ms609/TreeDist

Issues

• Plotting large (400 taxa) trees with VisualizeMatching

  #124 opened a month ago by ammaraziz
  5

• Islands vignette

  #126 opened 25 days ago by ms609
  0

• Use SIMD to improve performance (?)

  #84 opened 2 years ago by ms609
  0

• Check for clustering with Hopkins statistic

  #95 opened a month ago by ms609
  1

• using a benchmark tree correctly with distance functions

  #116 opened a month ago by jc17659
  3

• Memory Leak and Output Stalling when Processing Large Datasets with TreeDistance()

  #123 opened 2 months ago by qwer62667771
  5

• Other tree distances to discuss / incorporate

  #122 opened 2 months ago by ms609
  0

• Island hunting (Silva & Wilkinson 2021)

  #110 opened 3 months ago by ms609
  0

• The definition of RobinsonFoulds()

  #117 opened 4 months ago by Cassie818
  2

• Information-theoretic approaches to consensus trees

  #111 opened 7 months ago by ms609
  0

• SPR project

  #88 opened 2 years ago by ms609
  0

• Trees with different leaves:

  #44 opened a year ago by cdp-rna
  15

• Calculating adjusted R2 values from ClusteringInfoDistance() after randomization?

  #65 opened a year ago by Jigyasa3
  2

• VisualizeMatching

  #86 opened a year ago by rforster1
  1

• Error with `VisualizeMatching`

  #103 opened a year ago by Sidduppal
  4

• Warn when tips don't match?

  #106 opened a year ago by ms609
  0

• LAPJV

  #105 opened a year ago by ms609
  0

• The Treedist distance matrix output of Generalized RF and Nye et al. methods are zero

  #102 opened a year ago by Jigyasa3
  3

• LAPJV with non-square matrices

  #25 opened a year ago by ms609
  0

• Comparing trees with non-identical tips

  #92 opened 2 years ago by roblanf
  4

• When no. of tips in species tree and gene tree dont match. Adding new tips to the species tree

  #97 opened 2 years ago by Jigyasa3
  2

• MapTrees() with multiple batches

  #98 opened 2 years ago by ms609
  0

• thinnedTrees() with multiple tree batches

  #99 opened 2 years ago by ms609
  0

• Adapt for weighted trees

  #96 opened 2 years ago by ms609
  0

• polytomies allowed in the genetree?

  #94 opened 2 years ago by Jigyasa3
  1

• `Plot3` documentation

  #53 opened 2 years ago by ms609
  0

• Replace \insertRef with \insertCite inline citations

  #75 opened 2 years ago by ms609
  0

• Pathtrees

  #87 opened 2 years ago by ms609
  0

• Replace projection warning?

  #85 opened 2 years ago by ms609
  0

• Suggestion: how to compare tree with subsampled trees, thanks

  #81 opened 2 years ago
  2

• Dimension goodness plotter fails with batches

  #83 opened 2 years ago by ms609
  0

• input tree one by one?

  #82 opened 2 years ago
  2

• where is your shiny app for treedist?

  #80 opened 2 years ago by liamxg
  2

• How does CID affect DREAM outcomes?

  #74 opened 3 years ago by ms609
  0

• Visualize MST stress

  #68 opened 3 years ago by ms609
  0

• Use lighter Rcpp?

  #71 opened 3 years ago by ms609
  0

• Acknowledge another Generalized RF distance

  #70 opened 3 years ago by ms609
  0

• Hypervolume comparison in app

  #67 opened 3 years ago by ms609
  0

• Rooted trees or unrooted trees?

  #58 opened 3 years ago by Jigyasa3
  4

• Internalize multi-tree comparisons in C++

  #57 opened 3 years ago by ms609
  0

• protoclust required for vignette

  #46 opened 3 years ago by ms609
  0

• Add SSV metric to `MapTrees()`

  #51 opened 3 years ago by ms609
  0

• MapTrees() updates

  #50 opened 3 years ago by ms609
  0

• Check for duplicate edges in trees when comparing

  #47 opened 4 years ago by ms609
  0

• Match identical splits first

  #36 opened 4 years ago by ms609
  1

• Faster RF with multiple trees

  #37 opened 4 years ago by ms609
  0

• Arboreal matchings not tested

  #27 opened 4 years ago by ms609
  0

• NNI dist performance

  #22 opened 4 years ago by ms609
  0

• Replace `int` with `int_fastXX_t`

  #20 opened 4 years ago by ms609
  0

• MASTSize failure

  #17 opened 4 years ago by ms609
  0