This function takes the list of possible states (l), and the parameters of a cladogenesis model (s, v, j, y) (which are the relative weights of each of type of cladogenic range inheritance event) and, for each ancestral state, sums the weights of allowed descendant events. Dividing the weights in each row, by the sum of the weights for that row, provides the absolute probabilities of each transition, conditional on the ancestral state for that row.
1 2 3 4 5 6 
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. 
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...) 
The inputs Rcpp_leftprobs
and
Rcpp_rightprobs
are basically irrelevant here, but
retained for symmetry with the other functions. In
effect, this function is identical with
rcpp_calc_anclikes_sp
except that
Rcpp_leftprobs
and Rcpp_rightprobs
are
arrays of 1s of length(l)
, i.e.
length(number_of_states)
.
This function is no longer used in BioGeoBEARS
,
but has been retained to enable easy counting of the
number of events. When all nonzeroprobability events
are of equal probability (e.g. as in LAGRANGE; Ree &
Smith 2008) the function could be used for normalization,
but it is safer to use
rcpp_calc_anclikes_sp
or one of the faster
COOlike equivalents.
Rsp_rowsums
A vector of size (numstates) giving
the number of events of nonzero probability for each
ancestral states.
Nicholas Matzke matzke@berkeley.edu
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>.
rcpp_calc_anclikes_sp
,
rcpp_calc_anclikes_sp_COOprobs
,
rcpp_calc_anclikes_sp_COOweights_faster
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

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