section_the_tree: Section a tree for stratified analysis
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

Description Usage Arguments Value Note Author(s) References See Also Examples

View source: R/BioGeoBEARS_stratified_v1.R

A utility function for stratified analysis. Sections the tree into a series of strata. Each stratum may have one or more subtrees (APE phylo3 objects, *WITH* root edges) and/or branch segments (which are just represented as numeric values, indicating the length of the sub-branch, i.e. the time-width of the stratum, if the branch crosses the whole stratum.

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  section_the_tree(inputs, make_master_table = FALSE,
    plot_pieces = TRUE, cut_fossils = TRUE,
    fossils_older_than = 0.6)

`inputs`	The list of inputs for stratified analysis
`make_master_table`	If desired, make an `inputs$master_table` containing the correspondance between the original tree and the sectioned pieces.
`plot_pieces`	If `TRUE`, plot the tree chunks (but not isolated branch segments) as they are created.
`cut_fossils`	If `TRUE` (default), the program is stopped if there are fossils, i.e. tips older than 0.6 my (default). Users should use codedrop.tip or an external program to clip fossils out of the tree. PLEASE NOTE that several times I have experienced miserable long nights due, apparently, to `drop.tip` producing weird tree structures, resulting in weird Newick files, without me realizing it. The solution is usually to open the Newick file in something like `FigTree`, resort the branches, and save to a new Newick file. Fossils have now been implemented in stratified analysis; this was complicated, as it involves inserting new branches in chopped trees.
`fossils_older_than`	Tips that are older than `fossils_older_than` will be marked as `TRUE` in a column called `fossil`. This is not currently set to 0, because Newick files can have slight precision issues etc. that mean not all tips quite come to zero. You can attempt to fix this with `extend_tips_to_ultrametricize` (but make sure you do not inappropriately average in fossils!!).

inputs with inputs$tree_sections_list added.

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster

Matzke_2012_IBS

prt, chainsaw2, drop.tip

test=1

Loading required package: rexpokit
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve

Loading required package: Rcpp
Loading required package: cladoRcpp
Loading required package: ape
Loading required package: phylobase

Attaching package: 'phylobase'

The following object is masked from 'package:ape':

    edges