zero branch lengths actually allowed, most of the time

JuliaPhylo · Jul 6, 2022 · 0100906 · 0100906
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commit 0100906
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Showing 2 changed files with 13 additions and 9 deletions.
diff --git a/src/traits.jl b/src/traits.jl
@@ -386,7 +386,7 @@ end
 function checkBranchLengths(net::HybridNetwork)
     branches = [e.number for e in net.edge]
     undefined = branches[[e.length == -1.0 for e in net.edge]]
-    negatives = branches[[e.length <= 0 for e in net.edge]]
+    negatives = branches[[e.length < 0 for e in net.edge]]
     str = "The variance-covariance matrix of the network is not defined, and the phylogenetic regression cannot be done."
     if (length(undefined) > 0)
         error(string("Branches ", undefined, " have no length in the network. ", str))

diff --git a/test/test_lm.jl b/test/test_lm.jl
@@ -629,19 +629,23 @@ end
 ###############################################################################
 @testset "Undefined branch length" begin
     ## No branch length
-    net = readTopology("(A,((B:1,#H1:1::0.1):1,(C:1,(D:1)#H1:1::0.9):1):0.5);");
+    net = readTopology("(A:2.5,((B,#H1:1::0.1):1,(C:1,(D:1)#H1:1::0.9):1):0.5);");
     dfr = DataFrame(trait = [11.6,8.1,10.3,9.1], tipNames = ["A","B","C","D"]);
-    @test_throws ErrorException("Branches [1] have no length in the network. The variance-covariance matrix of the network is not defined, and the phylogenetic regression cannot be done.") phylolm(@formula(trait ~ 1), dfr, net);
+    @test_throws ErrorException("Branches [2] have no length in the network. The variance-covariance matrix of the network is not defined, and the phylogenetic regression cannot be done.") phylolm(@formula(trait ~ 1), dfr, net);
     ## Negative branch length
-    net.edge[1].length = -0.5;
-    @test_throws ErrorException("Branches [1] have a negative or zero length in the network. The variance-covariance matrix of the network is not defined, and the phylogenetic regression cannot be done.") phylolm(@formula(trait ~ 1), dfr, net);
+    net.edge[2].length = -0.5;
+    @test_throws ErrorException("Branches [2] have a negative or zero length in the network. The variance-covariance matrix of the network is not defined, and the phylogenetic regression cannot be done.") phylolm(@formula(trait ~ 1), dfr, net);
     ## Zero branch length
-    net.edge[1].length = 0.0;
-    @test_throws ErrorException("Branches [1] have a negative or zero length in the network. The variance-covariance matrix of the network is not defined, and the phylogenetic regression cannot be done.") phylolm(@formula(trait ~ 1), dfr, net);
+    net.edge[2].length = 0.0;
+    fit = phylolm(@formula(trait ~ 1), dfr, net);
+    @test loglikelihood(fit) ≈ -6.245746681512051
     ## Non zero branch length
-    net.edge[1].length = 0.1;
+    net.edge[2].length = 0.1;
     fit = phylolm(@formula(trait ~ 1), dfr, net);
-    @test loglikelihood(fit) ≈ -6.522868090996417
+    @test loglikelihood(fit) ≈ -6.2197697662066815
+    ## Illicit zero branch length
+    net.edge[1].length = 0.0;
+    @test_throws PosDefException phylolm(@formula(trait ~ 1), dfr, net);
 end
 
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