Englishing docstrings ✏️

src/measures/functioning.jl

@@ -13,10 +13,10 @@ over the `last` timesteps. `kwargs...` are optional arguments passed to
 
   - `solution`: output of `simulate()` or `solve()`
   - `threshold`: biomass threshold below which a species is considered extinct. Set to 0 by
-    debault and it is recommended to let as this. It is recommended to change the threshold
+    default and it is recommended to leave as this. It is recommended to change the threshold
     using [`ExtinctionCallback`](@ref) in [`simulate`](@ref).
 
-# Examples
+# Examples:
 
 ```jldoctest
 julia> foodweb = FoodWeb([0 0; 1 0]);
@@ -48,9 +48,9 @@ end
 """
     richness(n::AbstractVector; threshold = 0)
 
-When applied to a vector of biomass, returns the number of biomass above `threshold`
+When applied to a vector of biomass, returns the number of biomasses above `threshold`
 
-# Examples
+# Examples:
 
 ```jldoctest
 julia> richness([0, 1])
@@ -65,7 +65,7 @@ richness(n::AbstractVector; threshold = 0) = sum(n .> threshold)
 """
     species_persistence(solution; kwargs...)
 
-Returns the average proportion of species having a biomass superior or equal to threshold
+Returns the average proportion of species having a biomass greater than or equal to threshold
 over the `last` timesteps.
 
 `kwargs...` arguments are forwarded to [`extract_last_timesteps`](@ref). See
@@ -75,7 +75,7 @@ When applied to a vector of biomass, e.g.
 `species_persistence(n::Vector; threshold = 0)`, it returns the proportion of
 species which biomass is above `threshold`.
 
-# Examples
+# Examples:
 
 ```jldoctest
 julia> foodweb = FoodWeb([0 0; 0 0]; quiet = true);
@@ -111,15 +111,15 @@ species_persistence(n::AbstractVector; threshold = 0) = richness(n; threshold) /
 
 Returns a named tuple of total and species biomass, averaged over the `last` timesteps.
 
-# Arguments
+# Arguments:
 
 `kwargs...` arguments are forwarded to [`extract_last_timesteps`](@ref). See
 [`extract_last_timesteps`](@ref) for the argument details.
 
 Can also handle a species x time biomass matrix, e.g. `biomass(mat::AbstractMatrix;)` or a
 vector, e.g. `biomass(vec::AbstractVector;)`.
 
-# Examples
+# Examples:
 
 ```jldoctest
 julia> foodweb = FoodWeb([0 0; 1 0]);
@@ -160,7 +160,7 @@ over the `last` timesteps.
 
 Can also handle a vector, e.g. shannon_diversity(n::AbstractVector; threshold = 0)
 
-# Reference
+# Reference:
 
 https://en.wikipedia.org/wiki/Diversity_index#Shannon_index
 """
@@ -194,7 +194,7 @@ over the `last` timesteps.
 
 Can also handle a vector, e.g. simpson(n::AbstractVector; threshold = 0)
 
-# Reference
+# Reference:
 
 https://en.wikipedia.org/wiki/Diversity_index#Simpson_index
 """
@@ -219,14 +219,14 @@ end
 """
     evenness(solution; threshold = 0, kwargs...)
 
-Computes the average Pielou evenness, over the `last` timesteps.
+Computes the average Pielou evenness over the `last` timesteps.
 
 `kwargs...` arguments are forwarded to [`extract_last_timesteps`](@ref). See
 [`extract_last_timesteps`](@ref) for the argument details.
 
 Can also handle a vector, e.g. `evenness(n::AbstractVector; threshold = 0)`
 
-# Reference
+# Reference:
 
 https://en.wikipedia.org/wiki/Species_evenness
 """
@@ -250,13 +250,13 @@ end
     producer_growth(solution; kwargs...)
 
 Returns the average growth rates of producers over the `last` timesteps as as well as the
-average (`mean`) and the standard deviation (`std`). It also returns  by all the growth
+average (`mean`) and the standard deviation (`std`). It also returns all the growth
 rates (`all`) as a species x timestep matrix (as the solution matrix).
 
 kwargs... arguments are forwarded to [`extract_last_timesteps`](@ref). See
 [`extract_last_timesteps`](@ref) for the argument details.
 
-# Examples
+# Examples:
 
 ```jldoctest
 julia> foodweb = FoodWeb([0 1 1; 0 0 0; 0 0 0]);
@@ -332,13 +332,13 @@ get_parameters(sol) = sol.prob.p.params
     trophic_structure(solution; threshold = 0, idxs = nothing, kwargs...)
 
 Returns the maximum, mean and weighted mean trophic level averaged over the `last`
-timesteps. It also returns the adjacency matrix containing only the living species and the
-vector of the living species at the last timestep.
+timesteps. It also returns the adjacency matrix containing only the living species and a
+vector of the living species' identities at the last timestep.
 
 kwargs... arguments are forwarded to [`extract_last_timesteps`](@ref). See
 [`extract_last_timesteps`](@ref) for the argument details.
 
-# Examples
+# Examples:
 
 ```jldoctest
 julia> foodweb = FoodWeb([0 0 0; 0 0 0; 1 1 0]);
@@ -447,7 +447,7 @@ kwargs... arguments are forwarded to [`extract_last_timesteps`](@ref). See
 These functions also handle biomass vectors associated with a network, as well as
 a vector of trophic levels (See examples).
 
-# Examples
+# Examples:
 
 ```jldoctest
 julia> A = [0 0; 1 0];
@@ -565,15 +565,15 @@ end
 """
     living_species(solution::Solution; threshold = 0, idxs = nothing, 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
+Returns vectors of living species names and their indices within the original network.
+Living species are those with an average biomass above `threshold` over
 the `last` timesteps. `kwargs...` are optional arguments passed to
 [`extract_last_timesteps`](@ref).
 
 `kwargs...` arguments are forwarded to [`extract_last_timesteps`](@ref). See
 [`extract_last_timesteps`](@ref) for the argument details.
 
-# Examples
+# Examples:
 
 ```jldoctest
 julia> foodweb = FoodWeb([0 1 1; 0 0 0; 0 0 0]);
@@ -616,7 +616,7 @@ timesteps.
 `kwargs...` arguments are forwarded to [`extract_last_timesteps`](@ref). See
 [`extract_last_timesteps`](@ref) for the argument details.
 
-# Examples
+# Examples:
 
 ```jldoctest
 julia> foodweb = FoodWeb([0 0; 1 0]);

src/measures/stability.jl

@@ -5,7 +5,7 @@ Various measures of stability.
 """
     species_cv(solution::Solution; threshold = 0, last = "10%", kwargs...)
 
-Computes the temporal coefficient of variation of species biomass and its average.
+Computes the temporal coefficient of variation of species biomass and calculates the mean.
 
 See [`coefficient_of_variation`](@ref) for the details.
 """
@@ -52,7 +52,7 @@ Loreau & de Mazancourt (2008).
 
 See [`coefficient_of_variation`](@ref) for the argument details.
 
-# Reference
+# Reference:
 
 Loreau, M., & de Mazancourt, C. (2008). Species Synchrony and Its Drivers :
 Neutral and Nonneutral Community Dynamics in Fluctuating Environments. The
@@ -151,13 +151,13 @@ unbiaised estimator of the variance.
 
 See [`richness`](@ref) for the argument details.
 
-# Reference
+# 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
+# Examples:
 
 ```jldoctest
 julia> foodweb = FoodWeb([0 1 1; 0 0 0; 0 0 0]); # Two producers and one consumer

src/measures/structure.jl

@@ -7,7 +7,7 @@ richness(net::EcologicalNetwork) = richness(get_trophic_adjacency(net))
 richness(A::AbstractMatrix) = size(A, 1)
 
 """
-Connectance of network: number of links / (number of species)^2
+Connectance of network: number of links / (number of species)²
 """
 connectance(A::AbstractMatrix) = sum(A) / richness(A)^2
 connectance(foodweb::FoodWeb) = connectance(foodweb.A)
@@ -34,7 +34,7 @@ isproducer(i, net::FoodWeb) = isproducer(i, net.A)
 isproducer(i, net::MultiplexNetwork) = isproducer(i, net.layers[:trophic].A)
 
 """
-Return indexes of the producers of the given `network`.
+Return indices of the producers of the given `network`.
 """
 producers(net) = filter(isproducer, net)
 producers(A::AbstractMatrix) = (1:richness(A))[all(A .== 0; dims = 2)|>vec]
@@ -44,9 +44,9 @@ producers(A::AbstractMatrix) = (1:richness(A))[all(A .== 0; dims = 2)|>vec]
 """
     predators_of(i, network)
 
-Return indexes of the predators of species `i` for the given `network`.
+Return indices of the predators of species `i` for the given `network`.
 
-# Examples
+# Examples:
 
 ```jldoctest
 julia> foodweb = FoodWeb([0 0 0; 1 0 0; 1 1 0]);
@@ -78,7 +78,7 @@ ispredator(i, net::FoodWeb) = ispredator(i, net.A)
 ispredator(i, net::MultiplexNetwork) = ispredator(i, net.layers[:trophic].A)
 
 """
-Return indexes of the predators of the given `network`.
+Return indices of the predators of the given `network`.
 """
 predators(net::EcologicalNetwork) = filter(ispredator, net)
 #### end ####
@@ -87,9 +87,9 @@ predators(net::EcologicalNetwork) = filter(ispredator, net)
 """
     preys_of(i, network)
 
-Return indexes of the preys of species `i` for the given `network`.
+Return indices of the preys of species `i` for the given `network`.
 
-# Examples
+# Examples:
 
 ```jldoctest
 julia> foodweb = FoodWeb([0 0 0; 0 0 0; 1 1 0]);
@@ -117,7 +117,7 @@ isprey(i, net::FoodWeb) = isprey(i, net.A)
 isprey(i, net::MultiplexNetwork) = isprey(i, net.layers[:trophic].A)
 
 """
-Return indexes of the preys of the network (`net`).
+Return indices of the preys of the network (`net`).
 """
 preys(net::EcologicalNetwork) = filter(isprey, net)
 preys(A::AbstractSparseMatrix) = [i for i in 1:size(A, 1) if !isempty(A[:, i].nzval)]
@@ -269,7 +269,7 @@ trophic_classes() = (:producers, :intermediate_consumers, :top_predators)
 
 Remove a list of species from a `FoodWeb`, a `MultiplexNetwork` or an adjacency matrix.
 
-# Examples
+# Examples:
 
 Adjacency matrix.
 

src/measures/utils.jl

@@ -7,7 +7,7 @@ Utility functions for functions in measures
 
 Returns the biomass matrix of species x time over the `last` timesteps.
 
-# Arguments
+# Arguments:
 
   - `last`: the number of last timesteps to consider. A percentage can also be also be
     provided as a `String` ending by `%`. Defaulted to 1.
@@ -17,7 +17,7 @@ Returns the biomass matrix of species x time over the `last` timesteps.
 See [`richness`](@ref) for the other arguments. If `idxs` is an integer,
 it returns a vector of the species biomass instead of a matrix.
 
-# Examples
+# Examples:
 
 ```jldoctest
 julia> fw = FoodWeb([0 0; 1 0]);
@@ -179,7 +179,7 @@ end
 
 Returns a tuple with species having a biomass above `threshold` at the end of a simulation.
 
-# Examples
+# Examples:
 
 ```jldoctest
 julia> foodweb = FoodWeb([0 0; 0 0]; quiet = true);