palaeoware/trevosim: TREvoSim v2.0.0

This is the release of a new version (v2.0.0) of TREvoSim. The first release and the underlying model was described in detail in the following paper:

Keating, J.N., Sansom, R.S., Sutton, M.D., Knight, C.G. & Garwood, R.J. 2020. Morphological phylogenetics evaluated using novel evolutionary simulations. Systematic Biology 69(5): 897-912. doi:10.1093/sysbio/syaa012

Version 2.0.0 accompanies the preprint and paper below:

Mongiardino Koch, N., Garwood, R.J. & Parry, L.A. Preprint. Fossils improve phylogenetic analyses of morphological characters. bioRxiv. doi: 10.1101/2020.12.03.410068v1 Mongiardino Koch, N., Garwood, R.J. & Parry, L.A. 2021. Fossils improve phylogenetic analyses of morphological characters. Proceedings of the Royal Society B: Biological Sciences

The code is archived on zenodo.org:

Documentation:

• TREvoSim Online Documentation

Change log:

The changes in v2.0.0 are described and discussed fully in the associated paper. In brief, these allow TREvoSim v2.0.0 trees and data to achieve benchmarks calculated from twelve total evidence analyses, as well as respresenting ongoing development of the package. Changes are:

• Addition of multiple playing fields option. Playing fields can have independent or identical environments.
• The option to overwrite a random individual when a juveniles is returned to the playing field (instead of the least fit one).
• User control of the fitness target in the fitness algorithm (see Keating et al. 2020).
• A fitness histogram functionality to assess the fitness landscape in the simulation.
• User control of the strength of selection (see Mongiardino Koch et al. 2021 for discussion).
• Multiple environments per playing field. Organism fitness is assessed against each environment, and the fitness of an organism is defined by the environment they are best suited to.
• The code has been refactored (the biggest change being to the underlying data structures/classes), and the simulation now uses Qt QRandomGenerator tools rather than incorporating random data.
• A user-accessible test suite has been added.

Release information: Windows

A zip containing all required binaries can be downloaded from the assets below. Alternatively an installer is provided. See notes below:

Note 1: The .zip archive contains an executable TREvoSim_2.0.0.exe. The .zip can be extracted and the program run by double clicking this.exe file in the ./bin folder. All the required libraries have been included and are found in the ./bin folder.

Mac

A zip containing TREovSim can be downloaded from the assets below. To install the software, drag and drop the required .app folder(s) into the Applications folder. You may be required to the approve the software in security and privacy settings before it will launch.

Linux

Any Linux users willing to test a Linux build should contact palaeoware@gmail.com.