TREvoSim v3.0.0

This release is a new major version (v3.0.0) 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 and associated changes were introduced in the paper: Mongiardino Koch, N., Garwood, R.J. & Parry, L.A. 2021. Fossils improve phylogenetic analyses of morphological characters. Proceedings of the Royal Society B: 288(1950):20210044. doi: 10.1098/rspb.2021.0044 Version 3.0.0 and all new additions are described in detail in a paper in the Journal of Open Source Software, associated with this release: Garwood, R.J., Spencer, A.R.T., Bates, C.T.M., Callender-Crowe, L.M, Dunn, F.S., Halliday, T.J.D., Keating, J.N., Mongiardino Koch, N., Parry, L.A., Sansom, R.S., Smith, T.J., Sutton, M.D. & Vanteghem, T. 2024. TREvoSim v3: An individual based simulation for generating trees and character data. JOSS. The code is archived on zenodo.org: https://doi.org/10.5281/zenodo.13358420. Documentation: TREvoSim Online Documentation Change log: The changes in v3.0.0 are described and discussed fully in the associated paper. In brief, these include: New character options New default simulation parameters Ecosystem engineering functionality An expanding playing field mode New logging capabilities The option to match fitness peaks across environments A no selection mode Mixing of organisms between playing fields Perturbations (periods of accelerated environmental change) The ability to run the simulation for a user-defined number of iterations, as opposed to for set number of species Abstraction of the fitness algorithm from the genome via many-to-one mapping (stochastic layer) A test suite integrated into the software build Binaries The following binaries are available for download (installation instructions are present in the documentation): MacOS TREvoSim_v3.0.0_Installer_MacOS.dmg image containing the TREvoSim and TREvoSimTest applications and a drag n' drop installer. Windows x64-bit TREvoSim_v3.0.0_Installer_Winx64.exe containing the TREvoSim and TREvoSimTest applications.