REvoSim v3: A fast evolutionary simulation tool with ecological processes

This is a patch release for the REvoSim software implementing changes from the review of v3.0.0 for The Journal of Open Source Software, and a few other minor improvements. The model, and initial release was been described in detail in the following paper:

Garwood, R.J., Spencer A.R.T. and Sutton, M.D., 2019. REvoSim: Organism-level simulation of macro- and microevolution. Palaeontology 62(3),339-355. https://doi.org/10.1111/pala.12420

Additions in this release are described in the following paper:

Furness, E.N., Garwood, R.J. and Sutton, M.D., 2023. REvoSim v3: A fast evolutionary simulation tool with ecological processes. JOSS. Accepted.

The code is archived on zenodo.org:

Other relevant references: Furness E.N., Garwood R.J., Mannion P.D. & Sutton M.D. 2021. Evolutionary simulations clarify and reconcile biodiversity-disturbance models. Proceedings of the Royal Society B 288(1949):20210240. https://doi.org/10.1098/rspb.2021.0240 Furness, E.N., Garwood, R.J., Mannion, P. D. & Sutton, M.D. 2021. Productivity, niche availability, species richness and extinction risk: Untangling relationships using individual-based simulations. Ecology and Evolution 11(13): 8923-8940. https://doi.org/10.1002/ece3.7730

Documentation:

• REvoSim Online Documentation
• EnviroGen Online Documentation

Change log:

The following has been changed since the last release. All additions are fully outlined in the documentation.

REvoSim

• Updates to README files providing more details for building on both Windows and Linux
• Masks are now reset between runs on batch mode, and through button reset
• Pathogens are now reset between runs on batch mode, and through button reset
• Further details on time, species concepts, and exemplar usage have been added to the documentation
• More communication to the user has been added on save settings
• The log text has been added to the saved settings xml files
• New logging options for breed success, generation time, and species range have been added
• The above, and several other options have been added to the command line
• Splash image has been removed when running from commnad line

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 all REvoSim programs (REvoSim and EnviroGen). The .zip can be extracted and the programs run by double clicking the .exe files. All the required libraries have been included.

Note 2: The windows installer will not overwrite any pre-existing REvoSim installations.

Mac

A zip containing the REvoSim programs (REvoSim and EnviroGen) as DMGs can be downloaded from the assets below. The software can be run by double clicking on either. To install the software, drag and drop the required DMGs into the Applications folder. In both these cases you may be required to the approve the software in security and privacy settings before it will launch.

Note 1: Builds are x86-64, and so the software will not run at optimal speed on the new apple silicon Macs (tests suggest the speed is acceptable, however).

Linux

Any Linux users requiring a Linux build should contact palaeoware@gmail.com.