From 79ecc713c20dd5c7741056affcdf1b0a757990c4 Mon Sep 17 00:00:00 2001
From: Cecile Ane <cecileane@users.noreply.github.com>
Date: Thu, 7 Jul 2022 22:49:14 +0200
Subject: [PATCH] more specific name, docstring, cosmetic changes

---
 src/traits.jl   | 27 +++++++++++++++++----------
 test/test_lm.jl | 17 +++++++++--------
 2 files changed, 26 insertions(+), 18 deletions(-)

diff --git a/src/traits.jl b/src/traits.jl
index ff85b16c..98a68dd9 100644
--- a/src/traits.jl
+++ b/src/traits.jl
@@ -337,7 +337,9 @@ Returns an object of type [`MatrixTopologicalOrder`](@ref).
 """
 function sharedPathMatrix(net::HybridNetwork;
                           checkPreorder=true::Bool)
-    checkBranchLengths(net::HybridNetwork)
+    check_nonmissing_nonnegative_edgelengths(net,
+        """The variance-covariance matrix of the network is not defined.
+           A phylogenetic regression cannot be done.""")
     recursionPreOrder(net,
                       checkPreorder,
                       initsharedPathMatrix,
@@ -383,16 +385,21 @@ function initsharedPathMatrix(nodes::Vector{Node}, params)
     return(zeros(Float64,n,n))
 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]]
-    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))
+"""
+    check_nonmissing_nonnegative_edgelengths(net, str="")
+
+Throw an Exception if `net` has undefined edge lengths (coded as -1.0) or
+negative edge lengths. The error message indicates the number of the offending
+edge(s), followed by `str`.
+"""
+function check_nonmissing_nonnegative_edgelengths(net::HybridNetwork, str="")
+    if any(e.length == -1.0 for e in net.edge)
+        undefined = [e.number for e in net.edge if e.length == -1.0]
+        error(string("Branch(es) number ", join(undefined,","), " have no length.\n", str))
     end
-    if (length(negatives) > 0)
-        error(string("Branches ", negatives, " have a negative or zero length in the network. ", str))
+    if any(e.length < 0 for e in net.edge)
+        negatives = [e.number for e in net.edge if e.length < 0.0]
+        error(string("Branch(es) number ", join(negatives,","), " have negative length.\n", str))
     end
 end
 
diff --git a/test/test_lm.jl b/test/test_lm.jl
index f0b67da8..504b5d99 100644
--- a/test/test_lm.jl
+++ b/test/test_lm.jl
@@ -631,19 +631,20 @@ end
     ## No branch length
     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 [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);
+    @test_throws ErrorException("""Branch(es) number 2 have no length.
+        The variance-covariance matrix of the network is not defined.
+        A phylogenetic regression cannot be done.""") phylolm(@formula(trait ~ 1), dfr, net);
     ## Negative branch length
     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
+    @test_throws ErrorException("""Branch(es) number 2 have negative length.
+        The variance-covariance matrix of the network is not defined.
+        A phylogenetic regression cannot be done.""") phylolm(@formula(trait ~ 1), dfr, net);
+    ## Zero branch length: allowed
     net.edge[2].length = 0.0;
     fit = phylolm(@formula(trait ~ 1), dfr, net);
     @test loglikelihood(fit) ≈ -6.245746681512051
-    ## Non zero branch length
-    net.edge[2].length = 0.1;
-    fit = phylolm(@formula(trait ~ 1), dfr, net);
-    @test loglikelihood(fit) ≈ -6.2197697662066815
-    ## Illicit zero branch length
+    net.edge[2].length = 0.1; # back to non-zero
+    ## Illicit zero length for 1st edge: from root to single "outgroup" taxon
     net.edge[1].length = 0.0;
     @test_throws PosDefException phylolm(@formula(trait ~ 1), dfr, net);
 end