diff --git a/joss.06703/10.21105.joss.06703.crossref.xml b/joss.06703/10.21105.joss.06703.crossref.xml new file mode 100644 index 0000000000..673698c2f4 --- /dev/null +++ b/joss.06703/10.21105.joss.06703.crossref.xml @@ -0,0 +1,150 @@ + + + + 20241120202150-b2e24e02822bf2987dbab14f62121c610d6fc240 + 20241120202150 + + JOSS Admin + admin@theoj.org + + The Open Journal + + + + + Journal of Open Source Software + JOSS + 2475-9066 + + 10.21105/joss + https://joss.theoj.org + + + + + 11 + 2024 + + + 9 + + 103 + + + + Evoke: A Python package for evolutionary signalling +games + + + + Stephen Francis + Mann + + LOGOS Research Group, Universitat de Barcelona, Spain + Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany + + https://orcid.org/0000-0002-4136-8595 + + + Manolo + Martínez + + LOGOS Research Group, Universitat de Barcelona, Spain + + https://orcid.org/0000-0002-6194-7121 + + + + 11 + 20 + 2024 + + + 6703 + + + 10.21105/joss.06703 + + + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + + + + Software archive + 10.5281/zenodo.14185732 + + + GitHub review issue + https://github.com/openjournals/joss-reviews/issues/6703 + + + + 10.21105/joss.06703 + https://joss.theoj.org/papers/10.21105/joss.06703 + + + https://joss.theoj.org/papers/10.21105/joss.06703.pdf + + + + + + Communication and common +interest + Godfrey-Smith + PLOS Computational Biology + 11 + 9 + 10.1371/journal.pcbi.1003282 + 1553-7358 + 2013 + Godfrey-Smith, P., & Martínez, M. +(2013). Communication and common interest. PLOS Computational Biology, +9(11), e1003282. +https://doi.org/10.1371/journal.pcbi.1003282 + + + Signals: Evolution, learning, and +information + Skyrms + 10.1093/acprof:oso/9780199580828.001.0001 + 978-0-19-958082-8 + 2010 + Skyrms, B. (2010). Signals: +Evolution, learning, and information. Oxford University Press. +https://doi.org/10.1093/acprof:oso/9780199580828.001.0001 + + + EGTTools: Toolbox for evolutionary game +theory + Fernández Domingos + GitHub repository + 10.5281/zenodo.3687125 + 2020 + Fernández Domingos, E. (2020). +EGTTools: Toolbox for evolutionary game theory. In GitHub repository. +https://github.com/Socrats/EGTTools; GitHub. +https://doi.org/10.5281/zenodo.3687125 + + + Nashpy: 0.0.41 + Nashpy project developers + 10.5281/zenodo.10802174 + 2024 + Nashpy project developers. (2024). +Nashpy: 0.0.41. +https://doi.org/10.5281/zenodo.10802174 + + + + + + diff --git a/joss.06703/10.21105.joss.06703.pdf b/joss.06703/10.21105.joss.06703.pdf new file mode 100644 index 0000000000..047e1e0198 Binary files /dev/null and b/joss.06703/10.21105.joss.06703.pdf differ diff --git a/joss.06703/paper.jats/10.21105.joss.06703.jats b/joss.06703/paper.jats/10.21105.joss.06703.jats new file mode 100644 index 0000000000..5580b9730e --- /dev/null +++ b/joss.06703/paper.jats/10.21105.joss.06703.jats @@ -0,0 +1,221 @@ + + +
+ + + + +Journal of Open Source Software +JOSS + +2475-9066 + +Open Journals + + + +6703 +10.21105/joss.06703 + +Evoke: A Python package for evolutionary signalling +games + + + +https://orcid.org/0000-0002-4136-8595 + +Mann +Stephen Francis + + + + + +https://orcid.org/0000-0002-6194-7121 + +Martínez +Manolo + + +* + + + +LOGOS Research Group, Universitat de Barcelona, +Spain + + + + +Max Planck Institute for Evolutionary Anthropology, +Leipzig, Germany + + + + +* E-mail: + + +12 +8 +2024 + +9 +103 +6703 + +Authors of papers retain copyright and release the +work under a Creative Commons Attribution 4.0 International License (CC +BY 4.0) +2024 +The article authors + +Authors of papers retain copyright and release the work under +a Creative Commons Attribution 4.0 International License (CC BY +4.0) + + + +Python +evolutionary game theory +signalling games +sender-receiver framework +evolutionary simulations + + + + + + Summary +

Evoke is a Python library for evolutionary simulations + of signalling games. It offers a simple and intuitive API that can be + used to analyze arbitrary game-theoretic models, and to easily + reproduce and customize well-known results and figures from the + literature.

+

A signalling game is a special kind of mathematical game, a formal + representation of interactions between agents. In a signalling game, + the actions available to the players include sending and responding to + signals. The agents in games traditionally studied in game theory + develop strategies via such dynamics as reinforcement learning. In + contrast, evolutionary game theory investigates how strategies change + over time in populations undergoing evolutionary change such as + natural selection. Signalling games can be studied in the traditional + reinforcement-learning paradigm or in the evolutionary paradigm. Evoke + offers methods for both kinds of game dynamic. Users are able to + create signalling games and simulate the evolution of agents’ + strategies over time, using a range of game types and evolutionary and + learning dynamics.

+

Evoke also allows the user to recreate and customize figures from + the signalling game literature. Examples provided with Evoke include + figures from Skyrms + (2010) + and Godfrey-Smith & Martínez + (2013). + Users can contribute to the library by adding further examples from + the literature. This can be a useful way to become familiar with + Evoke, while at the same time increasing the benefit to other users. + Evoke can therefore serve as an educational tool (encouraging + understanding of existing literature) and a research resource + (promoting good practice and effective modelling techniques).

+
+ + Statement of need +

While there are Python packages devoted to game theory, such as + Nashpy + (Nashpy + project developers, 2024), and evolutionary game theory, such + as EGTtools + (Fernández + Domingos, 2020), to our knowledge there has not yet been a + Python package dedicated to the study of signalling games in the + context of both evolution and reinforcement learning. That is the gap + Evoke is intended to fill.

+

In the evolutionary game theory literature, models and results are + often developed with proprietary code. Evaluating and re-running + models can be difficult for readers, because custom-made software is + often not developed with other users in mind. Sometimes the model code + is not available at all.

+

It would be preferable to have a common framework that different + users can share. When new results are presented in a research article, + readers of that article could run the model and check the results for + themselves. Readers could also vary the parameters to obtain results + that were not reported in the original article, lending an air of + interactivity to published papers.

+

Built-in examples already shipped with Evoke include figures from + Skyrms + (2010). + These examples allow the user to change some of the input parameters + to Skyrms’s figures to see how different parameter values yield + different results. In a small way, this makes the book “interactive”: + in addition to the static figures on the page, the user can play with + the models in order to get a sense of the range of outcomes each model + can generate.

+
+ + Acknowledgements +

Many thanks to the reviewers and editors for their comments. This + work was supported by Juan de la Cierva grant FJC2020-044240-I and + María de Maeztu grant CEX2021-001169-M funded by + MICIU/AEI/10.13039/501100011033.

+
+ + + + + + + + Godfrey-SmithPeter + MartínezManolo + + Communication and common interest + PLOS Computational Biology + 2013 + 9 + 11 + 1553-7358 + 10.1371/journal.pcbi.1003282 + e1003282 + + + + + + + SkyrmsBrian + + Signals: Evolution, learning, and information + Oxford University Press + Oxford + 2010 + 978-0-19-958082-8 + 10.1093/acprof:oso/9780199580828.001.0001 + + + + + + Fernández DomingosElias + + EGTTools: Toolbox for evolutionary game theory + GitHub repository + https://github.com/Socrats/EGTTools; GitHub + 2020 + 10.5281/zenodo.3687125 + + + + + + Nashpy project developers + + Nashpy: 0.0.41 + 2024 + http://dx.doi.org/10.5281/zenodo.10802174 + 10.5281/zenodo.10802174 + + + + +