rcpp_calc_anclikes_sp {cladoRcpp}  R Documentation 
This function, given parameters on the Relative weight of different geographic range inheritance scenarios at cladogenesis (speciation) events, calculates the probability of each possible ancestral state given the probabilities of each possible combination of tip states.
rcpp_calc_anclikes_sp(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)
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...) 
The Python/C++ program LAGRANGE (Ree & Smith 2008) gives a fixed equal probability to each rangeinheritance scenario it allows:
(1) sympatric speciation with 1 area (e.g. A –> A,A);
(2) sympatric speciation where one species inherits the ancestral range, and the other inherits
a 1area subset of the ancestral range (e.g. ABC –> ABC,B);
(3) vicariant speciation with one daughter occupying an area of size 1 (e.g. ABCD –> ACD,B)
For example, if the ancestral range is ABC, the possible daughters are:
(Left, Right)
Vicariance: A,BC AB,C AC,B BC,A C,AB B,AC
Sympatric subset: A,ABC B,ABC C,ABC ABC,A ABC,B ABC,C
There are 12 possibilities, so LAGRANGE would give each a probability of 1/12, conditional on the ancestor having range ABC. All other imaginable scenarios are given probability 0 – e.g., sympatric speciation of a widespread range (ABC –> ABC,ABC), or jump dispersal leading to founderevent speciation (ABC –> ABC,D).
In BioGeoBEARS
, the relative probability (or weight) of these categories is set by the s
(sympatricsubset), v
(vicariance), j
(jump/founderevent), and y
(sympatricrangecopying) parameters. These parameters do not have to sum to 1, they just give the
relative weight of an event of each type. E.g., if s=1
, v=1
, j=0
, y=1
,
then each allowed sympatricrangecopying, sympatricsubset, and vicariance event is given equal probability
(this is the LAGRANGE cladogenesis model) .
The rcpp_calc_anclikes_sp
function gets slow for large state spaces, as every possible combination of states at Left and
Right branches is checked. Even in C++ this will get slow, as the (number of states) = 2^(number of areas)
,
and as the number of possible combinations of (ancestor, left,right) states is
(number of states)*(number of states)*(number of states)
.
Note: the maxent
parameters allow the user to specify the probability distribution for different range sizes of the
smallerranged descendant lineage. The defaults set these parameters so that the LAGRANGE model is implemented (the smaller
descendant always has range size 1).
See rcpp_calc_anclikes_sp_COOprobs
and rcpp_calc_anclikes_sp_COOweights_faster
for successively faster solutions to this problem.
This is the bytecompiled version of rcpp_calc_anclikes_sp_prebyte
.
rcpp_calc_anclikes_sp
is bytecompiled, which (might) make it faster.
For information on bytecompiling, see http://www.rstatistics.com/2012/04/speedupyourrcodeusingajustintimejitcompiler/ and cmpfun
in the compiler
package.
prob_ancestral_states
The probabilities of the ancestral states.
Nicholas Matzke matzke@berkeley.edu
rcpp_calc_anclikes_sp
, rcpp_calc_anclikes_sp_COOprobs
,
rcpp_calc_anclikes_sp_COOweights_faster
#bibliography /Dropbox/_njm/__packages/cladoRcpp_setup/cladoRcpp_refs.bib
@cite Matzke_2013
@cite Matzke_2014
@cite ReeSmith2008
# 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