datelife_result_sdm: Function to compute the SDM supertree (Criscuolo et al. 2006)...

Description Usage Arguments Details Value

View source: R/datelife_summary.R

Description

Function to compute the SDM supertree (Criscuolo et al. 2006) from a datelifeResult object.

Usage

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datelife_result_sdm(datelife_result, weighting = "flat",
  verbose = TRUE, clustering_method = "nj")

Arguments

datelife_result

An output of get_datelife_result function: A list of patristic matrices with names corresponding to original study citations.

weighting

A character vector indicating how much weight to give to each input tree in the SDM analysis. Choose one of:

weighting = "flat"

All trees have equal weighting.

weighting = "taxa"

Weight is proportional to number of taxa.

weighting = "inverse"

Weight is proportional to 1 / number of taxa.

verbose

Boolean. If TRUE, it gives printed updates to the user.

clustering_method

A character vector indicating the method to construct the tree. Options are "nj" for Neighbor-Joining and "upgma" for Unweighted Pair Group Method with Arithmetic Mean.

Details

Criscuolo A, Berry V, Douzery EJ, Gascuel O. SDM: a fast distance-based approach for (super) tree building in phylogenomics. Syst Biol. 2006. 55(5):740. doi: 10.1080/10635150600969872.

Value

A list of two elements:

phy

A phylo object with the output chronogram from SDM analysis.

data

A datelifeResult object with the chronograms that were used to construct the SDM tree.


phylotastic/datelife documentation built on Jan. 22, 2019, 12:29 a.m.