Calculate probability of ancestral states below a speciation event, given probabilities of the states on each descendant branch
Description
This is the prebyte compiled version of
rcpp_calc_anclikes_sp
.
rcpp_calc_anclikes_sp
is bytecompiled,
which (might) make it faster. See
rcpp_calc_anclikes_sp
for full description
and help.
Usage
1 2 3 4 5 6 7 
Arguments
Rcpp_leftprobs 
Probabilities of the states at the base of the left descendant branch 
Rcpp_rightprobs 
Probabilities of the states at the base of the right descendant branch 
l 
List of state indices (0based) 
s 
Relative weight of sympatric "subset"
speciation. Default 
v 
Relative weight of vicariant speciation. Default

j 
Relative weight of "founder event
speciation"/jump speciation. Default 
y 
Relative weight of fully sympatric speciation
(rangecopying). Default 
dmat 
If given, a matrix of rank numareas giving
multipliers for the probability of each dispersal event
between areas. Default NULL, which sets every cell of the

maxent01s 
Matrix giving the relative weight of
each possible descendant rangesize for the smaller range,
for a given ancestral rangesize, for a subsetsympatric
speciation event. Default is 
maxent01v 
Matrix giving the relative weight of
each possible descendant rangesize for the smaller range,
for a given ancestral rangesize, for a vicariance
speciation event. Default is 
maxent01j 
Matrix giving the relative weight of
each possible descendant rangesize for the smaller range,
for a given ancestral rangesize, for a founderevent
speciation event. Default is 
maxent01y 
Matrix giving the relative weight of
each possible descendant rangesize for the smaller range,
for a given ancestral rangesize, for a fullsympatric
(rangecopying) speciation event. Default is 
max_minsize_as_function_of_ancsize 
If given, any state with a range larger that this value will be given a probability of zero (for the branch with the smaller rangesize). This means that not every possible combination of ranges has to be checked, which can get very slow for large state spaces. 
Rsp_rowsums 
A vector of size (numstates) giving the sum of the relative probabilites of each combination of descendant states, assuming the probabilities of the left and rightstates are all equal (set to 1). This is thus the sum of the weights, and dividing by this normalization vector means that the each row of the speciation probability matrix will sum to 1. Default assumes the weights sum to 1 but this is not usually the case. Rsp_rowsums need only be calculated once per tree+model combination, stored, and then reused for each node in the tree, yielding significant time savings. 
printmat 
Should the probability matrix output be printed to screen? (useful for debugging, but can be dramatically slow in R.app for some reason for even moderate numbers of states; perhaps overrunning the line length...) 
Details
This function gets slow for large state spaces.
For information on bytecompiling, see
http://www.rstatistics.com/2012/04/speedupyourrcodeusingajustintimejitcompiler/
and cmpfun
in the
compiler
package.
Value
prob_ancestral_states
The probabilities of the
ancestral states.
Author(s)
Nicholas Matzke matzke@berkeley.edu
References
Matzke N (2012). "Founderevent speciation in BioGeoBEARS package dramatically improves likelihoods and alters parameter inference in DispersalExtinctionCladogenesis (DEC) analyses." _Frontiers of Biogeography_, *4*(suppl. 1), pp. 210. ISSN 19486596, Poster abstract published in the Conference Program and Abstracts of the International Biogeography Society 6th Biannual Meeting, Miami, Florida. Poster Session P10: Historical and PaleoBiogeography. Poster 129B. January 11, 2013, <URL: http://phylo.wikidot.com/matzke2013internationalbiogeographysocietyposter>.
Ree RH and Smith SA (2008). "Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis." _Systematic Biology_, *57*(1), pp. 414. <URL: http://dx.doi.org/10.1080/10635150701883881>, <URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18253896>.
See Also
rcpp_calc_anclikes_sp
Examples
1 2 3 4 5  # For the basic logic of a probablistic cladogenesis model, see
?rcpp_calc_anclikes_sp
# For examples of running the functions, see the comparison of all functions at:
# ?cladoRcpp
