treats: a modular R package for simulating trees and traits

Abstract

Simulating biological realistic data is an important step to understand and investigate biodiversity. Simulated data can be used to generate null, base line or neutral models. These can be used either in comparison to observed data to estimate the mechanisms that generated the data. Or they can be used to explore, understand and develop theoretical advances by proposing toy models. In evolutionary biology, simulations often involve the need of an evolutionary process where descent with modification is at the core of how the simulated data are generated. These evolutionary processes can then be nearly infinitely modified to include complex processes that affect the simulations such as traits co-evolution, competition mechanisms or mass extinction events. Here I present the treats package, a modular R package for trees and traits simulations. This package is based on a simple birth death algorithm from which all steps can easily be modified by users. treats also provides a tidy interface through the treats object, allowing users to easily run reproducible simulations. It also comes with an extend manual regularly updated following users' questions or suggestions