Merge pull request #94 from natetrux/master

Distance Metrics Documentation
eaton-lab · Sep 4, 2024 · f9eb409 · f9eb409
2 parents cb2f6fd + 11a9245
commit f9eb409
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diff --git a/docs/docs-drafts.ipynb b/docs/docs-drafts.ipynb
diff --git a/docs/node-distance.ipynb b/docs/node-distance.ipynb
diff --git a/docs/tree-distance.ipynb b/docs/tree-distance.ipynb
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -99,15 +99,15 @@ nav:
       # - composite plots
       # - Modifying axes style: ...
 
-    - Consensus Trees: ...
+    #- Consensus Trees: ...
     # - Species/Demographic Trees: ...
-    # - Admixture/Networks: ...
+    # - Admixture/Networks: ... # TO DO
 
     # - <i>.mod</i> - tree modifications:
     - <i>.mod</i> - tree modification:
       - rooting trees: rooting.ipynb
       - topology changes: mod-topology.ipynb
-      - edge/dist changes: mod-edges.ipynb
+      - edge/dist changes: mod-edges.ipynb #TO DO
       # - Tree moves: ...
 
     - <i>.enum</i> - tree enumeration:
@@ -116,9 +116,9 @@ nav:
       - quadripartition methods: quadripartitions.ipynb
       # - other: ...
 
-    - <i>.distance</i> - tree/node dists:
-      - node distances: ...
-      - tree distances: ...
+    - <i>.distance</i> - tree/node dists: # TO DO
+      - node distances: node-distance.ipynb
+      - tree distances: tree-distance.ipynb
 
     - <i>.pcm</i> - evol analyses:
       - Continuous traits: ...
@@ -130,7 +130,7 @@ nav:
       # - MulTree analysis: ...
       # - Tree inference: ...
 
-    - <i>.annotate</i> - add to drawings: ...
+    - <i>.annotate</i> - add to drawings: ... # TO DO
 
     - <i>.rtree</i> - random trees: random-trees.ipynb  
 

diff --git a/toytree/distance/_src/quartet_dist.py b/toytree/distance/_src/quartet_dist.py
@@ -54,7 +54,7 @@ def get_quartet_resolutions_table(tree: ToyTree, df: bool = False) -> np.ndarray
     assert len(snames) == len(set(snames)), "duplicate tip names are not allowed"
 
     # an empty array to enumerate all quartets and their resolutions
-    ntips = toytree.enum.get_n_quartets(tree.ntips)
+    ntips = toytree.enum.get_num_quartets(tree.ntips)
     arr = np.zeros(ntips, dtype=np.int_)
 
     # a dict to map {tipset: resolved} as {frozenset(abcd): tuple(abcd)}

diff --git a/toytree/distance/_src/treedist.py b/toytree/distance/_src/treedist.py
@@ -80,7 +80,6 @@
     "get_treedist_rfg_msi",
     "get_treedist_rfg_spi",
     "get_treedist_rfg_mci",
-    "get_treedist_rfg_jac",
 ]