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 3  make_relprob_matrix_bi(states_list = default_states_list(),
split_ABC = FALSE, splitval = "",
code_for_overlapping_subsets = NA, printwarn = 1)

states_list 
A list of states, where each state consists of a list of areas. A default example list is provided. 
split_ABC 

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 
printwarn 
If 
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.
NOTE: This function is veeeeeeery slow, even for only 3
areas (i.e. 2^3=8
geographic ranges). It is
mostly useful for illustration. See
cladoRcpp
for drastic
improvements in calculating cladogenesis models.
probmat
A matrix of strings, where each cell
contains the parameters describing the conditional
probability of that ancestorâ€“>(Left descendant,Right
descendant) range inheritance scenario.
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_spmat_row
1 2 3 4 5 6 
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