Better function names for output + corrected = false for std()

BecksLab · Feb 21, 2023 · 9a44039 · 9a44039
1 parent 7470ef8
commit 9a44039
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Showing 4 changed files with 18 additions and 29 deletions.
diff --git a/src/EcologicalNetworksDynamics.jl b/src/EcologicalNetworksDynamics.jl
@@ -62,7 +62,7 @@ export cascademodel
 export ClassicResponse
 export connectance
 export cpad
-export cv
+export coefficient_of_variation
 export DefaultGrowthParams
 export DefaultMaxConsumptionParams
 export DefaultMetabolismParams
@@ -128,7 +128,6 @@ export shannon_diversity
 export simpson
 export simulate
 export species_persistence
-export species_richness
 export trophic_levels
 export trophic_structure
 

diff --git a/src/measures/functioning.jl b/src/measures/functioning.jl
@@ -81,7 +81,7 @@ When applied to a vector of biomass, e.g.
 species which biomass is above `threshold`.
 
 When applied to a vector of biomass, e.g.
-species_persistence(n::Vector; threshold = eps()), it returns the proportion of
+`species_persistence(n::Vector; threshold = eps())`, it returns the proportion of
 species which biomass is above `threshold`.
 
 # Examples
@@ -134,8 +134,8 @@ Returns a named tuple of total and species biomass, averaged over the last `last
 Can also handle a species x time biomass matrix, e.g. `biomass(mat::Matrix;)` or a
 vector, e.g. `biomass(vec::Vector;)`.
 
-Can also handle a species x time biomass matrix, e.g. biomass(mat::Matrix;) or a
-vector, e.g. biomass(vec::Vector;).
+Can also handle a species x time biomass matrix, e.g. `biomass(mat::Matrix;)` or a
+vector, e.g. `biomass(vec::Vector;)`.
 
 # Examples
 

diff --git a/src/measures/stability.jl b/src/measures/stability.jl
@@ -87,12 +87,6 @@ Thibaut, L. M., & Connolly, S. R. (2013). Understanding diversity–stability
 relationships : Towards a unified model of portfolio effects. Ecology Letters,
 16(2), 140‑150. https://doi.org/10.1111/ele.12019
 
-# Reference
-
-Thibaut, L. M., & Connolly, S. R. (2013). Understanding diversity–stability
-relationships : Towards a unified model of portfolio effects. Ecology Letters,
-16(2), 140‑150. https://doi.org/10.1111/ele.12019
-
 # Examples
 
 ```jldoctest

diff --git a/test/measures/test-functioning.jl b/test/measures/test-functioning.jl
@@ -46,8 +46,8 @@ end
     sim_zero = simulates(params, [0, 0]; verbose = false)
 
     # Total biomass should converge to K
-    @test biomass(sim_one_sp; last = 1).total ≈ get_parameters(sim_one_sp).environment.K[2] rtol =
-        0.001
+    @test biomass(sim_one_sp; last = 1).total ≈
+    get_parameters(sim_one_sp).environment.K[2] rtol = 0.001
 
     # Species sub selection works
     @test biomass(sim_one_sp; last = 1, idxs = [1]).sp[1] ≈
@@ -73,34 +73,30 @@ end
     # Other hill diversity numbers
     ## Shannon
     @test shannon_diversity(sim_two_sp[:, end]) ==
-          shannon_diversity(sim_two_sp; last = 1) ==
-          log(2)
+    shannon_diversity(sim_two_sp; last = 1) == log(2)
 
     @test shannon_diversity(sim_one_sp[:, end]) ==
-          shannon_diversity(sim_one_sp; last = 1) ≈
-          0.0 # 0 entropy if 1 species only
+    shannon_diversity(sim_one_sp; last = 1) ≈ 0.0 # 0 entropy if 1 species only
 
     @test isnan(shannon_diversity(sim_zero[:, end])) ==
-          isnan(shannon_diversity(sim_zero; last = 1)) # Not defined for 0 species
+    isnan(shannon_diversity(sim_zero; last = 1)) # Not defined for 0 species
 
     ## Simpson
     @test simpson(sim_two_sp[:, end]) ==
           simpson(sim_two_sp; last = 1) ==
           1 / sum(2 .^ [1 / 2, 1 / 2])
     @test simpson(sim_one_sp[:, end]) ==
           simpson(sim_one_sp; last = 1) ==
-          1 / sum(2 .^ 1) ==
-          0.5# 0.5 if 1 species only
-
-    # Not defined for 0 species
-    @test isnan(simpson(sim_zero[:, end])) == isnan(simpson(sim_zero; last = 1))
+          1 / sum(2 .^ 1) == 0.5# 0.5 if 1 species only
+    @test isnan(simpson(sim_zero[:, end])) ==
+    isnan(simpson(sim_zero; last = 1)) # Not defined for 0 species
 
     # Community evenness
-    # Maximum equity of species biomass
-    @test evenness(sim_two_sp[:, end]) == evenness(sim_two_sp; last = 1) ≈ 1.0
-    # Should be NaN if 1 species
-    @test isnan(evenness(sim_one_sp[:, end])) == isnan(evenness(sim_one_sp; last = 1))
-    # Should be NaN if 0 species
-    @test isnan(evenness(sim_zero[:, end])) == isnan(evenness(sim_zero; last = 1))
+    @test evenness(sim_two_sp[:, end]) ==
+    evenness(sim_two_sp; last = 1) ≈ 1.0 # Maximum equity of species biomass
+    @test isnan(evenness(sim_one_sp[:, end])) ==
+    isnan(evenness(sim_one_sp; last = 1))# Should be NaN if 1 species
+    @test isnan(evenness(sim_zero[:, end])) ==
+    isnan(evenness(sim_zero; last = 1))# Should be NaN if 0 species
 
 end