calc_linked_params_BioGeoBEARS_model_object: Update parameters that are deterministic functions of free...
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

Description Usage Arguments Details Value Note Author(s) References See Also Examples

This function updates the linked parameters (which are listed as neither "fixed" nor "free" in params_table$type; i.e., they are equations which are calculated from #' the fixed and free parameters, which should have already been set by other functions).

1 2	calc_linked_params_BioGeoBEARS_model_object(BioGeoBEARS_model_object, update_init = FALSE)

`BioGeoBEARS_model_object`	The BioGeoBEARS_model object, of class `BioGeoBEARS_model`
`update_init`	If `TRUE`, put the estimates into the initial values in the `params_table`. Default: `FALSE`.

params_table$type is typically stored in: BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table.

BioGeoBEARS_model_object Updated version of the BioGeoBEARS_model object, of class BioGeoBEARS_model.

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster

Matzke_2012_IBS

define_BioGeoBEARS_model_object define_BioGeoBEARS_run

# Define a BioGeoBEARS run object
BioGeoBEARS_run_object = define_BioGeoBEARS_run()
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table

# Set 'j' to be free, i.e. as in a DEC+J model (adding jump dispersal
# to the LAGRANGE DEC model)
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","type"] = "free"
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","init"] = 0.25
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table["j","est"] = 0.25

# Display result
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table

# Update the other parameters
BioGeoBEARS_run_object$BioGeoBEARS_model_object =
calc_linked_params_BioGeoBEARS_model_object(
BioGeoBEARS_model_object=BioGeoBEARS_run_object$BioGeoBEARS_model_object)

# Display result
BioGeoBEARS_run_object$BioGeoBEARS_model_object@params_table