+function is a link function that maps the ODE solution to the expected number of infections we also
+apply the `LogExpFunctions.softplus` function to ensure that the expected number of infections is non-negative.
+Note that the `softplus` function is a smooth approximation to the ReLU function `x -> max(0, x)`.
+The utility of this approach is that small negative output from the ODE solver (e.g. ~ -1e-10) will be
+mapped to small positive values, without needing to use strict positivity constraints in the model.
+
+First, we define the `ODEProcess` object which combines the SIR model with the `sol2infs` link
+function and the solver options.
+
+```jldoctest sirexample; output = false
+using Turing, LogExpFunctions
+N = 1000.0
+
+sir_process = ODEProcess(
+    params = sirparams,
+    sol2infs = sol -> softplus.(N .* sol[2, :]),
+    solver_options = Dict(:verbose => false, :saveat => 1.0)
+)
+nothing
+
+# output
+
+```
+
+Second, we define a `PoissionError` observation model for linking the  the number of infections.
+
+```jldoctest sirexample; output = false
+pois_obs = PoissonError()
+nothing
+
+# output
+
+```
+
+Next, we create a `Turing` model for the full generative process: this solves the ODE model for
+the latent infections and then samples the observed infections from a Poisson distribution with this
+as the average.
+
+NB: The `nothing` argument is a dummy latent process, e.g. a log-Rt time series, that is not
+used in the SIR model, but might be used in other models.
+
+```jldoctest sirexample; output = false
+@model function fit_ode_model(data)
+    @submodel I_t = generate_latent_infs(sir_process, nothing)
+    @submodel y_t = generate_observations(pois_obs, data, I_t)
+
+    return y_t
+end
+nothing
+
+# output
+
+```
+
+We can generate some test data from the model by passing `missing` as the argument to the model.
+This tells `Turing` that there is no data to condition on, so it will sample from the prior parameters
+and then generate infections. In this case, we do it in a way where we cache the sampled parameters
+as `θ` for later use.
+
+```jldoctest sirexample; output = false
+# Sampled parameters
+gen_mdl = fit_ode_model(missing)
+θ = rand(gen_mdl)
+test_data = (gen_mdl | θ)()
+nothing
+
+# output
+
+```
+
+Now, we can refit the model but this time we condition on the test data. We suppress the
+output of the sampling process to keep the output clean, but you can remove the `@suppress` macro.
+
+```jldoctest sirexample; output = false
+using Suppressor
+inference_mdl = fit_ode_model(test_data)
+chn = Suppressor.@suppress sample(inference_mdl, NUTS(), 2_000)
+summarize(chn)
+nothing
+
+# output
+
+```
+
+We can compare the summarized chain to the sampled parameters in `θ` to see that the model is
+fitting the data well and recovering a credible interval containing the true parameters.
+
+# Custom ODE models
+
+To define a custom ODE model, you need to define:
+
+- Some `CustomModel <: AbstractTuringLatentModel` struct
+    that contains the ODE problem as a field called `prob`, as well as sufficient fields to
+    define or sample the parameters of the ODE model.
+- A method for `EpiAwareBase.generate_latent(params::CustomModel, Z_t)` that generates the
+    initial condition and parameters of the ODE model, potentially conditional on a sample from a latent process `Z_t`.
+    This method must return a `Tuple` `(u0, p)` where `u0` is the initial condition and `p` is the parameters.
+
+Here is an example of a simple custom ODE model for _specified_ exponential growth:
+
+```jldoctest customexample; output = false
+using EpiAware, Turing, OrdinaryDiffEq
+# Define a simple exponential growth model for testing
+function expgrowth(du, u, p, t)
+    du[1] = p[1] * u[1]
+end
+
+r = log(2) / 7 # Growth rate corresponding to 7 day doubling time
+
+# Define the ODE problem using SciML
+prob = ODEProblem(expgrowth, [1.0], (0.0, 10.0), [r])
+
+# Define the custom parameters struct
+struct CustomModel <: AbstractTuringLatentModel
+    prob::ODEProblem
+    r::Float64
+    u0::Float64
+end
+custom_ode = CustomModel(prob, r, 1.0)
+
+# Define the custom generate_latent function
+@model function EpiAwareBase.generate_latent(params::CustomModel, n)
+    return ([params.u0], [params.r])
+end
+nothing
+
+# output
+
+```
+
+This model is not random! But we can still use it to generate latent infections.
+
+```jldoctest customexample; output = false
+# Define the ODEProcess
+expgrowth_model = ODEProcess(
+    params = custom_ode,
+    sol2infs = sol -> sol[1, :]
+)
+infs = generate_latent_infs(expgrowth_model, nothing)()
+nothing
+
+# output
+
+```
+"""
+@kwdef struct ODEProcess{
+    P <: AbstractTuringLatentModel, S, F <: Function, D <:
+                                                      Union{Dict, NamedTuple}} <:
+              EpiAwareBase.AbstractTuringEpiModel
+    "The ODE problem and parameters, where `P` is a subtype of `AbstractTuringLatentModel`."
+    params::P
+    "The solver used for the ODE problem. Default is `AutoVern7(Rodas5())`, which is an auto
+    switching solver aimed at medium/low tolerances."
+    solver::S = AutoVern7(Rodas5())
+    "A function that maps the solution object of the ODE to infection counts."
+    sol2infs::F
+    "The extra solver options for the ODE problem. Can be either a `Dict` or a `NamedTuple`
+    containing the solver options."
+    solver_options::D = Dict(:verbose => false, :saveat => 1.0)
+end
+
+@doc raw"""
+Implement the `generate_latent_infs` function for the `ODEProcess` model.
+
+This function remakes the ODE problem with the provided initial conditions and parameters,
+    solves it using the specified solver, and then transforms the solution into latent infections
+    using the `sol2infs` function.
+
+# Example usage with predefined SIR model
+
+In this example we define an `ODEProcess` object using the predefined `SIRParams` model and
+generate an expected infection time series using SIR model parameters sampled from their priors.
+
+```jldoctest; output = false
+using EpiAware, OrdinaryDiffEq, Distributions, Turing, LogExpFunctions
+
+# Create an instance of SIRParams
+sirparams = SIRParams(
+    tspan = (0.0, 100.0),
+    infectiousness = LogNormal(log(0.3), 0.05),
+    recovery_rate = LogNormal(log(0.1), 0.05),
+    initial_prop_infected = Beta(1, 99)
+)
+
+#Population size
+
+N = 1000.0
+
+sir_process = ODEProcess(
+    params = sirparams,
+    sol2infs = sol -> softplus.(N .* sol[2, :]),
+    solver_options = Dict(:verbose => false, :saveat => 1.0)
+)
+
+generated_It = generate_latent_infs(sir_process, nothing)()
+nothing
+
+# output
+
+```
+
+"""
+@model function EpiAwareBase.generate_latent_infs(epi_model::ODEProcess, Z_t)
+    prob, solver, sol2infs, solver_options = epi_model.params.prob,
+    epi_model.solver, epi_model.sol2infs, epi_model.solver_options
+    n = isnothing(Z_t) ? 0 : size(Z_t, 1)
+
+    @submodel u0, p = generate_latent(epi_model.params, n)
+
+    _prob = remake(prob; u0 = u0, p = p)
+    sol = solve(_prob, solver; solver_options...)
+    I_t = sol2infs(sol)
+
+    return I_t
+end