bump compat for PhyloNetworks to 0.16, drop earlier versions (#25)

fixes #24

Project.toml

@@ -23,7 +23,7 @@ CSV = "0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.10"
 DataFrames = "0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 1.0"
 NLopt = "0.5.1, 0.6"
 PhyloCoalSimulations = "0.1,1"
-PhyloNetworks = "0.15.2"
+PhyloNetworks = "0.16.0"
 SpecialFunctions = "0.8, 0.9, 0.10, 1.0, 2"
 StaticArrays = "0.9, 0.10, 0.11, 0.12, 1.0"
 StatsFuns = "0.7, 0.8, 0.9, 1"

README.md

@@ -4,7 +4,8 @@
 
 ## overview
 
-`QuartetNetworkGoodnessFit` is a Julia package, providing tools to measure the
+`QuartetNetworkGoodnessFit` is a Julia package for phylogenetic networks analyses using four-taxon subsets.
+It includes tools to measure the
 goodness of fit of a phylogenetic network to data on subsets of 4 tips.
 It depends on the [PhyloNetworks](https://github.com/crsl4/PhyloNetworks.jl)
 package.

docs/Project.toml

@@ -5,6 +5,7 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterMarkdown = "997ab1e6-3595-5248-9280-8efb232c3433"
 PhyloCoalSimulations = "53f7b83a-06b5-4910-9a21-1896bf762ade"
 PhyloNetworks = "33ad39ac-ed31-50eb-9b15-43d0656eaa72"
+QuartetNetworkGoodnessFit = "1382f7fc-2744-4d9d-8ec6-1e3efdec0746"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]

docs/make.jl

@@ -4,7 +4,7 @@ using QuartetNetworkGoodnessFit
 DocMeta.setdocmeta!(QuartetNetworkGoodnessFit, :DocTestSetup, :(using QuartetNetworkGoodnessFit); recursive=true)
 
 makedocs(
-    sitename = "QuartetNetwork GoF.jl",
+    sitename = "QGoF",
     authors = "Cécile Ané and Ruoyi Cai",
     format = Documenter.HTML(prettyurls = get(ENV, "CI", nothing) == "true"), # easier local build
     modules = [QuartetNetworkGoodnessFit],

docs/src/index.md

@@ -1,10 +1,11 @@
-# QuartetNetworkGoodnessFit.jl
+# Quarnet GoF --or simply QGoF
 
-
-Julia
+QuartetNetworkGoodnessFit.jl is a Julia
 [package](https://github.com/cecileane/QuartetNetworkGoodnessFit.jl)
+for phylogenetic networks analyses using four-taxon subsets.
+It includes tools
 to measure the goodness of fit
-of a phylogenetic network to data on subsets of 4 tips.
+of a candidate network to data on subsets of 4 tips.
 It depends on the [PhyloNetworks](https://github.com/crsl4/PhyloNetworks.jl)
 package.
 

src/quarnetconcordancefactors.jl

@@ -183,7 +183,7 @@ function network_expectedCF_4taxa!(net::HybridNetwork, fourtaxa, inheritancecorr
     function isexternal(ib) # is bcc[ib] of degree 2 and adjacent to an external edge?
         # yes if: 1 single exit adjacent to a leaf
         length(exitnodes[ib]) != 1 && return false
-        ch = PhyloNetworks.getChildren(exitnodes[ib][1])
+        ch = getchildren(exitnodes[ib][1])
         return length(ch) == 1 && ch[1].leaf
     end
     for ib in reverse(bloborder)
@@ -203,19 +203,19 @@ function network_expectedCF_4taxa!(net::HybridNetwork, fourtaxa, inheritancecorr
         preorder!(net)
         # find a lowest hybrid node and # of taxa below it
         hyb = net.nodes_changed[findlast(n -> n.hybrid, net.nodes_changed)]
-        funneledge = [e for e in hyb.edge if PhyloNetworks.getParent(e) === hyb]
+        funneledge = [e for e in hyb.edge if getparent(e) === hyb]
         ispolytomy = length(funneledge) > 1
         funneldescendants = union([PhyloNetworks.descendants(e) for e in funneledge]...)
         ndes = length(funneldescendants)
-        n2 = (ispolytomy ? hyb : PhyloNetworks.getChild(funneledge[1]))
+        n2 = (ispolytomy ? hyb : getchild(funneledge[1]))
         ndes > 2 && n2.leaf && error("2+ descendants below the lowest hybrid, yet n2 is a leaf. taxa: $(fourtaxa)")
     end
     if ndes > 2 # simple formula for qCF: find cut edge and its length
         # inheritance correlation has no impact
         # pool of cut edges below. contains NO external edge, bc n2 not leaf (if reticulation), nice tree ow
         cutpool = (net.numHybrids == 0 ? net.edge :
-                    [e for e in n2.edge if PhyloNetworks.getParent(e) === n2])
-        filter!(e -> !PhyloNetworks.getChild(e).leaf, cutpool)
+                    [e for e in n2.edge if getparent(e) === n2])
+        filter!(e -> !getchild(e).leaf, cutpool)
         net.numHybrids > 0 || length(cutpool) <= 1 ||
             error("2+ cut edges, yet 4-taxon tree, degree-3 root and no degree-2 nodes. taxa: $(fourtaxa)")
         sistertofirst = 2    # arbitrarily correct if 3-way polytomy (no cut edge)
@@ -235,7 +235,7 @@ function network_expectedCF_4taxa!(net::HybridNetwork, fourtaxa, inheritancecorr
     ndes > 0 || error("weird: hybrid node has no descendant taxa")
     # by now, there are 1 or 2 taxa below the lowest hybrid
     qCF = MVector{3,Float64}(0.0,0.0,0.0) # mutated later
-    parenthedge = [e for e in hyb.edge if PhyloNetworks.getChild(e) === hyb]
+    parenthedge = [e for e in hyb.edge if getchild(e) === hyb]
     all(h.hybrid for h in parenthedge) || error("hybrid $(hyb.number) has a parent edge that's a tree edge")
     parenthnumber = [p.number for p in parenthedge]
     nhe = length(parenthedge)
@@ -269,10 +269,10 @@ function network_expectedCF_4taxa!(net::HybridNetwork, fourtaxa, inheritancecorr
     # no coalescence on cut-edge: delete it and extract parental networks
     ispolytomy || PhyloNetworks.shrinkedge!(net, funneledge[1])
     # shrinkedge! requires PhyloNetworks v0.15.2
-    childedge = [e for e in hyb.edge if PhyloNetworks.getParent(e) === hyb]
+    childedge = [e for e in hyb.edge if getparent(e) === hyb]
     length(childedge) == 2 ||
       error("2-taxon subtree, but not 2 child edges after shrinking the cut edge.")
-    all(PhyloNetworks.getChild(e).leaf for e in childedge) ||
+    all(getchild(e).leaf for e in childedge) ||
       error("2-taxon subtree, cut-edge shrunk, but the 2 edges aren't both external")
     childnumber = [e.number for e in childedge]
     for i in 1:nhe
@@ -291,8 +291,8 @@ function network_expectedCF_4taxa!(net::HybridNetwork, fourtaxa, inheritancecorr
             # detach childedge[2] from hyb and attach it to hyb's parent j
             pej_index = findfirst(e -> e.number == parenthnumber[j], simplernet.edge)
             pej = simplernet.edge[pej_index]
-            pn = PhyloNetworks.getParent(pej)
-            hn = PhyloNetworks.getChild(pej) # hyb node, but in simplernet
+            pn = getparent(pej)
+            hn = getchild(pej) # hyb node, but in simplernet
             ce2_index = findfirst(e -> e.number == childnumber[2], simplernet.edge)
             ce2 = simplernet.edge[ce2_index]
             PhyloNetworks.removeEdge!(hn,ce2)

src/utils.jl

@@ -35,8 +35,8 @@ function ultrametrize!(net::HybridNetwork, verbose::Bool)
     dr[1] = 0.0 # root
     for i in 2:length(net.nodes_changed) # pre-order
         @inbounds n = net.nodes_changed[i]
-        e = PhyloNetworks.getMajorParentEdge(n)
-        p = PhyloNetworks.getParent(e)
+        e = getparentedge(n)
+        p = getparent(e)
         pi = findfirst(x -> x===p, net.nodes_changed)
         drmaj = dr[pi]    # distance to root of major parent
         if !n.hybrid # n is a tree node. only 1 parent edge: e
@@ -47,8 +47,8 @@ function ultrametrize!(net::HybridNetwork, verbose::Bool)
             continue
         end
         # now: n is a hybrid node, with parent edges e and emin
-        emin = PhyloNetworks.getMinorParentEdge(n)
-        pmin = PhyloNetworks.getParent(emin)
+        emin = getparentedgeminor(n)
+        pmin = getparent(emin)
         pmini = findfirst(x -> x===pmin, net.nodes_changed)
         drmin = dr[pmini] # distance to root of minor parent
         majmissing = e.length == -1.0
@@ -101,7 +101,7 @@ function ultrametrize!(net::HybridNetwork, verbose::Bool)
     for i in 2:length(net.nodes_changed)
         @inbounds n = net.nodes_changed[i]
         n.leaf || continue
-        e = PhyloNetworks.getMajorParentEdge(n)
+        e = getparentedge(n)
         if e.length == -1.0
             e.length = height - dr[i]
         elseif !isapprox(dr[i], height)