log_likelihood: Log Likelihood of a fitted object

In PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

Log Likelihood of a fitted object

Description

log_likelihood computes the log likelihood of some parameters.

Usage

log_likelihood(x, ...)

## S3 method for class 'params_process'
log_likelihood(x, Y_data, phylo, ...)

## S3 method for class 'PhyloEM'
log_likelihood(x, ...)

Arguments

x	an object of class params_process or PhyloEM.
...	for a PhyloEM object, further arguments to be passed on to params_process.PhyloEM (to choose which parameters to extract from the results, see documentation of this function).
Y_data	matrix of data at the tips, size p x ntaxa. Each line is a trait, and each column is a tip. The column names are checked against the tip names of the tree.
phylo	a phylogenetic tree, class phylo. incidence.matrix.full. Can be specified to avoid extra computations.

Value

The log likelihood of the data with the provided parameters on the tree.

Methods (by class)

• params_process: params_process object

• PhyloEM: PhyloEM object

See Also

params_process, PhyloEM

PhylogeneticEM documentation built on Aug. 31, 2022, 9:16 a.m.