section_the_tree(inputs, make_master_table = FALSE, plot_pieces = TRUE, cut_fossils = TRUE, fossils_older_than = 0.6)inputs$master_table containing the correspondance
between the original tree and the sectioned pieces.TRUE, plot the tree chunks
(but not isolated branch segments) as they are created.TRUE (default), the program
is stopped if there are fossils, i.e. tips older than 0.6
my (default). Users should use
codedrop.tip or an external program to clip
fossils out of the tree. PLEASE NOTE that several times I
have experienced miserable long nights due, apparently,
to drop.tip producing weird tree
structures, resulting in weird Newick files, without me
realizing it. The solution is usually to open the Newick
file in something like FigTree, resort the
branches, and save to a new Newick file. Fossils have now
been implemented in stratified analysis; this was
complicated, as it involves inserting new branches in
chopped trees.fossils_older_than will be marked as TRUE
in a column called fossil. This is not currently
set to 0, because Newick files can have slight precision
issues etc. that mean not all tips quite come to zero.
You can attempt to fix this with
extend_tips_to_ultrametricize (but make
sure you do not inappropriately average in fossils!!).inputs with inputs$tree_sections_list
added.
Matzke_2012_IBS
prt, chainsaw2,
drop.tip