bump compat for Functors to 0.4 (#189)

CI: setup-r removed from test job, @v2 in docs job Co-authored-by: CompatHelper Julia <[email protected]> Co-authored-by: Cecile Ane <[email protected]>
JuliaPhylo · Dec 9, 2022 · 4ee407a · 4ee407a
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commit 4ee407a
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -26,7 +26,6 @@ jobs:
           - x64
     steps:
       - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
@@ -44,15 +43,15 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v2
         with:
           file: lcov.info
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
       - run: echo "LD_LIBRARY_PATH=$(R RHOME)/lib" >> $GITHUB_ENV
       - uses: julia-actions/setup-julia@v1
         with:

diff --git a/Project.toml b/Project.toml
@@ -35,7 +35,7 @@ DataFrames = "1.3"
 DataStructures = "0.9, 0.10, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18"
 Distributions = "0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25"
 FASTX = "1.1, 2"
-Functors = "0.2, 0.3"
+Functors = "0.2, 0.3, 0.4"
 GLM = "1.1, 1.2, 1.3, 1.4"
 NLopt = "0.5.1, 0.6"
 StaticArrays = "0.8.3, 0.9, 0.10, 0.11, 0.12, 1.0"

diff --git a/src/addHybrid_snaq.jl b/src/addHybrid_snaq.jl
@@ -344,14 +344,6 @@ addHybridizationUpdateSmart!(net::HybridNetwork, N::Integer) = addHybridizationU
 
 
 # ----------------------------------- add alternative hybridizations found in bootstrap ------------------------------------
-## function to add the top hybridizations (not in best network)
-## found in bootstrap networks
-## it modifies the network and BSe to add the new edge number,
-## it also adds a new column 0/1, with 1 if the edge is not present in the original estimated network
-## cutoff=10, only show hybridizations with bootstrap support>10%
-## top=3, only show the top three alternative hybridizations (sorted by bootstrap support)
-## can we put in a different color in the plot?
-## Cecile: you could add a new option to our RCall-based plot function to take a vector of colors.
 """
     addAlternativeHybridizations!(net::HybridNetwork, BSe::DataFrame;
                                   cutoff=10::Number, top=3::Int)
@@ -360,11 +352,18 @@ Modify the network `net` (the best network estimated with snaq) by adding other
 that are present in the bootstrap networks. By default, it will only consider hybrid edges with
 more than 10% bootstrap support (`cutoff`) and it will only include the three top hybridizations
 (`top`) sorted by bootstrap support.
-The function also modifies the dataframe `BSe` obtained with `hybridBootstrapSupport`. In the original
-`BSe` dataframe, hybrid edges that do not appear in the best network have a missing number.
+
+The function also modifies the dataframe `BSe`. In the original `BSe`,
+supposedly obtained with `hybridBootstrapSupport`, hybrid edges that do not
+appear in the best network have a missing number.
 After the hybrid edges are added with `addAlternativeHybridizations`, `BSe` is modified to include the
-edge numbers of the newly added hybrid edges. Note that the function only adds the hybrid edges as minor to
-keep the underlying tree topology.
+edge numbers of the newly added hybrid edges.
+To distinguish hybrid edges present in the original network versus new edges,
+an extra column of true/false values is also added to `BSe`, named "alternative",
+with true for newly added edges absent from the original network.
+
+The hybrid edges added to `net` are added as minor edges, to keep the underlying
+major tree topology.
 
 # example