Usage
calc_loglike_for_optim_stratified(params, BioGeoBEARS_run_object, phy, tip_condlikes_of_data_on_each_state, print_optim = TRUE, areas_list, states_list, force_sparse = FALSE, cluster_already_open = FALSE)
Arguments
params
A vector of parameters for optimization.
BioGeoBEARS_run_object
Object containing the run
parameters, and the model.
tip_condlikes_of_data_on_each_state
Conditional
likelihoods at tips. 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.
print_optim
If TRUE (default), print the
optimization steps as ML estimation progresses.
areas_list
A list of the desired area
names/abbreviations/letters (?).
states_list
A list of the possible
states/geographic ranges, in 0-based index form.
force_sparse
Should sparse matrix exponentiation
be used? Default FALSE.
cluster_already_open
The cluster object, if it has
already been started.