Merge pull request #23 from jangevaare/dev

v0.4.7

.travis.yml

@@ -1,18 +1,16 @@
-# Documentation: http://docs.travis-ci.com/user/languages/julia/
+## Documentation: http://docs.travis-ci.com/user/languages/julia/
+codecov: true
 language: julia
 os:
   - linux
   - osx
 julia:
   - 1.1
-  - 1.2
-  - 1.3
+  - 1.4
   - nightly
 notifications:
   email: false
 matrix:
   allow_failures:
     - julia: nightly
-  fast_finish: true
-after_success:
-  - julia -e 'using Pkg; Pkg.add("Coverage"); using Coverage; Codecov.submit(process_folder())'
+  fast_finish: true

Project.toml

@@ -1,7 +1,7 @@
 name = "Pathogen"
 uuid = "c8189ad9-0349-5cbb-98f2-579781f27e5c"
 authors = ["Justin Angevaare <justinangevaare@gmail.com>"]
-version = "0.4.6"
+version = "0.4.7"
 
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"

src/Pathogen.jl

@@ -15,41 +15,47 @@ module Pathogen
   import StatsBase.mean,
          ProgressMeter.next!
 
-  # Types
-  include("types/EpidemicModel.jl")
-  include("types/DiseaseState.jl")
-  include("types/Population.jl")
-  include("types/Events/Event.jl")
-  include("types/Events/Events.jl")
-  include("types/Events/EventExtents.jl")
-  include("types/Events/EventObservations.jl")
-  include("types/Events/EventRates.jl")
-  include("types/Risks/AbstractRisk.jl")
-  include("types/Risks/RiskFunctions.jl")
-  include("types/Risks/RiskParameters.jl")
-  include("types/Risks/RiskPriors.jl")
-  include("types/Transmissions/Transmission.jl")
-  include("types/Transmissions/TransmissionNetwork.jl")
-  include("types/Transmissions/TransmissionRates.jl")
-  include("types/Simulation.jl")
-  include("types/MarkovChain.jl")
-  include("types/MCMC.jl")
-  include("types/Transmissions/TransmissionNetworkDistribution.jl")
+  # Core
+  include("core/EpidemicModel.jl")
+  include("core/DiseaseState.jl")
+  include("core/Population.jl")
+  include("core/Events/Event.jl")
+  include("core/Events/Events.jl")
+  include("core/Events/EventRates.jl")
+  include("core/Risks/AbstractRisk.jl")
+  include("core/Risks/RiskFunctions.jl")
+  include("core/Risks/RiskParameters.jl")
+  include("core/Transmissions/Transmission.jl")
+  include("core/Transmissions/TransmissionNetwork.jl")
+  include("core/Transmissions/TransmissionRates.jl")
+  include("core/initialize.jl")
+  include("core/update!.jl")
 
-  # Functions
-  include("functions/_pathway_from.jl")
-  include("functions/_pathway_to.jl")
-  include("functions/_accept.jl")
-  include("functions/_bounds.jl")
-  include("functions/generate.jl")
-  include("functions/initialize.jl")
-  include("functions/observe.jl")
-  include("functions/update!.jl")
-  include("functions/simulate!.jl")
-  include("functions/loglikelihood.jl")
-  include("functions/logpriors.jl")
-  include("functions/start!.jl")
-  include("functions/iterate!.jl")
+  # Simulation
+  include("simulation/Simulation.jl")
+  include("simulation/generate.jl")
+  include("simulation/simulate!.jl")
+  include("simulation/update!.jl")
+  include("simulation/EventObservations.jl")
+  include("simulation/observe.jl")
+
+  # Inference
+  include("inference/TransmissionNetworkDistribution.jl")
+  include("inference/RiskPriors.jl")
+  include("inference/EventExtents.jl")
+  include("inference/MarkovChain.jl")
+  include("inference/MCMC.jl")
+  include("inference/_pathway_from.jl")
+  include("inference/_pathway_to.jl")
+  include("inference/_accept.jl")
+  include("inference/_bounds.jl")
+  include("inference/generate.jl")
+  include("inference/initialize.jl")
+  include("inference/update!.jl")
+  include("inference/loglikelihood.jl")
+  include("inference/logpriors.jl")
+  include("inference/start!.jl")
+  include("inference/iterate!.jl")
 
   # Visualization
   include("visualization/epidemic_curve.jl")

src/types/Events/Event.jl → src/core/Events/Event.jl

@@ -1,11 +1,6 @@
 abstract type AbstractEvent end
 
 struct NoEvent <: AbstractEvent
-  time::Float64
-
-  function NoEvent()
-    return new(Inf)
-  end
 end
 
 struct Event{T <: EpidemicModel} <: AbstractEvent
@@ -26,10 +21,14 @@ struct Event{T <: EpidemicModel} <: AbstractEvent
   end
 end
 
-function _time(x::AbstractEvent) where T <: EpidemicModel
+function _time(x::Event{T}) where T <: EpidemicModel
   return x.time
 end
 
+function _time(x::NoEvent)
+  return Inf
+end
+
 # function Base.copy(x::Event{T}) where T <: EpidemicModel
 #   return Event{T}(copy(x.time), copy(x.id), copy(x.new_state))
 # end

src/types/Transmissions/TransmissionRates.jl → src/core/Transmissions/TransmissionRates.jl

@@ -18,10 +18,10 @@ struct TransmissionRates
   end
 end
 
-function Base.copy(x::TransmissionRates)
-  return TransmissionRates(copy(x.external),
-                           copy(x.internal))
-end
+# function Base.copy(x::TransmissionRates)
+#   return TransmissionRates(copy(x.external),
+#                            copy(x.internal))
+# end
 
 function Base.sum(x::TransmissionRates)
   return sum(x.external) + sum(x.internal)

src/core/initialize.jl

@@ -0,0 +1,48 @@
+function initialize(::Type{TransmissionRates},
+                    states::Vector{DiseaseState},
+                    pop::Population,
+                    rf::RiskFunctions{T},
+                    rp::RiskParameters{T}) where T <: EpidemicModel
+  n_ids = length(states)
+  tr = TransmissionRates(n_ids)
+  for i in findall(states .== Ref(State_S))
+    # External exposure
+    #tr.external[i] = rf.susceptibility(rp.susceptibility, pop, i) * rf.sparks(rp.sparks, pop, i)
+    tr.external[i] = rf.sparks(rp.sparks, pop, i)
+    # Internal exposure
+    for k in findall(states .== Ref(State_I))
+      tr.internal[k, i] = rf.susceptibility(rp.susceptibility, pop, i) *
+                          rf.infectivity(rp.infectivity, pop, i, k) *
+                          rf.transmissibility(rp.transmissibility, pop, k)
+    end
+  end
+  @debug "Initialization of $T TransmissionRates complete" external = tr.external ∑external = sum(tr.external) internal = tr.internal ∑internal = sum(tr.internal)
+  return tr
+end
+
+function initialize(::Type{EventRates},
+                    tr::TransmissionRates,
+                    states::Vector{DiseaseState},
+                    pop::Population,
+                    rf::RiskFunctions{T},
+                    rp::RiskParameters{T}) where T <: EpidemicModel
+  n_ids = length(states)
+  rates = EventRates{T}(n_ids)
+  for i = 1:n_ids
+    if states[i] == State_S
+      if T in [SEIR; SEI]
+        rates.exposure[i] = tr.external[i] + sum(tr.internal[:,i])
+      elseif T in [SIR; SI]
+        rates.infection[i] = tr.external[i] + sum(tr.internal[:,i])
+      end
+    elseif states[i] == State_E
+      rates.infection[i] = rf.latency(rp.latency, pop, i)
+    elseif states[i] == State_I
+      if T in [SEIR; SIR]
+        rates.removal[i] = rf.removal(rp.removal, pop, i)
+      end
+    end
+  end
+  @debug "Initialization of $T EventRates complete" rates = rates[_state_progressions[T][2:end]]
+  return rates
+end

src/core/update!.jl

@@ -0,0 +1,120 @@
+function update!(events::Events{T},
+                 event::Event{T}) where T <: EpidemicModel
+  events[event.new_state][event.individual] = event.time
+  return events
+end
+
+function update!(states::Vector{DiseaseState},
+                 event::Event{T}) where T <: EpidemicModel
+  states[event.individual] = event.new_state
+  return states
+end
+
+function update!(net::TransmissionNetwork,
+                 xfer::ExogenousTransmission)
+  net.external[xfer.individual] = true
+  return net
+end
+
+function update!(net::TransmissionNetwork,
+                 xfer::EndogenousTransmission)
+  net.internal[xfer.source, xfer.individual] = true
+  return net
+end
+
+function update!(net::TransmissionNetwork,
+                 xfer::NoTransmission)
+  return net
+end
+
+function update!(tr::TransmissionRates,
+                 event::Event{T},
+                 states::Vector{DiseaseState},
+                 pop::Population,
+                 rf::RiskFunctions{T},
+                 rp::RiskParameters{T};
+                 xzero::Bool=false) where T <: EpidemicModel
+  id = event.individual
+  if _new_transmission(event) && xzero
+    tr.external[id] = 0.0
+    tr.internal[:, id] .= 0.0
+  end
+  if event.new_state == State_I
+    transmissibility = rf.transmissibility(rp.transmissibility, pop, id)
+    @simd for i in findall(states .== Ref(State_S))
+      tr.internal[id, i] = rf.susceptibility(rp.susceptibility, pop, i) *
+                           rf.infectivity(rp.infectivity, pop, i, id) *
+                           transmissibility
+    end
+  elseif event.new_state == State_R
+    @simd for i in findall(states .== Ref(State_S))
+      tr.internal[id, i] = 0.0
+    end
+  end
+  return tr
+end
+
+function update!(rates::EventRates{T},
+                 tr::TransmissionRates,
+                 event::Event{T},
+                 states::Vector{DiseaseState},
+                 pop::Population,
+                 rf::RiskFunctions{T},
+                 rp::RiskParameters{T}) where T <: EpidemicModel
+  id = event.individual
+  if event.new_state == State_E
+    rates.exposure[id] = 0.0
+    rates.infection[id] = rf.latency(rp.latency, pop, id)
+    @logmsg LogLevel(-5000) "Exposure rate total for i = $id updated"  λ = rates.exposure[id]
+    @logmsg LogLevel(-5000) "Infection rate for i = $id updated" λ = rates.infection[id]
+  elseif event.new_state == State_I
+    rates.infection[id] = 0.0
+    @logmsg LogLevel(-5000) "Infection rate for i = $id updated" λ = rates.infection[id]
+    if T in [SEIR; SIR]
+      rates.removal[id] = rf.removal(rp.removal, pop, id)
+      @logmsg LogLevel(-5000) "Removal rate for i = $id updated" λ = rates.removal[id]
+    end
+    if T in [SEIR; SEI]
+      @simd for i in findall(states .== Ref(State_S))
+        # This assumes `TransmissionRates` already updated!
+        rates.exposure[i] += tr.internal[id, i]
+        @logmsg LogLevel(-5000) "Exposure rate total for i = $id updated"  λ = rates.exposure[id]
+      end
+    elseif T in [SIR; SI]
+      @simd for i in findall(states .== Ref(State_S))
+        # This assumes `TransmissionRates` already updated!
+        rates.infection[i] += tr.internal[id, i]
+        @logmsg LogLevel(-5000) "Infection rate total for i = $id updated"  λ = rates.infection[id]
+      end
+    end
+  elseif event.new_state == State_R
+    rates.removal[id] = 0.0
+    @logmsg LogLevel(-5000) "Removal rate for i = $id updated" λ = rates.removal[id]
+    if T == SEIR
+      @simd for i in findall(states .== Ref(State_S))
+        # This assumes `TransmissionRates` already updated!
+        rates.exposure[i] = sum(tr.internal[:, i])
+        @logmsg LogLevel(-5000) "Exposure rate total for i = $i updated"  λ = rates.exposure[i]
+      end
+    elseif T == SIR
+      @simd for i in findall(states .== Ref(State_S))
+        # This assumes `TransmissionRates` already updated!
+        rates.infection[i] = sum(tr.internal[:, i])
+        @logmsg LogLevel(-5000) "Infection rate for i = $i updated" λ = rates.infection[i]
+      end
+    end
+  end
+  return rates
+end
+
+function update!(tr::TransmissionRates,
+                 rates::EventRates{T},
+                 event::Event{T},
+                 states::Vector{DiseaseState},
+                 pop::Population,
+                 rf::RiskFunctions{T},
+                 rp::RiskParameters{T}) where T <: EpidemicModel
+  update!(tr, event, states, pop, rf, rp)
+  update!(rates, tr, event, states, pop, rf, rp)
+  return tr, rates
+end