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REvoSim and EnviroGen v3.0.0
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@RussellGarwood RussellGarwood released this 05 Mar 13:52
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v3.0.0
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This is the public release of a new version of the REvoSim software with major updates, alongside minor improvements to the EnviroGen utility package. 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 v3.0.0: A fast evolutionary simulation tool with ecological processes. JOSS. Submitted.

The code is archived on zenodo.org: DOI

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:

Change log:

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

REvoSim

  • Systems. REvoSim processes (e.g. fitness, mutation, breeding, species ID) have been placed into structures called systems, which can be applied to user-defined portions of organism genomes.
  • New genome architecture. Organisms now comprise a configurable number of 32-bit genome “words”- organisms, and different word combinations can be utilised by REvoSim’s different systems.
  • Pathogens. There is now a mechanism by which pathogens can be applied, killing individuals within the simulation. These can either drift, or evolve towards virulence.
  • Masks for variables. A mechanism by which images can be used to spatially control the variables within a simulation has been added.
  • Ecology added. Inter-organism interactions are now possible within the software. These are achieved through two mechanisms, and can alter organism fitness, or result in the transfer of energy between individuals.
  • Additional seeding options. Associated with ecology, simulations can now be seeded with three or five species, known to form a food-chain in some interactions settings, and a trophic level is calculated for individuals.
  • Logging. The software logging system has been rewritten for increased versatility - for the running log the software now allows a user to define a header, grid-level statistics, species level statistics which are output at polling iterations.
  • Species ID. The species identification algorithm has been recoded to improve performance.
  • Breeding. Organism breeding modes now include obligate as well as facultative sexual reproduction, asexual reproduction, and variable. In the latter a portion of the organism genome defines the probability of breeding sexually v.s asexually, allowing the level of recombination to evolve.
  • Mutation. Similar to the variable breeding option, there is now a variable mutation mode in which mutation rate is under control of the genome and so can evolve.
  • Random numbers. The random number system has been updated to employ the QRandomGenerator Class.
  • Command line. REvoSim can now be launched from the command line, all options can be modified at launch, and runs initiated.
  • Tests. Software tests have been added, and can outputs can be inspected by the user.

EnviroGen

  • Random numbers. The random number system has been updated to employ the QRandomGenerator Class.
  • Fixed numerous bugs.

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.

Assets 5