plot_batch_profile_lik: Plot Batch Profile Likelihoods
In thej022214/corHMM: Hidden Markov Models of Character Evolution

plot_batch_profile_lik

R Documentation

Plot Batch Profile Likelihoods

Description

Plots profile likelihoods for each parameter in a batch from the output of a profile corHMM object, displaying the log-likelihoods across parameter values and indicating the maximum likelihood estimate (MLE) and the 95% confidence interval.

Usage

plot_batch_profile_lik( corhmm_profile, 
                        n_cols = NULL,
                        n_rows = NULL, 
                        mar = c(5, 4, 4, 1) + 0.1,
                        ci_level = 1.96, 
                        polygon_col = "lightgrey", 
                        line_col = "black", 
                        line_type = "l", 
                        mle_col = "blue", 
                        ci_line_col = "black", 
                        ci_line_type = "dashed", 
                        axis_tick_length = -0.2, 
                        label_cex = 0.7,
                        ylim=NULL)

Arguments

`corhmm_profile`	a list containing profile likelihood tables for each parameter and the corHMM object with MLE and loglik attributes.
`n_cols`	optional; number of columns for the plotting layout. If NULL, automatically calculated based on the number of parameters.
`n_rows`	optional; number of rows for the plotting layout. If NULL, automatically calculated based on the number of parameters.
`mar`	margins around the plot. Defaults to c(5, 4, 4, 1) + 0.1.
`ci_level`	z-value for the 95% confidence interval. Defaults to 1.96.
`polygon_col`	color of the polygon under the curve. Defaults to "lightgrey".
`line_col`	color of the profile likelihood curve. Defaults to "black".
`line_type`	type of the profile likelihood curve. Defaults to "l".
`mle_col`	color of the MLE point. Defaults to "blue".
`ci_line_col`	color of the 95% CI line. Defaults to "black".
`ci_line_type`	line type for the 95% CI line. Defaults to "dashed".
`axis_tick_length`	length of the axis ticks, with negative values indicating ticks pointing inwards. Defaults to -0.2.
`label_cex`	character expansion size for labels, affecting the size of text labels. Defaults to 0.7.

Details

This function generates a series of plots for the profile likelihood of each parameter in the input corHMM model object. It visualizes the log-likelihood across the range of parameter values, highlights the maximum likelihood estimate (MLE), and denotes the 95% confidence interval with a horizontal dashed line. The function is designed to accommodate the batch analysis of multiple parameters, organizing the plots in a specified layout and allowing for extensive customization of plot aesthetics.

Value

Generates and displays a grid of profile likelihood plots, one for each parameter in the input model, with visual cues for MLE and confidence intervals.