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Introduction

This repository contains the code that describes most analyses presented in:

Fine PVA, Zapata F , and Daly DC. (2014) Investigating processes of Neotropical rain forest tree diversification by examining the evolution and historical biogeography of the Protieae (Burseraceae). Evolution 68: 1988-2004. doi:10.1111/evo.12414.

Dependencies

These scripts require R and several libraries. See code in scripts for details.

Running the analyses

The analyses are broken into a series of scripts. Some scripts run analyses, others regenerate figures. See scripts for details.

Is this a fully executable paper?

This manuscript is partially executable. The code explicitly describes how several analysis steps were completed but is not entirely sufficient on its own to re-execute the whole paper. There are several reasons for this:

  • Figure 1 was prepared manually.

  • The code provided here includes paths to already processed files, including phylogenetic trees and data files.

Data

The data/ directory contains all the none phylogenetic data and pre-processed files for analyses. The phylogenetic_data directory contains all the tree and samples of trees necessary to run the analyses.