Define global convenience Solution type alias.

BecksLab · Apr 18, 2023 · f413f66 · f413f66
1 parent 2316c2c
commit f413f66
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Showing 4 changed files with 12 additions and 10 deletions.
diff --git a/Project.toml b/Project.toml
@@ -13,6 +13,6 @@ EcologicalNetworks = "f03a62fe-f8ab-5b77-a061-bb599b765229"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 Mangal = "b8b640a6-63d9-51e6-b784-5033db27bef2"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
+SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
-
diff --git a/src/EcologicalNetworksDynamics.jl b/src/EcologicalNetworksDynamics.jl
@@ -37,7 +37,10 @@ using OrderedCollections
 using SparseArrays
 using Statistics
 using Decimals
+using SciMLBase
 
+# Convenience aliases.
+const Solution = SciMLBase.AbstractODESolution
 
 # Include scripts
 include(joinpath(".", "macros.jl"))

diff --git a/src/measures/functioning.jl b/src/measures/functioning.jl
@@ -525,7 +525,7 @@ function aggregate_trophic_level(op_name, aggregate_function)
     return quote
 
         @doc $docstring function $op_trophic_level(
-            solution::SciMLBase.ODESolution;
+            solution::Solution;
             threshold = 0,
             kwargs...,
         )
@@ -568,7 +568,7 @@ end
 
 
 """
-    living_species(solution; threshold, kwargs...)
+    living_species(solution::Solution; threshold, kwargs...)
 
 Returns the vectors of alive species and their indices in the original network.
 Living species are the ones having, in average, a biomass above `threshold` over
@@ -596,7 +596,7 @@ julia> B0 = [0, 0.5, 0.5];
 ```
 """
 function living_species(
-    solution::SciMLBase.ODESolution;
+    solution::Solution;
     threshold = 0,
     idxs = nothing,
     kwargs...,

diff --git a/src/measures/stability.jl b/src/measures/stability.jl
@@ -3,14 +3,13 @@ Various measures of stability
 =#
 
 """
-    species_cv(solution; threshold, kwargs...)
+    species_cv(solution::Solution; threshold, kwargs...)
 
 Computes the temporal coefficient of variation of species biomass and its average.
 
 See [`coefficient_of_variation`](@ref) for the details.
 """
-function species_cv(solution::SciMLBase.ODESolution; threshold = 0, last = "10%", kwargs...)
-
+function species_cv(solution::Solution; threshold = 0, last = "10%", kwargs...)
     measure_on = extract_last_timesteps(solution; last, kwargs...)
     # Fetch species that are alive, whose avg biomass is > threshold
     living_sp = living_species(measure_on; threshold)
@@ -54,7 +53,7 @@ Neutral and Nonneutral Community Dynamics in Fluctuating Environments. The
 American Naturalist, 172(2), E48‑E66. https://doi.org/10.1086/589746
 """
 function synchrony(
-    solution::SciMLBase.ODESolution;
+    solution::Solution;
     threshold = 0,
     last = "10%",
     corrected = true,
@@ -96,7 +95,7 @@ Compute the temporal Coefficient of Variation of community biomass.
 See [`coefficient_of_variation`](@ref) for the argument details.
 """
 function community_cv(
-    solution::SciMLBase.ODESolution;
+    solution::Solution;
     threshold = 0,
     last = "10%",
     corrected = true,
@@ -164,7 +163,7 @@ julia> B0 = [0, 0.5, 0.5]; # Two producers
 ```
 """
 function coefficient_of_variation(
-    solution;
+    solution::Solution;
     threshold = 0,
     last = "10%",
     corrected = true,