log_transform_parameters: Log Transform Parameter Samples

In topolow: Force-Directed Euclidean Embedding of Dissimilarity Data

Log Transform Parameter Samples

Description

Reads parameter samples from a CSV file and applies a log transformation to specified parameter columns (e.g., N, k0, cooling_rate, c_repulsion).

Note: As of version 2.0.0, this function is primarily for backward compatibility with existing parameter files. The initial_parameter_optimization() function now returns log-transformed parameters directly, eliminating the need for this separate transformation step in the normal workflow.

Usage

log_transform_parameters(samples_file, output_file = NULL)

Arguments

samples_file	Character. Path to the CSV file containing the parameter samples.
output_file	Character. Optional path to save the transformed data as a new CSV file.

Details

This function is maintained for users who have existing parameter files from older versions of the package or who need to work with parameter files that contain original-scale parameters. In the current workflow:

• initial_parameter_optimization() –> returns log-transformed parameters directly

• run_adaptive_sampling() –> works with log-transformed parameters

• euclidean_embedding() –> works with original-scale parameters

If you are working with the current workflow (using Euclidify() or calling initial_parameter_optimization() directly), you typically do not need to call this function.

Value

A data.frame with the log-transformed parameters. If output_file is specified, the data frame is also written to a file and returned invisibly.

Note

Backward Compatibility Note: This function is maintained for compatibility with existing workflows and parameter files. For new workflows, consider using initial_parameter_optimization() which returns log-transformed parameters directly.

Examples

# This example uses a sample file included with the package.
sample_file <- system.file("extdata", "sample_params.csv", package = "topolow")

# Ensure the file exists before running the example
if (nzchar(sample_file)) {
  # Transform the data from the sample file and return as a data frame
  transformed_data <- log_transform_parameters(sample_file, output_file = NULL)

  # Display the first few rows of the transformed data
  print(head(transformed_data))
}

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