If things are nontrivial, move them from here into their own issue. This is not a complete list from any of these packages, but things that jumped out as being needed. More to add probably. Some of the help pages for the functions below list multiple functions.
Ape functions (tree manipulation)
[ ] bind.tree (Binds Trees)
[x] branching.times (Branching Times of a Phylogenetic Tree)
[x] collapse.singles (Collapse Single Nodes)
[x] drop.tip (Remove Tips in a Phylogenetic Tree)
[x] is.binary.tree (Test for Binary Tree)
[ ] is.monophyletic (Is Group Monophyletic)
[x] is.ultrametric (Test if a Tree is Ultrametric)
[ ] ladderize (Ladderize a Tree)
[ ]mrca (Find Most Recent Common Ancestors Between Pairs)
[ ]multi2di (Collapse and Resolve Multichotomies)
[ ] node.depth (Depth and Heights of Nodes and Tips)
for this, probably depends how it will be used: could be useful
on a per-node basis and could be useful as a complete output.
But I need to know how output from the tree will be used first
really. The information is there already.
[x] rotate (Swapping Sister Clades) (done for binary trees only)
[ ]rotateContr (reorder nodes to give tip order)
Tree comparison (all.equal.phylo) type support that takes into account node rotation is also potentially very useful.
Phytools functions (tree manipulation; not sure about these)
[ ] applyBranchLengths (?)
[ ] bind.tip (see ape::bind.tree, and work out why this is needed)
[ ] collapse.to.star (Collapse a subtree to a star phylogeny)
[ ] drop.leaves (does not seem that useful)
diversitree functions (tree manipulation)
[ ] get.descendants (tips and or nodes)
[ ] ancestors
[x] branching.heights, branching.depth
I/O
[x] nexus trees (to and from) (basic version done, but see #29)
[x] ape trees (to and from, better and faster)
from ape is done, to ape remains.
Tree simulation
should I include a bd tree simulator to help with examples, and as an exercise in how to write one?
Starting to verge intro tree inference territory
[ ] gammaStat (Gamma-Statistic of Pybus and Harvey)
[ ] pic (Phylogenetically Independent Contrasts)
[ ] vcv (Phylogenetic Variance-covariance or Correlation Matrix)
Totally inference territory
[ ] bm via pruning; simulation and inference, as a demo. (mostly done)
richfitz
commented
10 years ago
If things are nontrivial, move them from here into their own issue. This is not a complete list from any of these packages, but things that jumped out as being needed. More to add probably. Some of the help pages for the functions below list multiple functions.
bind.tree(Binds Trees)branching.times(Branching Times of a Phylogenetic Tree)collapse.singles(Collapse Single Nodes)drop.tip(Remove Tips in a Phylogenetic Tree)is.binary.tree(Test for Binary Tree)is.monophyletic(Is Group Monophyletic)is.ultrametric(Test if a Tree is Ultrametric)ladderize(Ladderize a Tree)mrca(Find Most Recent Common Ancestors Between Pairs)multi2di(Collapse and Resolve Multichotomies)node.depth(Depth and Heights of Nodes and Tips)rotate(Swapping Sister Clades) (done for binary trees only)rotateContr(reorder nodes to give tip order)Tree comparison (all.equal.phylo) type support that takes into account node rotation is also potentially very useful.
applyBranchLengths(?)bind.tip(see ape::bind.tree, and work out why this is needed)collapse.to.star(Collapse a subtree to a star phylogeny)drop.leaves(does not seem that useful)get.descendants(tips and or nodes)ancestorsbranching.heights,branching.depthgammaStat(Gamma-Statistic of Pybus and Harvey)pic(Phylogenetically Independent Contrasts)vcv(Phylogenetic Variance-covariance or Correlation Matrix)