Calculate probability of ancestral states below a speciation event, given probabilities of the states on each descendant branch

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Description

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.

Usage

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  rcpp_calc_anclikes_sp_prebyte(Rcpp_leftprobs,
    Rcpp_rightprobs, l, s = 1, v = 1, j = 0, y = 1,
    dmat = NULL, maxent01s = NULL, maxent01v = NULL,
    maxent01j = NULL, maxent01y = NULL,
    max_minsize_as_function_of_ancsize = NULL,
    Rsp_rowsums = rep(1, length(Rcpp_leftprobs)),
    printmat = FALSE)

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 (0-based)

s

Relative weight of sympatric "subset" speciation. Default s=1 mimics LAGRANGE model.

v

Relative weight of vicariant speciation. Default v=1 mimics LAGRANGE model.

j

Relative weight of "founder event speciation"/jump speciation. Default j=0 mimics LAGRANGE model.

y

Relative weight of fully sympatric speciation (range-copying). Default y=1 mimics LAGRANGE model.

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 dmat matrix to value 1. Users may construct their own parameterized dmat (for example, making dmat a function of distance) for inclusion in ML or Bayesian analyses.

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 NULL, which means the script will set up the LAGRANGE model (one descendent always has range size 1).

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 NULL, which means the script will set up the LAGRANGE model (one descendent always has range size 1).

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 NULL, which means the script will set up the LAGRANGE model (one descendent always has range size 1).

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 NULL, which means the script will set up the LAGRANGE model (one descendent always has range size 1).

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...)

Details

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.

Value

prob_ancestral_states The probabilities of the ancestral states.

Author(s)

Nicholas Matzke matzke@berkeley.edu

References

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>.

See Also

rcpp_calc_anclikes_sp

Examples

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# 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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