Merge pull request #128 from CDCgov/issue53

Issue 53: First pass at differenced AR

EpiAware/src/EpiAware.jl

@@ -48,7 +48,7 @@ export spread_draws, scan, create_discrete_pmf
 include("EpiLatentModels/EpiLatentModels.jl")
 using .EpiLatentModels
 
-export RandomWalk, default_rw_priors
+export RandomWalk, AR
 
 include("EpiInfModels/EpiInfModels.jl")
 using .EpiInfModels

EpiAware/src/EpiAwareBase/EpiAwareBase.jl

@@ -10,6 +10,7 @@ export AbstractModel, AbstractEpiModel, AbstractLatentModel,
        AbstractObservationModel, generate_latent,
        generate_latent_infs, generate_observations
 
+include("docstrings.jl")
 include("types.jl")
 include("functions.jl")
 

EpiAware/src/EpiAwareBase/docstrings.jl

@@ -0,0 +1,24 @@
+@template (FUNCTIONS, METHODS, MACROS) = """
+                                             $(TYPEDSIGNATURES)
+                                         $(DOCSTRING)
+                                         """
+
+@template (TYPES) = """
+                        $(TYPEDEF)
+                    $(DOCSTRING)
+
+                    ---
+                    ## Fields
+                    $(TYPEDFIELDS)
+                    """
+
+@template MODULES = """
+$(DOCSTRING)
+
+---
+## Exports
+$(EXPORTS)
+---
+## Imports
+$(IMPORTS)
+"""

EpiAware/src/EpiAwareUtils/EpiAwareUtils.jl

@@ -14,6 +14,7 @@ using DocStringExtensions, QuadGK
 
 export scan, spread_draws, create_discrete_pmf
 
+include("docstrings.jl")
 include("prior-tools.jl")
 include("distributions.jl")
 include("scan.jl")

EpiAware/src/EpiAwareUtils/docstrings.jl

@@ -0,0 +1,24 @@
+@template (FUNCTIONS, METHODS, MACROS) = """
+                                             $(TYPEDSIGNATURES)
+                                         $(DOCSTRING)
+                                         """
+
+@template (TYPES) = """
+                        $(TYPEDEF)
+                    $(DOCSTRING)
+
+                    ---
+                    ## Fields
+                    $(TYPEDFIELDS)
+                    """
+
+@template MODULES = """
+$(DOCSTRING)
+
+---
+## Exports
+$(EXPORTS)
+---
+## Imports
+$(IMPORTS)
+"""

EpiAware/src/EpiInfModels/EpiInfModels.jl

@@ -13,6 +13,7 @@ using Turing, Distributions, DocStringExtensions, LinearAlgebra
 export EpiData, DirectInfections, ExpGrowthRate, Renewal,
        R_to_r, r_to_R
 
+include("docstrings.jl")
 include("epidata.jl")
 include("directinfections.jl")
 include("expgrowthrate.jl")

EpiAware/src/EpiInfModels/docstrings.jl

@@ -0,0 +1,24 @@
+@template (FUNCTIONS, METHODS, MACROS) = """
+                                             $(TYPEDSIGNATURES)
+                                         $(DOCSTRING)
+                                         """
+
+@template (TYPES) = """
+                        $(TYPEDEF)
+                    $(DOCSTRING)
+
+                    ---
+                    ## Fields
+                    $(TYPEDFIELDS)
+                    """
+
+@template MODULES = """
+$(DOCSTRING)
+
+---
+## Exports
+$(EXPORTS)
+---
+## Imports
+$(IMPORTS)
+"""

EpiAware/src/EpiInference/EpiInference.jl

@@ -10,6 +10,7 @@ using DynamicPPL, DocStringExtensions
 
 export manypathfinder
 
+include("docstrings.jl")
 include("manypathfinder.jl")
 
 end

EpiAware/src/EpiInference/docstrings.jl

@@ -0,0 +1,24 @@
+@template (FUNCTIONS, METHODS, MACROS) = """
+                                             $(TYPEDSIGNATURES)
+                                         $(DOCSTRING)
+                                         """
+
+@template (TYPES) = """
+                        $(TYPEDEF)
+                    $(DOCSTRING)
+
+                    ---
+                    ## Fields
+                    $(TYPEDFIELDS)
+                    """
+
+@template MODULES = """
+$(DOCSTRING)
+
+---
+## Exports
+$(EXPORTS)
+---
+## Imports
+$(IMPORTS)
+"""

EpiAware/src/EpiLatentModels/EpiLatentModels.jl

@@ -8,8 +8,10 @@ using ..EpiAwareBase
 
 using Turing, Distributions, DocStringExtensions
 
-export RandomWalk, default_rw_priors
+export RandomWalk, AR
 
+include("docstrings.jl")
 include("randomwalk.jl")
-
+include("autoregressive.jl")
+include("utils.jl")
 end

EpiAware/src/EpiLatentModels/autoregressive.jl

@@ -0,0 +1,95 @@
+@doc raw"
+The autoregressive (AR) model struct.
+
+# Constructors
+- `AR(damp_prior::Distribution, std_prior::Distribution, init_prior::Distribution; p::Int = 1)`: Constructs an AR model with the specified prior distributions for damping coefficients, standard deviation, and initial conditions. The order of the AR model can also be specified.
+
+- `AR(; damp_priors::Vector{D} = [truncated(Normal(0.0, 0.05))], std_prior::Distribution = truncated(Normal(0.0, 0.05), 0.0, Inf), init_priors::Vector{I} = [Normal()]) where {D <: Distribution, I <: Distribution}`: Constructs an AR model with the specified prior distributions for damping coefficients, standard deviation, and initial conditions. The order of the AR model is determined by the length of the `damp_priors` vector.
+
+- `AR(damp_prior::Distribution, std_prior::Distribution, init_prior::Distribution, p::Int)`: Constructs an AR model with the specified prior distributions for damping coefficients, standard deviation, and initial conditions. The order of the AR model is explicitly specified.
+
+# Examples
+
+```julia
+using Distributions
+using EpiAware
+ar = AR()
+ar_model = generate_latent(ar, 10)
+rand(ar_model)
+```
+"
+struct AR{D <: Sampleable, S <: Sampleable, I <: Sampleable, P <: Int} <:
+       AbstractLatentModel
+    "Prior distribution for the damping coefficients."
+    damp_prior::D
+    "Prior distribution for the standard deviation."
+    std_prior::S
+    "Prior distribution for the initial conditions"
+    init_prior::I
+    "Order of the AR model."
+    p::P
+    function AR(damp_prior::Distribution, std_prior::Distribution,
+            init_prior::Distribution; p::Int = 1)
+        damp_priors = fill(damp_prior, p)
+        init_priors = fill(init_prior, p)
+        return AR(; damp_priors = damp_priors, std_prior = std_prior,
+            init_priors = init_priors)
+    end
+
+    function AR(; damp_priors::Vector{D} = [truncated(Normal(0.0, 0.05), 0, 1)],
+            std_prior::Distribution = truncated(Normal(0.0, 0.05), 0.0, Inf),
+            init_priors::Vector{I} = [Normal()]) where {
+            D <: Distribution, I <: Distribution}
+        p = length(damp_priors)
+        damp_prior = _expand_dist(damp_priors)
+        init_prior = _expand_dist(init_priors)
+        return AR(damp_prior, std_prior, init_prior, p)
+    end
+
+    function AR(damp_prior::Distribution, std_prior::Distribution,
+            init_prior::Distribution, p::Int)
+        @assert p>0 "p must be greater than 0"
+        @assert length(damp_prior)==length(init_prior) "damp_prior and init_prior must have the same length"
+        @assert p==length(damp_prior) "p must be equal to the length of damp_prior"
+        new{typeof(damp_prior), typeof(std_prior), typeof(init_prior), typeof(p)}(
+            damp_prior, std_prior, init_prior, p
+        )
+    end
+end
+
+@doc raw"
+Generate a latent AR series.
+
+# Arguments
+
+- `latent_model::AR`: The AR model.
+- `n::Int`: The length of the AR series.
+
+# Returns
+- `ar::Vector{Float64}`: The generated AR series.
+- `params::NamedTuple`: A named tuple containing the generated parameters (`σ_AR`, `ar_init`, `damp_AR`).
+
+# Notes
+- The length of `damp_prior` and `init_prior` must be the same.
+- `n` must be longer than the order of the autoregressive process.
+"
+@model function EpiAwareBase.generate_latent(latent_model::AR, n)
+    p = latent_model.p
+    ϵ_t ~ MvNormal(ones(n - p))
+    σ_AR ~ latent_model.std_prior
+    ar_init ~ latent_model.init_prior
+    damp_AR ~ latent_model.damp_prior
+
+    @assert n>p "n must be longer than order of the autoregressive process"
+
+    # Initialize the AR series with the initial values
+    ar = Vector{Float64}(undef, n)
+    ar[1:p] = ar_init
+
+    # Generate the rest of the AR series
+    for t in (p + 1):n
+        ar[t] = damp_AR' * ar[(t - p):(t - 1)] + σ_AR * ϵ_t[t - p]
+    end
+
+    return ar, (; σ_AR, ar_init, damp_AR)
+end

EpiAware/src/EpiLatentModels/docstrings.jl

@@ -0,0 +1,24 @@
+@template (FUNCTIONS, METHODS, MACROS) = """
+                                             $(TYPEDSIGNATURES)
+                                         $(DOCSTRING)
+                                         """
+
+@template (TYPES) = """
+                        $(TYPEDEF)
+                    $(DOCSTRING)
+
+                    ---
+                    ## Fields
+                    $(TYPEDFIELDS)
+                    """
+
+@template MODULES = """
+$(DOCSTRING)
+
+---
+## Exports
+$(EXPORTS)
+---
+## Imports
+$(IMPORTS)
+"""

EpiAware/src/EpiLatentModels/randomwalk.jl

@@ -1,11 +1,6 @@
-struct RandomWalk{D <: Sampleable, S <: Sampleable} <: AbstractLatentModel
-    init_prior::D
-    std_prior::S
-end
-
-function default_rw_priors()
-    return (:var_RW_prior => truncated(Normal(0.0, 0.05), 0.0, Inf),
-        :init_rw_value_prior => Normal()) |> Dict
+@kwdef struct RandomWalk{D <: Sampleable, S <: Sampleable} <: AbstractLatentModel
+    init_prior::D = Normal()
+    std_prior::S = truncated(Normal(0.0, 0.05), 0.0, Inf)
 end
 
 @model function EpiAwareBase.generate_latent(latent_model::RandomWalk, n)

EpiAware/src/EpiLatentModels/utils.jl

@@ -0,0 +1,6 @@
+function _expand_dist(dist::Vector{D} where {D <: Distribution})
+    d = length(dist)
+    product_dist = all(first(dist) .== dist) ?
+                   filldist(first(dist), d) : arraydist(dist)
+    return product_dist
+end

EpiAware/src/EpiObsModels/EpiObsModels.jl

@@ -12,6 +12,7 @@ using Turing, Distributions, DocStringExtensions, SparseArrays
 
 export DelayObservations, default_delay_obs_priors
 
+include("docstrings.jl")
 include("delayobservations.jl")
 include("utils.jl")
 

EpiAware/src/EpiObsModels/docstrings.jl

@@ -0,0 +1,24 @@
+@template (FUNCTIONS, METHODS, MACROS) = """
+                                             $(TYPEDSIGNATURES)
+                                         $(DOCSTRING)
+                                         """
+
+@template (TYPES) = """
+                        $(TYPEDEF)
+                    $(DOCSTRING)
+
+                    ---
+                    ## Fields
+                    $(TYPEDFIELDS)
+                    """
+
+@template MODULES = """
+$(DOCSTRING)
+
+---
+## Exports
+$(EXPORTS)
+---
+## Imports
+$(IMPORTS)
+"""