diff --git a/core/MarkovProcesses.jl b/core/MarkovProcesses.jl
index e547640d4d41a7a0b2c7645e08e8786cf11d9074..914b006e458f6b83ce5bfb87797c377a8ad5dd45 100644
--- a/core/MarkovProcesses.jl
+++ b/core/MarkovProcesses.jl
@@ -10,7 +10,7 @@ export Distribution, Product, Uniform, Normal
# Common types and constructors
export Observations, AbstractTrajectory, Trajectory, SynchronizedTrajectory
-export Model, ContinuousTimeModel, SynchronizedModel, ModelPrior
+export Model, ContinuousTimeModel, SynchronizedModel, ParametricModel
export LHA, StateLHA, Edge
# Trajectory related methods
@@ -25,19 +25,23 @@ export load_automaton, get_index, get_value, length_var, isaccepted
# Model related methods
export simulate, set_param!, get_param, set_observed_var!, observe_all!
-export set_time_bound!, getproperty, draw!
+export set_time_bound!, getproperty, draw!, draw_model!
export isbounded, isaccepted, check_consistency
export load_model, get_module_path
# Utils
export get_module_path, cosmos_get_values, load_plots
+# Algorithms
+export automaton_abc
+
include("common.jl")
include("trajectory.jl")
include("lha.jl")
include("model.jl")
include("utils.jl")
+include(get_module_path() * "/algorithms/automaton_abc.jl")
end
diff --git a/core/common.jl b/core/common.jl
index be1a32f8eadffdc9a01fa99a50277106f881e381..a0026fb5fbc84b183e90fbb77fd8b1a630e55c67 100644
--- a/core/common.jl
+++ b/core/common.jl
@@ -32,7 +32,7 @@ struct Trajectory <: AbstractTrajectory
transitions::Vector{Transition}
end
-struct ModelPrior
+struct ParametricModel
m::Model
map_l_param_dist::Dict{Vector{String},Distribution}
end
@@ -105,11 +105,16 @@ LHA(A::LHA, map_var::Dict{String,Int}) = LHA(A.l_transitions, A.l_loc, A.Λ,
Base.:*(m::ContinuousTimeModel, A::LHA) = SynchronizedModel(m, A)
Base.:*(A::LHA, m::ContinuousTimeModel) = SynchronizedModel(m, A)
-function ModelPrior(m::Model, priors::Tuple{Vector{String},Distribution}...)
+function ParametricModel(m::Model, priors::Tuple{Vector{String},Distribution}...)
map = Dict{Vector{String},Distribution}()
for prior in priors
+ check_vars = true
+ for var in prior[1]
+ check_vars = check_vars && var in keys(get_proba_model(m).map_param_idx)
+ end
+ @assert check_vars
map[prior[1]] = prior[2]
end
- return ModelPrior(m, map)
+ return ParametricModel(m, map)
end
diff --git a/core/model.jl b/core/model.jl
index 0a305c3fcb878f4fb2ddae6add7d099190ed1e8a..359133dba01e47cf777da21dcc55888716da7efc 100644
--- a/core/model.jl
+++ b/core/model.jl
@@ -286,16 +286,31 @@ function getproperty(m::ContinuousTimeModel, sym::Symbol)
end
get_proba_model(m::ContinuousTimeModel) = m
get_proba_model(sm::SynchronizedModel) = sm.m
+get_observed_var(m::ContinuousTimeModel) = m.g
+get_observed_var(sm::SynchronizedModel) = (sm.m).g
# Prior methods
-function draw!(Π::ModelPrior)
- dict_dist = Π.map_l_param_dist
+function draw_model!(pm::ParametricModel)
+ dict_dist = pm.map_l_param_dist
for l_name in keys(dict_dist)
if length(l_name) == 1
- set_param!(get_proba_model(Π.m), l_name[1], rand(dict_dist[l_name]))
+ set_param!(get_proba_model(pm.m), l_name[1], rand(dict_dist[l_name]))
else
- set_param!(get_proba_model(Π.m), l_name, rand(dict_dist[l_name]))
+ set_param!(get_proba_model(pm.m), l_name, rand(dict_dist[l_name]))
end
end
end
+function dim_free_param(pm::ParametricModel)
+ return 1
+end
+
+function draw!(vec_p::Vector{Float64}, pm::ParametricModel)
+end
+
+function draw!(mat_p::Matrix{Float64}, pm::ParametricModel)
+end
+
+function prior_density!(wl::Vector{Float64}, mat_p::Matrix{Float64}, pm::ParametricModel)
+end
+
diff --git a/core/plots.jl b/core/plots.jl
index b2092ef7f4468ef042a475dbc13e8369ed2d3341..4e50cfd2444d9d96dd7999f0dcf9056a02e0b6e2 100644
--- a/core/plots.jl
+++ b/core/plots.jl
@@ -1,7 +1,16 @@
import Plots: plot, plot!, scatter!
-import Plots: palette, display, png, close
+import Plots: current, palette, display, png, close
+"""
+ `plot(σ, var...; plot_transitions=false)`
+
+Plot a simulated trajectory σ. var... is a tuple of stirng variables.
+`plot(σ)` will plot all the variables simulated in σ
+whereas `plot(σ, "I", "R")` only plots the variables I and R of the trajectory (if it exists).
+If `plot_transitions=true`, a marker that corresponds to a transition of the model will be plotted
+at each break of the trajectory.
+"""
function plot(σ::AbstractTrajectory, vars::String...; filename::String = "", plot_transitions = false)
# Setup
palette_tr = palette(:default)
diff --git a/core/utils.jl b/core/utils.jl
index c403635c85567a464600399d7d9eba0875c4aa6a..ff0d6bea939575a8db5084a9ace3383164e1f307 100644
--- a/core/utils.jl
+++ b/core/utils.jl
@@ -1,6 +1,10 @@
get_module_path() = dirname(dirname(pathof(@__MODULE__)))
+function create_results_dir()
+ return "./"
+end
+
function cosmos_get_values(name_file::String)
output_file = open(name_file)
dict_values = Dict{String}{Float64}()
diff --git a/tests/automaton_abc/R1.jl b/tests/automaton_abc/R1.jl
new file mode 100644
index 0000000000000000000000000000000000000000..1e3da5aa54d89ffe11f43555903b4dc802a4cfa9
--- /dev/null
+++ b/tests/automaton_abc/R1.jl
@@ -0,0 +1,11 @@
+
+using MarkovProcesses
+
+load_model("ER")
+load_automaton("automaton_F")
+A_F = create_automaton_F(ER, 50.0, 75.0, 0.025, 0.05, "P")
+sync_ER = A_F*ER
+pm_sync_ER = ParametricModel(sync_ER, (["k3"], Uniform(0.0, 100.0)))
+
+automaton_abc(pm_sync_ER)
+
diff --git a/tests/run_unit.jl b/tests/run_unit.jl
index a384dcb288e0879e736960ecead45c40be5dee84..e67bfff5bc391c1ef70d380a5dc7f51832b693ab 100644
--- a/tests/run_unit.jl
+++ b/tests/run_unit.jl
@@ -2,27 +2,36 @@
using Test
@testset "Unit tests" begin
- @test include("unit/load_model.jl")
- @test include("unit/load_model_bench.jl")
- @test include("unit/load_module.jl")
- @test include("unit/simulate_sir.jl")
- @test include("unit/simulate_sir_bounded.jl")
- @test include("unit/simulate_er.jl")
+ @test include("unit/absorbing_x0.jl")
+
@test include("unit/change_obs_var_sir.jl")
@test include("unit/change_obs_var_sir_2.jl")
+ @test include("unit/check_model_consistency.jl")
+ @test include("unit/check_trajectory_consistency.jl")
+ @test include("unit/create_automata.jl")
+ @test include("unit/create_models.jl")
+
+ @test include("unit/dist_lp.jl")
+ @test include("unit/dist_lp_var.jl")
+
@test include("unit/getindex_access_trajectory.jl")
@test include("unit/is_always_bounded_sir.jl")
- @test include("unit/length_obs_var.jl")
- @test include("unit/dist_lp_var.jl")
- @test include("unit/dist_lp.jl")
+
@test include("unit/l_dist_lp.jl")
- @test include("unit/check_trajectory_consistency.jl")
- @test include("unit/check_model_consistency.jl")
+ @test include("unit/length_obs_var.jl")
+ @test include("unit/load_model.jl")
+ @test include("unit/load_model_bench.jl")
+ @test include("unit/load_module.jl")
+ @test include("unit/long_sim_er.jl")
+
+ @test include("unit/model_prior.jl")
+ @test include("unit/observe_all.jl")
+
+
@test include("unit/set_param.jl")
@test include("unit/side_effects_1.jl")
- @test include("unit/create_models.jl")
- @test include("unit/create_automata.jl")
- @test include("unit/model_prior.jl")
- @test include("unit/absorbing_x0.jl")
+ @test include("unit/simulate_sir.jl")
+ @test include("unit/simulate_sir_bounded.jl")
+ @test include("unit/simulate_er.jl")
end
diff --git a/tests/unit/model_prior.jl b/tests/unit/model_prior.jl
index 0b04b511c521794b41397c00f92c246421931e1b..b634aec8df83e6c377b0ac546254fb91c8b5e8ee 100644
--- a/tests/unit/model_prior.jl
+++ b/tests/unit/model_prior.jl
@@ -5,16 +5,16 @@ load_model("ER")
test_all = true
load_model("ER")
-prior1 = ModelPrior(ER, (["k2"], Uniform(2.0, 4.0)))
-draw!(prior1)
+prior1 = ParametricModel(ER, (["k2"], Uniform(2.0, 4.0)))
+draw_model!(prior1)
test_all = test_all && 2.0 <= ER["k2"] <= 4.0
-prior2 = ModelPrior(ER, (["k3","k2"], Product(Uniform.([2.5,6.0], [3.5,7.0]))))
-draw!(prior2)
+prior2 = ParametricModel(ER, (["k3","k2"], Product(Uniform.([2.5,6.0], [3.5,7.0]))))
+draw_model!(prior2)
test_all = test_all && 2.5 <= ER["k3"] <= 3.5 && 6.0 <= ER["k2"] <= 7.0
-prior3 = ModelPrior(ER, (["k3"], Uniform(10.0, 11.0)), (["k2"], Uniform(13.0, 14.0)))
-draw!(prior3)
+prior3 = ParametricModel(ER, (["k3"], Uniform(10.0, 11.0)), (["k2"], Uniform(13.0, 14.0)))
+draw_model!(prior3)
test_all = test_all && 10.0 <= ER["k3"] <= 11.0 && 13.0 <= ER["k2"] <= 14.0
return test_all
diff --git a/tests/unit/observe_all.jl b/tests/unit/observe_all.jl
index 3608bfc4ca812d598b81c92992b5ae15422afac4..ff3b5f3ca4fa37b40ff20b9f7ad9188108b2a045 100644
--- a/tests/unit/observe_all.jl
+++ b/tests/unit/observe_all.jl
@@ -7,5 +7,5 @@ load_model("SIR")
observe_all!(ER)
observe_all!(SIR)
-return ER.g == ["E", "S", "ER", "P"] && SIR.g == ["S", "I", "R"]
+return (ER.g == ["E", "S", "ES", "P"] && SIR.g == ["S", "I", "R"])