From 1f722aaa53552ae0066b8d98a55b83102fb3b4b1 Mon Sep 17 00:00:00 2001
From: "michael d. catchen" <mdcatchen@gmail.com>
Date: Sat, 6 Jul 2024 10:47:05 -0400
Subject: [PATCH] samplers, last commit before network api rework

---
 src/realizable.jl |  8 ++++++-
 src/realize.jl    |  2 +-
 src/samplers.jl   | 58 ++++++++++++++++++++++++++++++++---------------
 3 files changed, 48 insertions(+), 20 deletions(-)

diff --git a/src/realizable.jl b/src/realizable.jl
index b639eb7..4edf1b9 100644
--- a/src/realizable.jl
+++ b/src/realizable.jl
@@ -36,7 +36,13 @@ function realizable(
     E = nfl.energy / unique_localities
     _scale = map(x -> _rate_matrix(x, θ, relabd_mat, E), net)
 
-    adj = sum(adjacency.(filter(!isnothing, _scale.network)))
+    adj = nothing
+    if typeof(_scale) <: Global 
+        adj = adjacency(_scale) 
+    else 
+        adj = sum(adjacency.(filter(x->!isnothing(x), _scale.network)))
+    end 
+    
     mw = SpeciesInteractionNetwork(net.metaweb.nodes, Binary(adj))
 
 
diff --git a/src/realize.jl b/src/realize.jl
index 5b61662..0f4fa26 100644
--- a/src/realize.jl
+++ b/src/realize.jl
@@ -12,7 +12,7 @@ end
 function realize(net::Network{Realizable,SC}) where {SC}
     _scale = map(_realize, net)
 
-    mw_adj = sum(adjacency.(filter(!isnothing, _scale.network)))
+    mw_adj = SC <: Global ? adjacency(_scale.network) : sum(adjacency.(filter(!isnothing, _scale.network)))
 
     mw = SpeciesInteractionNetwork(
         net.metaweb.nodes,
diff --git a/src/samplers.jl b/src/samplers.jl
index a2a1d92..abc12e1 100644
--- a/src/samplers.jl
+++ b/src/samplers.jl
@@ -1,39 +1,61 @@
 
 struct Static end
 
-@kwdef struct SpeciesInteractionSampler
+@kwdef struct SpeciesInteractionSampler{R,P}
     _feasibility_model = NicheModel()
-    _range_model = Static
-    _phenology_model = Static
+    _range_model::R = Static()
+    _phenology_model::P = Static()
     _abundance_model = NormalizedLogNormal()
     _realization_model = NeutrallyForbiddenLinks()
     _detection_model = RelativeAbundanceScaled()
 end
 
-struct Sample{L,A,D,G,T,Z,DT}
+struct Sample{L,D}
     λ::L
-    abd::A
-    δ::D
-    γ::G
-    θ::T
-    ζ::Z
-    detected::DT
+  #  abd::A
+  #  δ::D
+  #  γ::G
+  #  θ::T
+  #  ζ::Z
+    detected::D
 end
 Base.show(io::IO, s::Sample) = tprint(io, "Sample with FNR = $(falsenegativerate(s))")
 
+struct SampleSet{S<:Sample}
+    set::Vector{S}
+end
+Base.length(s::SampleSet) = length(s.set)
+falsenegativerate(s::SampleSet) = mean(falsenegativerate.(s.set))
+Base.show(io::IO, set::SampleSet) = tprint(io, "$(length(set)) samples with FNR = $(falsenegativerate(set))")
+
+
 function sample(sampler::SpeciesInteractionSampler, n::Integer)
-    [sample(sampler) for _ in 1:n]
+    SampleSet([sample(sampler) for _ in 1:n])
 end
 falsenegativerate(s::S) where {S<:Sample} = 1 - (sum(adjacency(s.detected.metaweb) .> 0) / sum(adjacency(s.λ.metaweb)))
 
-function sample(sampler::SpeciesInteractionSampler)
+_get_possible(::SpeciesInteractionSampler{R,P}, λ) where {R<:Static, P<:Static} = λ
+_get_possible(sampler::SpeciesInteractionSampler{R,P}, λ) where {R<:RangeGenerator, P<:Static} = begin 
+    ranges = generate(sampler._range_model, richness(λ))
+    possible(λ, ranges)
+end
+_get_possible(sampler::SpeciesInteractionSampler{R,P}, λ) where {R<:Static, P<:PhenologyGenerator} = begin
+    phen = generate(sampler._phenology_model, richness(λ))
+    possible(λ, phen)
+end
+_get_possible(sampler::SpeciesInteractionSampler{R,P}, λ) where {R<:RangeGenerator, P<:PhenologyGenerator} = begin
+    ranges = generate(sampler._range_model, richness(λ))
+    phen = generate(sampler._phenology_model, richness(λ))
+    possible(λ, ranges, phen)
+end
+
+function sample(sampler::SpeciesInteractionSampler{R,S}) where {R,S}
     λ = generate(sampler._feasibility_model)
     abd = generate(sampler._abundance_model, λ)
     δ = detectability(sampler._detection_model, λ, abd)
-    if sampler._range_model == Static && sampler._phenology_model <: Static
-        θ = realizable(sampler._realization_model, λ, abd)
-        ζ = realize(θ)
-        D = detect(ζ, δ)
-        Sample(λ, abd, δ, λ, θ, ζ, D)
-    end
+    γ = _get_possible(sampler, λ)
+    θ = realizable(sampler._realization_model, γ, abd)
+    ζ = realize(θ)
+    D = detect(ζ, δ)
+    return Sample(λ, D)
 end