Linking pattern to process using phylogenies—insights from a comparison of eight simulation models

Allen H. Hurlbert*, Juliano Sarmento Cabral, Rampal S. Etienne, Oskar Hagen, Shan Huang, Yun-Ting Jang, Thijs Janzen, Antonin Machac, Pedro Santos Neves, Mikael Pontarp, David Storch, Liang Xu, Florian Hartig*

*Equally contributing lead authors

This repository contains code underlying the comparison of 8 eco-evolutionary simulation models and the evaluation of links between eco-evolutionary processes and phylogenetic patterns.

Organization

Folders

trees
--uniform_sampling_experiment: all simulated phylogenetic trees used in the study, with file names in the form mm_xxxxx.tre where mm is the simulation model abbreviation, and xxxx is a unique simulation ID.
--empirical: 16 empirical trees for 8 pairs of sister clades (4 pairs of mammals and 4 pairs of birds)

derived_tree_data
--simulation_parameter_keys.csv: key to the parameters used across the 8 different models, specifying which process the parameter was related to, its name, its description, and the direction (sign) of its relation to the stated process
--USE_treeStats.txt: 70+ tree metrics calculated from the treestats R package for all simulated trees
--process_parameter_values_and_tree_metrics_sign_corrected.csv: all simulated trees, their parameter settings grouped by relevant process and sign-corrected as necessary to standardize the direction of effect, and their 70+ tree metrics
--empiricalSisterClades_treeStats.txt: 70+ tree metrics calculated from the treestats R package for each empirical tree
--scaled_predictions_empirical_trees.csv: for each combination of empirical tree, simulation model, and eco-evolutionary process, the inferred parameter value (value) related to that process based on a random forest trained on trees simulated by that model, as well as the value rescaled to vary between 0 and 1 (scaledValue) based on the minimum and maximum parameter values actually used across all simulations.

code
--analysis_functions.r: functions used for calculating tree stats and for aligning parameters with processes.

figures
--manuscript figures

Analysis workflow

Analysis.qmd: Complete analysis workflow given the USE_treeStats.txt and empiricalSisterClades_treeStats.txt output