Description Usage Arguments Details Value Author(s) References See Also Examples
This is the pre-byte compiled version of
rcpp_calc_anclikes_sp
.
rcpp_calc_anclikes_sp
is byte-compiled,
which (might) make it faster. See
rcpp_calc_anclikes_sp
for full description
and help.
1 2 3 4 5 6 7 |
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 (0-based) |
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
(range-copying). 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 subset-sympatric
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 founder-event
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 full-sympatric
(range-copying) 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 right-states 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 re-used 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...) |
This function gets slow for large state spaces.
For information on byte-compiling, see
http://www.r-statistics.com/2012/04/speed-up-your-r-code-using-a-just-in-time-jit-compiler/
and cmpfun
in the
compiler
package.
prob_ancestral_states
The probabilities of the
ancestral states.
Nicholas Matzke matzke@berkeley.edu
Matzke N (2012). "Founder-event speciation in BioGeoBEARS package dramatically improves likelihoods and alters parameter inference in Dispersal-Extinction-Cladogenesis (DEC) analyses." _Frontiers of Biogeography_, *4*(suppl. 1), pp. 210. ISSN 1948-6596, Poster abstract published in the Conference Program and Abstracts of the International Biogeography Society 6th Biannual Meeting, Miami, Florida. Poster Session P10: Historical and Paleo-Biogeography. Poster 129B. January 11, 2013, <URL: http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster>.
Ree RH and Smith SA (2008). "Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis." _Systematic Biology_, *57*(1), pp. 4-14. <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>.
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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