{"id":34603957,"url":"https://github.com/yoavram/milpitas","last_synced_at":"2026-05-26T12:32:50.984Z","repository":{"id":149271670,"uuid":"73962912","full_name":"yoavram/Milpitas","owner":"yoavram","description":"Ram, Liberman \u0026 Feldman (2018) Vertical and Oblique Transmission under Fluctuating Selection, PNAS","archived":false,"fork":false,"pushed_at":"2018-02-17T07:52:56.000Z","size":49578,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-12-26T01:46:22.507Z","etag":null,"topics":["cultural-evolution","evolution","evolution-simulation","non-vertical-transmission","population-genetics"],"latest_commit_sha":null,"homepage":"https://doi.org/10.1073/pnas.1719171115","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/yoavram.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":"2016-11-16T21:30:39.000Z","updated_at":"2019-07-31T09:27:38.000Z","dependencies_parsed_at":"2023-09-03T10:18:59.719Z","dependency_job_id":null,"html_url":"https://github.com/yoavram/Milpitas","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/yoavram/Milpitas","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/yoavram%2FMilpitas","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/yoavram%2FMilpitas/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/yoavram%2FMilpitas/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/yoavram%2FMilpitas/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/yoavram","download_url":"https://codeload.github.com/yoavram/Milpitas/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/yoavram%2FMilpitas/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33520609,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T03:12:49.672Z","status":"ssl_error","status_checked_at":"2026-05-26T03:12:47.976Z","response_time":63,"last_error":"SSL_read: 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":["cultural-evolution","evolution","evolution-simulation","non-vertical-transmission","population-genetics"],"created_at":"2025-12-24T13:04:06.313Z","updated_at":"2026-05-26T12:32:50.978Z","avatar_url":"https://github.com/yoavram.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Vertical and Oblique Transmission under Fluctuating Selection\n## Yoav Ram, Uri Liberman, and Marcus W. Feldman, PNAS 2018\n\nThis repository contains supporting material for\n\n\u003e   Ram, Liberman \u0026 Feldman (2018) _Vertical and Oblique Transmission under Fluctuating Selection_, Proc Natl Acad Sci USA. DOI: [10.1073/pnas.1719171115](https://doi.org/10.1073/pnas.1719171115)\n\nThe notebook file [`figures.ipynb`](https://github.com/yoavram/Milpitas/blob/master/notebooks/figures.ipynb) includes Python source code for reproduction of the manuscript figures.\n\n## Run the notebook\n\nYou can interact with the notebooks on your own machine.\n\n### Install dependencies\n\nThe easiest way to install the dependencies is to install [Anaconda](https://www.anaconda.com/download/).\nYou should use Python 3, preferably with version 3.5 or higher.\nThe notebook will probably not work on Python 2.\n\nAll required packages should then be available.\nHowever, if you get an `ImportError` due to a package not being installed, the following command will install all requirements using conda:\n\n```sh\nconda install jupyter numpy scipy matplotlib pandas seaborn sympy numba \n```\n\nYou also need to install [rakott](https://github.com/yoavram/rakott) and [matplotlib_colorbar](https://github.com/ppinard/matplotlib-colorbar):\n```sh\npip install https://github.com/yoavram/rakott.git\npip install matplotlib_colorbar\n```\n\n### Get the source code repository\n\nYou can download all the source code by clicking the _Clone or Download_ button and choosing _Download ZIP_. Then extract the ZIP to a folder on your machine.\n\nIf you use `git` you can clone the repo using:\n\n```sh\ngit clone https://github.com/yoavram/Milpitas.git\n```\n\n### Run the notebook\n\nStart a Jupyter notebook server inside the repo folder:\n\n```sh\ncd \u003cpath to folder\u003e\njupyter notebook\n```\n\nYour browser should open automatically. \nOpen the `notebooks` folder and choose the notebook file `figures.ipynb` file.\n\n## Troubleshooting\n\nUse the [Issues](https://github.com/yoavram/Milpitas/issues) page to report problems or suggest improvements or contact [Yoav Ram](mailto:yoav@yoavram.com).\n\nLicense\n-------\n\nThis work is licensed under a Creative Commons Attribution-ShareAlike 4.0\nInternational License.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fyoavram%2Fmilpitas","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fyoavram%2Fmilpitas","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fyoavram%2Fmilpitas/lists"}