plot_logLik: Plot Log-Likelihood function of the model

In USCbiostats/phylogenetic: Statistical Inference and Prediction of Annotations in Phylogenetic Trees

Plot Log-Likelihood function of the model

Description

Plot Log-Likelihood function of the model

Usage

plot_logLik(x, sets, ...)

## S3 method for class 'aphylo'
plot_logLik(x, sets, ...)

## S3 method for class 'formula'
plot_logLik(x, sets, ...)

## S3 method for class 'aphylo_estimates'
plot_logLik(x, sets, ...)

Arguments

x	An object of class aphylo()
sets	(optional) Character matrix of size ⁠2 x # of combinations⁠. contains the names of the pairs to plot. If nothing passed, the function will generate all possible combinations as combn(names(params), 2).
...	Aditional parameters to be passed to plotfun.

Value

NULL (invisible). Generates a plot of the loglikelihood of the model.

Examples

# Loading data
data(fakeexperiment)
data(faketree)
O <- new_aphylo(fakeexperiment[,2:3], tree = as.phylo(faketree))

# Baseline plot (all parameters but Pi)
plot_logLik(O)

# No psi parameter
plot_logLik(O ~ mu_d + Pi + eta)

USCbiostats/phylogenetic documentation built on Oct. 28, 2023, 7:23 a.m.