Merge 19ff59d into d1a21d4

src/aggregators/aggregators.jl

@@ -188,6 +188,38 @@ needs_vartojumps_map(aggregator::RSSACR) = true
 supports_variablerates(aggregator::AbstractAggregatorAlgorithm) = false
 supports_variablerates(aggregator::Coevolve) = true
 
+# true if aggregator supports hops, e.g. diffusion
 is_spatial(aggregator::AbstractAggregatorAlgorithm) = false
 is_spatial(aggregator::NSM) = true
 is_spatial(aggregator::DirectCRDirect) = true
+
+# return the fastest aggregator out of the available ones
+function select_aggregator(jumps::JumpSet; vartojumps_map=nothing, jumptovars_map=nothing, dep_graph=nothing, spatial_system=nothing, hopping_constants=nothing)
+
+    # detect if a spatial SSA should be used
+    !isnothing(spatial_system) && !isnothing(hopping_constants) && return DirectCRDirect
+
+    # if variable rate jumps are present, return one of the two SSAs that support them
+    if num_vrjs(jumps) != 0
+        any(isbounded, vrjs) && return Coevolve
+        return Direct
+    end
+
+    # if the number of jumps is small, return the Direct
+    num_jumps(jumps) < 10 && return Direct
+
+    # if there are only massaction jumps, we can build the species-jumps dependency graphs
+    can_build_dependency_graphs = num_crjs(jumps) == 0 && num_vrjs(jumps) == 0
+    have_species_to_jumps_dependency_graphs = !isnothing(vartojumps_map) && !isnothing(jumptovars_map)
+
+    # if we have the species-jumps dependency graphs or can build them, use one of the Rejection-based methods
+    if can_build_dependency_graphs || have_species_to_jumps_dependency_graphs
+        num_jumps(jumps) < 100 && return RSSA
+        return RSSACR
+    # if we have the jumps-jumps dependency graph, use the Composition-Rejection Direct method
+    elseif !isnothing(dep_graph)
+        return DirectCR
+    else
+        return Direct
+    end
+end

src/problem.jl

@@ -171,9 +171,12 @@ function JumpProblem(prob, aggregator::AbstractAggregatorAlgorithm, jumps::Abstr
                      kwargs...)
     JumpProblem(prob, aggregator, JumpSet(jumps...); kwargs...)
 end
-function JumpProblem(prob, jumps::JumpSet; kwargs...)
-    JumpProblem(prob, NullAggregator(), jumps; kwargs...)
+function JumpProblem(prob, jumps::JumpSet; vartojumps_map=nothing, jumptovars_map=nothing, dep_graph=nothing, spatial_system=nothing, hopping_constants=nothing, kwargs...)
+    aggregator = select_aggregator(jumps::JumpSet; vartojumps_map=vartojumps_map, jumptovars_map=jumptovars_map, dep_graph=dep_graph, spatial_system=spatial_system, hopping_constants=hopping_constants)
+    return JumpProblem(prob, aggregator(), jumps; vartojumps_map=vartojumps_map, jumptovars_map=jumptovars_map, dep_graph=dep_graph, spatial_system=spatial_system, hopping_constants=hopping_constants, kwargs...)
 end
+# this makes it easier to test the aggregator selection
+JumpProblem(prob, aggregator::NullAggregator, jumps::JumpSet; kwargs...) = JumpProblem(prob, jumps; kwargs...)
 
 make_kwarg(; kwargs...) = kwargs
 

test/geneexpr_test.jl

@@ -12,7 +12,7 @@ dotestmean = true
 doprintmeans = false
 
 # SSAs to test
-SSAalgs = (RDirect(), RSSACR(), Direct(), DirectFW(), FRM(), FRMFW(), SortingDirect(),
+SSAalgs = (JumpProcesses.NullAggregator(), RDirect(), RSSACR(), Direct(), DirectFW(), FRM(), FRMFW(), SortingDirect(),
            NRM(), RSSA(), DirectCR(), Coevolve())
 
 # numerical parameters
@@ -116,3 +116,12 @@ end
 #     end
 #     println()
 # end
+
+# no-aggregator tests
+jump_prob = JumpProblem(prob, majumps, save_positions = (false, false),
+                                      vartojumps_map = spec_to_dep_jumps,
+                                      jumptovars_map = jump_to_dep_specs, rng = rng)
+@test abs(runSSAs(jump_prob) - expected_avg) < reltol * expected_avg
+
+jump_prob = JumpProblem(prob, majumps, save_positions = (false, false), rng = rng)
+@test abs(runSSAs(jump_prob) - expected_avg) < reltol * expected_avg

test/linearreaction_test.jl

@@ -16,7 +16,7 @@ tf = 0.1
 baserate = 0.1
 A0 = 100
 exactmean = (t, ratevec) -> A0 * exp(-sum(ratevec) * t)
-SSAalgs = [RSSACR(), Direct(), RSSA()]
+SSAalgs = [RSSACR(), Direct(), RSSA(), JumpProcesses.NullAggregator()]
 
 spec_to_dep_jumps = [collect(1:Nrxs), []]
 jump_to_dep_specs = [[1, 2] for i in 1:Nrxs]

test/spatial/ABC.jl

@@ -56,6 +56,9 @@ jump_problems = JumpProblem[JumpProblem(prob, NSM(), majumps,
 push!(jump_problems,
       JumpProblem(prob, DirectCRDirect(), majumps, hopping_constants = hopping_constants,
                   spatial_system = grids[1], save_positions = (false, false), rng = rng))
+push!(jump_problems,
+      JumpProblem(prob, majumps, hopping_constants = hopping_constants,
+            spatial_system = grids[1], save_positions = (false, false), rng = rng))
 # setup flattenned jump prob
 push!(jump_problems,
       JumpProblem(prob, NRM(), majumps, hopping_constants = hopping_constants,