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4-fit_BD_truncated_PBD_trees

README.md

Fit BD Model to Truncated PBD-Simulated Trees with Trimmed Terminal Branches

Overview

This pipeline fits a Birth-Death (BD) model to truncated phylogenies based on trees simulated with the Protracted Birth-Death (PBD) model. The scripts are designed to run multiple replicates and combinations of parameters, primarily intended to be executed on a computing cluster.

Files

  • 1-fit_truncated_PBD_trees.Rmd: R Markdown file to fit a BD model adapted to truncated phylogenies on PBD-simulated trees.
  • 1-fit_truncated_PBD_trees.R: Script version of the .Rmd file.
  • 1-fit_truncated_PBD_trees.nb.html: HTML report generated from the 1-fit_truncated_PBD_trees.Rmd file.
  • 1-submission.sub: Job submission script for running the fitting process on a cluster.
  • 2-combine_CSVs.R: Script to combine the output CSV files (stored in "simulations_output/4-Truncated_PBD") from multiple replicates into a single CSV file for further analysis.
  • 3-plot_comparison.R: Script to generate comparison plots from the combined CSV data. These plots are used to visualize and compare the results of the model fitting process.

Usage

Fitting the BD Model

To fit the BD model to truncated PBD-simulated trees, run the following script on your local machine:

Rscript 1-fit_truncated_PBD_trees.R [parameter_row]

The parameter_row argument corresponds to the row in the parameter file "simulations_output/1-PBD/all_simulations_inference.csv".

Combining CSV Files

After running multiple replicates, combine the output CSV files into a single file using:

Rscript 2-combine_CSVs.R

The result will be stored as "simulations_output/4-Truncated_PBD/combined_long_df.csv".

Generating Comparison Plots

To generate comparison plots from the combined CSV data, run:

Rscript 3-plot_comparison.R

The resulting figures will be stored as "fig/SM_truncation_lambda.pdf" and "fig/SM_truncation_mu.pdf".