Description Usage Arguments Details Value Author(s) References See Also Examples
This function is a faster version of
rcpp_calc_anclikes_sp
. Like
rcpp_calc_anclikes_sp
, this function
calculates the conditional probability of every allowed
combination of ancestral range, left descendent range,
and right descendent range.
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 (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. |
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 improves upon
rcpp_calc_anclikes_sp
by returning a
COO-like list of the nonzero cells in the transition
matrix for the speciation event.
(COO = Coordinate list format for a matrix, see http://en.wikipedia.org/wiki/Sparse_matrix#Coordinate_list_.28COO.29
Whereas a COO-formatted square matrix stores, for each
nonzero cell, the row #, column #, and cell value,
rcpp_calc_anclikes_sp
returns lists
containing, for each nonzero cell:
1. 0-based index of the ancestral state
2. 0-based
index of the left state
3. 0-based index of the right
state
4. Value of the specified nonzero cell
Time savings over rcpp_calc_anclikes_sp
are
realized by skipping many ancestor/descendent
combinations which are impossible transitions on the
model, and neither recording, nor storing, nor passing
them. This becomes important with large state spaces.
list_weights_of_transitions
A list of 3 lists.
Each list has (numstates) items, representing the
ancestral states. List #1 gives the 0-based state index
for the nonzero left descendents of each ancestral state.
List #2 gives the 0-based state index for the nonzero
right descendents of each ancestral state. List #3 gives
the weight of each nonzero transition from each ancestral
state. Summing these weights within each ancestral state
for list #3 gives the total of the weights for each
ancestral state. Dividing the weights by the sum of
weights gives the conditional probability of each
descendent state, conditional on the ancestral state.
These conditional probabilities need only be calculated
once per tree+model combination, stored, and then re-used
for each node in the tree, yielding significant time
savings.
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>.
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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