plot_batch_profile_lik: Plot Batch Profile Likelihoods

In thej022214/corHMM: Hidden Markov Models of Character Evolution

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, 
  xlab="Parameter Value", 
  ...)

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.
ylim	a user-specified upper and lower limit to the y-axis.
xlab	user-specified x label
...	Additional arugments to be passed to plot.

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.

Author(s)

James D. Boyko

thej022214/corHMM documentation built on April 13, 2025, 9:37 a.m.