doctest failure in ~/work/PhyloCoalSimulations.jl/PhyloCoalSimulations.jl/src/simulatecoalescent_onepop.jl:29-49 ```jldoctest julia> PhyloCoalSimulations.simulatecoal_onepopulation!([], 2.0, 1) 1 julia> e1 = PhyloCoalSimulations.initializetip("s","1",1,""); julia> e2 = PhyloCoalSimulations.initializetip("s","2",2,""); julia> forest = [e1,e2]; julia> using Random; Random.seed!(7690); julia> PhyloCoalSimulations.simulatecoal_onepopulation!(forest, Inf, 3); julia> PhyloCoalSimulations.convert2tree!(forest[1].node[1]) HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: s2, s1 (s2:0.302,s1:0.302); ``` Subexpression: PhyloCoalSimulations.convert2tree!(forest[1].node[1]) Evaluated output: PhyloNetworks.HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: s2, s1 (s2:0.302,s1:0.302); Expected output: HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: s2, s1 (s2:0.302,s1:0.302); diff = Warning: Diff output requires color. HybridNetwork, PhyloNetworks.HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: s2, s1 (s2:0.302,s1:0.302);

doctest failure in ~/work/PhyloCoalSimulations.jl/PhyloCoalSimulations.jl/src/simulatecoalescent_network.jl:70-106 ```jldoctest simcoal julia> using PhyloNetworks julia> net = readTopology("(A:1,B:1);"); # branch lengths of 1 coalescent unit julia> using Random; Random.seed!(54321); # for replicability of examples below julia> simulatecoalescent(net, 2, 1) # 2 gene trees, 1 individual/species 2-element Vector{HybridNetwork}: HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: B, A (B:1.023,A:1.023); HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: B, A (B:2.328,A:2.328); julia> simulatecoalescent(net, 1, 3)[1] # 1 gene tree, 3 individuals/species HybridNetwork, Rooted Network 10 edges 11 nodes: 6 tips, 0 hybrid nodes, 5 internal tree nodes. tip labels: B_2, B_1, B_3, A_3, ... (((B_2:0.12,B_1:0.12):2.39,B_3:2.51):0.692,(A_3:0.518,(A_2:0.461,A_1:0.461):0.057):2.684); julia> simulatecoalescent(net, 1, Dict("A"=>2, "B"=>1))[1] # 2 individuals in A, 1 in B HybridNetwork, Rooted Network 4 edges 5 nodes: 3 tips, 0 hybrid nodes, 2 internal tree nodes. tip labels: B, A_2, A_1 (B:2.801,(A_2:0.344,A_1:0.344):2.457); ``` Subexpression: simulatecoalescent(net, 2, 1) # 2 gene trees, 1 individual/species Evaluated output: 2-element Vector{HybridNetwork}: PhyloNetworks.HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: B, A (B:1.023,A:1.023); PhyloNetworks.HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: B, A (B:2.328,A:2.328); Expected output: 2-element Vector{HybridNetwork}: HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: B, A (B:1.023,A:1.023); HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: B, A (B:2.328,A:2.328); diff = Warning: Diff output requires color. 2-element Vector{HybridNetwork}: HybridNetwork, PhyloNetworks.HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: B, A (B:1.023,A:1.023); HybridNetwork, PhyloNetworks.HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: B, A (B:2.328,A:2.328);

doctest failure in ~/work/PhyloCoalSimulations.jl/PhyloCoalSimulations.jl/src/simulatecoalescent_network.jl:70-106 ```jldoctest simcoal julia> using PhyloNetworks julia> net = readTopology("(A:1,B:1);"); # branch lengths of 1 coalescent unit julia> using Random; Random.seed!(54321); # for replicability of examples below julia> simulatecoalescent(net, 2, 1) # 2 gene trees, 1 individual/species 2-element Vector{HybridNetwork}: HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: B, A (B:1.023,A:1.023); HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: B, A (B:2.328,A:2.328); julia> simulatecoalescent(net, 1, 3)[1] # 1 gene tree, 3 individuals/species HybridNetwork, Rooted Network 10 edges 11 nodes: 6 tips, 0 hybrid nodes, 5 internal tree nodes. tip labels: B_2, B_1, B_3, A_3, ... (((B_2:0.12,B_1:0.12):2.39,B_3:2.51):0.692,(A_3:0.518,(A_2:0.461,A_1:0.461):0.057):2.684); julia> simulatecoalescent(net, 1, Dict("A"=>2, "B"=>1))[1] # 2 individuals in A, 1 in B HybridNetwork, Rooted Network 4 edges 5 nodes: 3 tips, 0 hybrid nodes, 2 internal tree nodes. tip labels: B, A_2, A_1 (B:2.801,(A_2:0.344,A_1:0.344):2.457); ``` Subexpression: simulatecoalescent(net, 1, 3)[1] # 1 gene tree, 3 individuals/species Evaluated output: PhyloNetworks.HybridNetwork, Rooted Network 10 edges 11 nodes: 6 tips, 0 hybrid nodes, 5 internal tree nodes. tip labels: B_2, B_1, B_3, A_3, ... (((B_2:0.12,B_1:0.12):2.39,B_3:2.51):0.692,(A_3:0.518,(A_2:0.461,A_1:0.461):0.057):2.684); Expected output: HybridNetwork, Rooted Network 10 edges 11 nodes: 6 tips, 0 hybrid nodes, 5 internal tree nodes. tip labels: B_2, B_1, B_3, A_3, ... (((B_2:0.12,B_1:0.12):2.39,B_3:2.51):0.692,(A_3:0.518,(A_2:0.461,A_1:0.461):0.057):2.684); diff = Warning: Diff output requires color. HybridNetwork, PhyloNetworks.HybridNetwork, Rooted Network 10 edges 11 nodes: 6 tips, 0 hybrid nodes, 5 internal tree nodes. tip labels: B_2, B_1, B_3, A_3, ... (((B_2:0.12,B_1:0.12):2.39,B_3:2.51):0.692,(A_3:0.518,(A_2:0.461,A_1:0.461):0.057):2.684);

doctest failure in ~/work/PhyloCoalSimulations.jl/PhyloCoalSimulations.jl/src/simulatecoalescent_network.jl:70-106 ```jldoctest simcoal julia> using PhyloNetworks julia> net = readTopology("(A:1,B:1);"); # branch lengths of 1 coalescent unit julia> using Random; Random.seed!(54321); # for replicability of examples below julia> simulatecoalescent(net, 2, 1) # 2 gene trees, 1 individual/species 2-element Vector{HybridNetwork}: HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: B, A (B:1.023,A:1.023); HybridNetwork, Rooted Network 2 edges 3 nodes: 2 tips, 0 hybrid nodes, 1 internal tree nodes. tip labels: B, A (B:2.328,A:2.328); julia> simulatecoalescent(net, 1, 3)[1] # 1 gene tree, 3 individuals/species HybridNetwork, Rooted Network 10 edges 11 nodes: 6 tips, 0 hybrid nodes, 5 internal tree nodes. tip labels: B_2, B_1, B_3, A_3, ... (((B_2:0.12,B_1:0.12):2.39,B_3:2.51):0.692,(A_3:0.518,(A_2:0.461,A_1:0.461):0.057):2.684); julia> simulatecoalescent(net, 1, Dict("A"=>2, "B"=>1))[1] # 2 individuals in A, 1 in B HybridNetwork, Rooted Network 4 edges 5 nodes: 3 tips, 0 hybrid nodes, 2 internal tree nodes. tip labels: B, A_2, A_1 (B:2.801,(A_2:0.344,A_1:0.344):2.457); ``` Subexpression: simulatecoalescent(net, 1, Dict("A"=>2, "B"=>1))[1] # 2 individuals in A, 1 in B Evaluated output: PhyloNetworks.HybridNetwork, Rooted Network 4 edges 5 nodes: 3 tips, 0 hybrid nodes, 2 internal tree nodes. tip labels: B, A_2, A_1 (B:2.801,(A_2:0.344,A_1:0.344):2.457); Expected output: HybridNetwork, Rooted Network 4 edges 5 nodes: 3 tips, 0 hybrid nodes, 2 internal tree nodes. tip labels: B, A_2, A_1 (B:2.801,(A_2:0.344,A_1:0.344):2.457); diff = Warning: Diff output requires color. HybridNetwork, PhyloNetworks.HybridNetwork, Rooted Network 4 edges 5 nodes: 3 tips, 0 hybrid nodes, 2 internal tree nodes. tip labels: B, A_2, A_1 (B:2.801,(A_2:0.344,A_1:0.344):2.457);

Process completed with exit code 1.