Description Usage Arguments Value Note Author(s) References See Also Examples
View source: R/BioGeoBEARS_stratified_v1.R
This function is the stratified version of
calc_loglike_sp
.
1 2 3 4 5 6 7 8 9 10 11 12  calc_loglike_sp_stratified(tip_condlikes_of_data_on_each_state,
phy, Qmat = NULL, spPmat = NULL,
min_branchlength = 1e21, return_what = "loglike",
probs_of_states_at_root = NULL, rootedge = TRUE,
sparse = FALSE, printlevel = 0, use_cpp = TRUE,
input_is_COO = FALSE, spPmat_inputs = NULL,
cppSpMethod = 3, cluster_already_open = NULL,
calc_ancprobs = FALSE, null_range_allowed = TRUE,
fixnode = NULL, fixlikes = NULL, inputs = inputs,
allareas = allareas, all_states_list = all_states_list,
return_condlikes_table = FALSE,
calc_TTL_loglike_from_condlikes_table = TRUE)

tip_condlikes_of_data_on_each_state 
A numeric matrix with rows representing tips, and columns representing states/geographic ranges. The cells give the likelihood of the observation data under the assumption that the tip has that state; typically this means that the known geographic range gets a '1' and all other states get a 0. 
phy 
A phylogeny object. The function converts it to pruningwise order. 
Qmat 
A Q transition matrix representing the
alongbranch model for the evolution of geographic range,
using parameters d (dispersal/range expansion),
e (extinction/range contraction/local
extirpation), and perhaps others (e.g. distance). This
matrix can be input in either dense or sparse (COO)
format, as specified by 
spPmat 
Default is 
min_branchlength 
Nodes with branches below this branchlength will not be treated as cladogenesis events; instead, they will be treated as if an OTU had been sampled from an anagenetic lineage, i.e. as if you had a direct ancestor. This is useful for putting fossils into the biogeography analysis, when you have fossil species that range through time. (Note: the proper way to obtain such trees, given that most phylogenetic methods force all OTUs to be tips rather than direct ancestors, is another question subject to active research. However, one method might be to just set a branchlength cutoff, and treat any branches sufficiently small as direct ancestors.) 
return_what 
What should be returned to the user? Options are "loglike" (the loglikelihood of the data under the tree, model, and model parameters), "nodelikes" (the scaled conditional likelihoods at the nodes), "rootprobs" (the relative probability of the geographic ranges/states at the root), or "all" (all of the above in a list). Typically the user will only want to return "loglike" while doing ML optimization, but then return "all" once the ML parameter values have been found. 
probs_of_states_at_root 
The prior probability of
the states/geographic ranges at the root. The default,

rootedge 
Should the root edge be included in the
calculation (i.e., calculate to the bottom of the root),
if a root edge is present? Default 
sparse 
Should sparse matrix exponentiation be
performed? This should be faster for very large matrices
(> 100200 states), however, the calculations appear to
be less accurate. The function will transform a dense
matrix to COO format (see

printlevel 
If >= 1, various amounts of intermediate output will be printed to screen. Note: Intermediate outputs from C++ and FORTRAN functions have been commented out, to meet CRAN guidelines. 
use_cpp 
Should the C++ routines from

input_is_COO 
Is the input Q matrix a sparse,
COOformatted matrix ( 
spPmat_inputs 
A list of parameters so that

cppSpMethod 
Three C++ methods from cladoRcpp for
calculating and using the cladogenesis probability
matrix. 1 is slowest but easiest to understand; 3 is
fastest. If 
cluster_already_open 
If the user wants to
distribute the matrix exponentiation calculations from
all the branches across a number of processors/nodes on a
cluster, specify the cluster here. E.g.

calc_ancprobs 
Should ancestral state estimation be performed (adds an uppass at the end). 
null_range_allowed 
Does the state space include
the null range? Default is 
fixnode 
If the state at a particular node is going to be fixed (e.g. for ML marginal ancestral states), give the node number. (Trial implementation for stratified analysis.) 
fixlikes 
The state likelihoods to be used at the fixed node. I.e. 1 for the fixed state, and 0 for the others. (Trial implementation for stratified analysis.) 
inputs 
A list of inputs containing the dispersal matrix for each time period, etc. 
allareas 
A list of all the areas in the total analysis 
all_states_list 
A list of all the stats in the total analysis (0based coding  ?) 
return_condlikes_table 
If 
calc_TTL_loglike_from_condlikes_table 
If TRUE, force making of the condlikes table, and use it to calculate the loglikelihood (default=TRUE; matches LAGRANGE). 
grand_total_likelihood The total loglikelihood of the
data on the tree (default). Or, if
return_condlikes_table==TRUE
, the function returns
calc_loglike_sp_stratified_results
, with
calc_loglike_sp_stratified_results$condlikes_table
and
calc_loglike_sp_stratified_results$grand_total_likelihood
as list items. This can be useful for debugging
stratified analyses, which have a lot of extra
bookkeeping that is easy to mess up.
Go BEARS!
(COO = Coordinate list format for a matrix, see http://en.wikipedia.org/wiki/Sparse_matrix#Coordinate_list_.28COO.29
Nicholas Matzke matzke@berkeley.edu
Matzke_2012_IBS
ReeSmith2008
Landis_Matzke_etal_2013_BayArea
calc_loglike_sp
,
rcpp_calc_anclikes_sp
,
rcpp_calc_anclikes_sp_COOprobs
,
rcpp_calc_anclikes_sp_COOweights_faster
,
mat2coo
,
rcpp_calc_anclikes_sp_COOweights_faster
1  testval=1

Loading required package: rexpokit
Loading required package: cladoRcpp
Loading required package: ape
Loading required package: phylobase
Attaching package: 'phylobase'
The following object is masked from 'package:ape':
edges
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