Description Usage Arguments Details Value Note Author(s) References See Also Examples
View source: R/BioGeoBEARS_basics_v1.R
Given the identity of the states/geographic ranges on the
left branch (Lstates
), right branch
(Rstates
), and ancestral areas
(ancareas_txt_tmp
), construct the (text version)
of the row of transition probabilities. This means that
each nonzero cell gets a v for a vicariance event,
a y for a sympatric speciation/rangecopying
event, a j for a founderevent/jump speciation
event, and an s for a sympatricsubset event.
1 2  make_spmat_row(Lstates, Rstates, ancareas_txt_tmp,
splitval = "", code_for_overlapping_subsets = NA)

Lstates 
A string listing the possible left states,
which will be split by 
Rstates 
A string listing the possible right
states, which will be split by 
ancareas_txt_tmp 
A string listing the possible
ancestral states, which will be split by

splitval 
The character to split on. 
code_for_overlapping_subsets 
Hypothetically, there
is no reason that a vicariance event could happen, e.g.
ABCâ€“>AB, BC. This is disallowed in 
This function is utilized by apply
in
other functions (e.g. ) in an attempt to speed up
calculation over rows. However, processing of text
formulas via apply
will never be fast
enough for large matrices; see
cladoRcpp
for optimized
functions.
This textbased matrix later gets evaluated by other
functions to calculate the numerical probabilities.
I.e., if j=0 and the other forms of speciation have
weights equal to each other, this is the LAGRANGE
cladogenesis model.
returncell
The text specifying the type of
transition.
Go BEARS!
Nicholas J. Matzke matzke@berkeley.edu
http://phylo.wikidot.com/matzke2013internationalbiogeographysocietyposter https://code.google.com/p/lagrange/
Matzke_2012_IBS
ReeSmith2008
size_species_matrix
,
make_relprob_matrix_bi
1  testval=1

Loading required package: rexpokit
Loading required package: cladoRcpp
Loading required package: ape
Loading required package: phylobase
Attaching package: 'phylobase'
The following object is masked from 'package:ape':
edges
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