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Estimate the extended phylogenetic independent contrast. Rather than normalize differences across nodes by branch lengths, differencesare normalized be the expected difference obtained from replicate simulations. This allows for greater model flexibility.

Originally reported by: Casey Dunn (Bitbucket: caseywdunn, GitHub: caseywdunn)

Need to get citation() working correctly. Created inst/CITATION as described in http://r-pkgs.had.co.nz/inst.html#inst-citation, but it isn't being parsed.

• Bitbucket: https://bitbucket.org/caseywdunn/hutan/issue/3

Originally reported by: Casey Dunn (Bitbucket: caseywdunn, GitHub: caseywdunn)

Takes a tree and a set of node numbers for tips. Returns TRUE if the tips form a monophyletic clade. Unrooted - a subtree can be monophyletic even if it includes the root.

• Bitbucket: https://bitbucket.org/caseywdunn/hutan/issue/1

Originally reported by: Casey Dunn (Bitbucket: caseywdunn, GitHub: caseywdunn)

• Bitbucket: https://bitbucket.org/caseywdunn/hutan/issue/4

Originally reported by: Casey Dunn (Bitbucket: caseywdunn, GitHub: caseywdunn)

Build the function decompose based on the following template.

#!r

#' Decomposes a single tree into a series of subtrees designated by internal
#' node numbers
#' 
#' @param phy The tree to be decomposed, as an ape phylo object
#' @param x A vector of internal node numbers. The tree phy will be cut on each branch 
#' that subtends each of these nodes.
#' @return A list of phylo objects 
decompose <- function( phy, x ){}

• Bitbucket: https://bitbucket.org/caseywdunn/hutan/issue/2

Create the function Create function map_frequency_to_subtree() that has the following behavior:

• Takes a set of trees with multiple sequences per taxon. Tips have name format taxon_1@1234 where taxon_1 is the taxon and 1234 is the sequence ID. Each taxon can have one or more sequences, which are differentiated by their ids. Creates a table of split frequencies seen in the tree.

• Takes a focal tree with one tip per taxon, and tip name taxon. e.g. taxon_1

• For each edge in focal tree (including terminal edges) identify the corresponding edge in the split frequency table. Map the frequency of that edge to the edge label in the focal tree. If the split was not found in the set then the edge label has value 0.

• Return the focal tree with edge labels.

Originally reported by: beroe (Bitbucket: beroe, GitHub: beroe)

is there a way to determine taxa that are outside the maximally inclusive monophyletic group in an unrooted tree, maybe by making some assumptions about distances?

• Bitbucket: https://bitbucket.org/caseywdunn/hutan/issue/5