plot.profile_likelihood: Plot Method for profile_likelihood Objects

In topolow: Force-Directed Euclidean Embedding of Dissimilarity Data

Plot Method for profile_likelihood Objects

Description

Creates a visualization of the profile likelihood for a parameter, showing the maximum likelihood estimates and the 95% confidence interval. It supports mathematical notation for parameter names for clearer plot labels.

Usage

## S3 method for class 'profile_likelihood'
plot(x, LL_max, width = 3.5, height = 3.5, save_plot = FALSE, output_dir, ...)

Arguments

x	A profile_likelihood object returned by profile_likelihood().
LL_max	The global maximum log-likelihood value from the entire sample set, used as the reference for calculating the confidence interval.
width, height	Numeric. The width and height of the output plot in inches.
save_plot	Logical. If TRUE, the plot is saved to a file.
output_dir	Character. The directory where the plot will be saved. Required if save_plot is TRUE.
...	Additional arguments passed to the plot function.

Details

The 95% confidence interval is determined using the likelihood ratio test, where the cutoff is based on the chi-squared distribution: LR(\theta_{ij}) = -2[log L_{max}(\theta_{ij}) - log L_{max}(\hat{\theta})]. The interval includes all parameter values \theta_{ij} for which LR(\theta_{ij}) \leq \chi^2_{1,0.05} \approx 3.84.

Value

A ggplot object representing the profile likelihood plot.

Examples

# This example can take more than 5 seconds to run.
# Create a sample data frame of MCMC samples
samples <- data.frame(
  log_N = log(runif(50, 2, 10)),
  log_k0 = log(runif(50, 1, 5)),
  log_cooling_rate = log(runif(50, 0.01, 0.1)),
  log_c_repulsion = log(runif(50, 0.1, 1)),
  NLL = runif(50, 20, 100)
)

# Calculate profile likelihood for the "log_N" parameter
pl_result <- profile_likelihood("log_N", samples, grid_size = 10)

# Provide the global maximum log-likelihood from the samples
LL_max <- max(-samples$NLL)

# The plot function requires the ggplot2 package
if (requireNamespace("ggplot2", quietly = TRUE)) {
  plot(pl_result, LL_max, width = 4, height = 3)
}

topolow documentation built on Aug. 31, 2025, 1:07 a.m.