Draft implementation of new SPR distance#175

Merged

ms609 merged 217 commits intomainfrom

Feb 12, 2026

Commits on Feb 22, 2022

Commits on Feb 23, 2022

A second way
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Faster path dist comparison
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sqrt; vec_diff_euclidean
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tests & checks
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cf. phangorn::path.dist
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How SPR is calcualted
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Whidden solutions
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Commits on Feb 28, 2022

Improve SPR distance
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Definite improvement over de O algo
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balance?
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Commits on Mar 1, 2022

Approximates rather than underestimates
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Split out deO approach
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confusion()
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Commits on Mar 2, 2022

Tree reduction
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ren
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TreeConflict→Reduce()
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rn
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Reduction rule 2
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Commits on Mar 4, 2022

gg_aunt fixes reduce_tree()
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Handle deletion of root leaf
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Drop >1 if requested
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Reduce
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Test root lift
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static root 1
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Lift logging
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lift log
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Success
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Commits on Mar 8, 2022

Root-lifting
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sibling rewritery
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Debugging glyphs
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Simplify test
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Renumber tips in situ
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Reduce → postorder
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KeepTipPostorder
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keep_and_reroot()
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keep_and_reroot
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rm dbg
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splits by tree
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rm i, j
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keep_and_reduce
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Commits on Jul 19, 2022

Commits on Jul 20, 2022

insertCite
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Commits on Jun 26, 2024

Merge branch 'master' into no-phangorn
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Merge; write
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document()
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PathDist _is_ faster than path.dist()
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Update test-tree_distance_path.R
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Merge branch 'master' into spr-dist
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Exact
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phangorn
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ms609/TreeDistData first
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Run on successful R CMD check
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workflow_dispatch:
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env
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phangorn (>= 2.2.1)
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Update memcheck.yml
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libicu66
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-commetn
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libicu66
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ms609/TreeTools
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phangorn 4.4 requires Matrix
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libicu-dev

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Combine apt installs

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Work backwards

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Reorder; rm duplication

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Def don't want show all leaks
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--errors-for-leak-kinds=definite
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Merge branch 'master' into no-phangorn
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rm comment
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* rm PathVectorR
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libicu66: obseleted?
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libcui66 BEFORE -dev?
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libicu66 REALLY first
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copyedit
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-libicu66
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-libcurl
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ws
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Github package install
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20.04
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Reinstall stringi
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latest
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Commits on Jun 27, 2024

Commits on Jun 28, 2024

Commits on Jan 15, 2026

Commits on Feb 3, 2026

Commits on Feb 4, 2026

Commits on Feb 5, 2026

Commits on Feb 6, 2026

Commits on Feb 9, 2026

First stab at lookup table for n = 7
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7
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Improve packing
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Rcpp ftw
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Manual fix for pectinate read
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Debugged
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ren
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mark 7
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Draft for pec
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mid draft
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lookup8
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Update spr-exact-8.R
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7ize
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First shape for 9s
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Quick bash at incorporating 8-leaves
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shape1
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shape2
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Correct shapes
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Commits on Feb 11, 2026

Require TreeTools 2.1.0
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Commits on Feb 12, 2026