BAMMlikelihood {BAMMtools}

Calculate BAMM likelihood

Description

Calculates the likelihood of a phylogeny exactly as is done by BAMM, given a set of events.

Usage

BAMMlikelihood(
  phy,
  eventdata,
  gen = "last",
  segLength = 0.02,
  sf = 1,
  return.intermediates = FALSE,
  e_prob_condition = "if_different",
  ...
)

Arguments

phy

Either an object of class phylo or the path to a tree file in newick format.

eventdata

A table of event data, as returned by BAMM, either as an object of class dataframe or as the path to an event_data file. Alternatively, a named numeric vector of length two holding speciation ("lambda") and extinction ("mu") rates for the constant-rate birth-death process.

gen

The BAMM generation for which the likelihood should be calculated. Can be an integer specifying a specific generation, or last, specifying the last generation, or all, in which case the likelihood will be calculated for all generations.

segLength

The relative segment length, exactly as defined for BAMM.

sf

The sampling fraction.

return.intermediates

Debugging option, returns augmented phylo objects for each generation, see Details.

e_prob_condition

Approach for how extinction probabilities are handled at nodes.

...

Additional arguments that will be passed to an internal function computeBAMMlikelihood.

Details

This function allows the user to check the likelihoods computed by BAMM using an independent R-based implementation. This is designed to provide a check on potential software bugs that might be introduced during future BAMM development and which might compromise the likelihood calculation. If you observe measurable discrepancies between the likelihood computed by this function and the corresponding likelihood returned by BAMM, please inform the BAMM development team.

Value

If return.intermediates == TRUE, then phylo objects are returned with the following components:

event_times

A list of length (number of nodes), where event_times[[k]] is the vector of absolute times, in order, of events that happened on a focal branch. If no event, it is NULL.

event_id

A list of length equal to number of nodes, as event_times, but holding the corresponding event id.

events

A dataframe giving parameters and associated nodes (and unique index values) of the event data.

node_event

The event governing the process realized at the node. This will be the first event encountered as one moves rootwards towards the tips from the focal node.

Author(s)

Dan Rabosky, Pascal Title

Examples

# a global sampling fraction of 0.98 was used in generating the whales
# dataset.
data(whales, events.whales, mcmc.whales)

x <- BAMMlikelihood(whales, events.whales, gen = 'last', sf = 0.98)

# Does the likelihood generated by BAMM match the R implementation?
identical(round(x, 3), mcmc.whales[nrow(mcmc.whales), 'logLik'])

# an example with a constant-rate birth-death process:
pars <- c(0.5, 0.45)
names(pars) <- c("lambda", "mu")
BAMMlikelihood(whales, pars, sf = 0.98)