{"id":34656492,"url":"https://github.com/andim/transitions-paper","last_synced_at":"2026-05-26T22:03:26.553Z","repository":{"id":72334724,"uuid":"86507183","full_name":"andim/transitions-paper","owner":"andim","description":"Source code accompanying the paper \"Transitions in optimal adaptive strategies for populations in fluctuating environments\"","archived":false,"fork":false,"pushed_at":"2017-08-18T22:58:03.000Z","size":1748,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-12-26T06:54:36.784Z","etag":null,"topics":["biophysics","openscience"],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/andim.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2017-03-28T21:04:32.000Z","updated_at":"2019-05-17T21:36:21.000Z","dependencies_parsed_at":null,"dependency_job_id":"3e2b2809-15d5-445a-a497-6cfe20249b74","html_url":"https://github.com/andim/transitions-paper","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/andim/transitions-paper","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andim%2Ftransitions-paper","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andim%2Ftransitions-paper/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andim%2Ftransitions-paper/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andim%2Ftransitions-paper/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/andim","download_url":"https://codeload.github.com/andim/transitions-paper/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andim%2Ftransitions-paper/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33540617,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"ssl_error","status_checked_at":"2026-05-26T15:22:15.568Z","response_time":63,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["biophysics","openscience"],"created_at":"2025-12-24T18:04:26.731Z","updated_at":"2026-05-26T22:03:26.506Z","avatar_url":"https://github.com/andim.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Transitions in optimal adaptive strategies for populations in fluctuating environments\n\nThis repository contains the source code associated with the manuscript\n\nMayer, Mora, Rivoire, Walczak : [Transitions in optimal adaptive strategies for populations in fluctuating environments](), Arxiv 2017\n\nIt allows reproduction of all numerical results reported in the manuscript.\n\n[![DOI](https://zenodo.org/badge/86507183.svg)](https://zenodo.org/badge/latestdoi/86507183)\n\n## Installation requirements\n\nThe code uses Python 2.7+.\n\nA number of standard scientific python packages are needed for the numerical simulations and visualizations. An easy way to install all of these is to install a Python distribution such as [Anaconda](https://www.continuum.io/downloads). The file `environment.yml` contains a list of the relevant packages in a format understood by Anaconda.\n\n- [numpy](http://github.com/numpy/numpy/)\n- [scipy](https://github.com/scipy/scipy)\n- [pandas](http://github.com/pydata/pandas)\n- [matplotlib](http://github.com/matplotlib/matplotlib)\n\nAdditionally the code also relies on these packages:\n\n- [scipydirect](http://github.com/andim/scipydirect/)\n- [noisyopt](http://github.com/andim/noisyopt)\n- [palettable](http://github.com/jiffyclub/palettable)\n\nAnd optionally for nicer progress output install:\n\n- [pyprind](http://github.com/rasbt/pyprind)\n\n## Running the code\n\nThe time stepping of the population dynamics is accelerated by a Cython module, which needs to be compiled first. To compile it run `make cython` in the `lib` directory. In the directories for the figures about the results in correlated environments launch `make run` followed by `make agg` to produce the underlying data. We provide both Jupyter notebooks with additional explanatory comments and plain python files for generating the figures.\n\nNote: As the simulations are stochastic you will not get precisely equivalent plots.\n\n## Contact\n\nIf you run into any difficulties running the code, feel free to contact us at `andimscience@gmail.com`.\n\n## License\n\nThe source code is freely available under an MIT license. The plots are licensed under a Creative commons attributions license (CC-BY).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandim%2Ftransitions-paper","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fandim%2Ftransitions-paper","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandim%2Ftransitions-paper/lists"}