{"id":25943795,"url":"https://github.com/emilydolson/evo_in_space","last_synced_at":"2026-01-28T15:32:24.496Z","repository":{"id":70781613,"uuid":"75765412","full_name":"emilydolson/evo_in_space","owner":"emilydolson","description":"Figures, scripts and data for paper \"Spatial resource heterogeneity creates local hotspots of evolutionary potential\"","archived":false,"fork":false,"pushed_at":"2018-02-25T06:34:14.000Z","size":12042,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-06-04T05:49:58.067Z","etag":null,"topics":["avida","biodiversity","evolution","evolutionary-computation","spatial-data-analysis"],"latest_commit_sha":null,"homepage":"","language":"TeX","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/emilydolson.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2016-12-06T19:46:54.000Z","updated_at":"2023-03-29T03:12:34.000Z","dependencies_parsed_at":"2023-04-22T01:48:23.342Z","dependency_job_id":null,"html_url":"https://github.com/emilydolson/evo_in_space","commit_stats":{"total_commits":93,"total_committers":4,"mean_commits":23.25,"dds":0.3655913978494624,"last_synced_commit":"419b34af6d54775c39863b8d171ac63ea9ed0594"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/emilydolson/evo_in_space","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/emilydolson%2Fevo_in_space","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/emilydolson%2Fevo_in_space/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/emilydolson%2Fevo_in_space/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/emilydolson%2Fevo_in_space/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/emilydolson","download_url":"https://codeload.github.com/emilydolson/evo_in_space/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/emilydolson%2Fevo_in_space/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28846342,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-28T15:15:36.453Z","status":"ssl_error","status_checked_at":"2026-01-28T15:15:13.020Z","response_time":57,"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":["avida","biodiversity","evolution","evolutionary-computation","spatial-data-analysis"],"created_at":"2025-03-04T07:18:55.564Z","updated_at":"2026-01-28T15:32:24.482Z","avatar_url":"https://github.com/emilydolson.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"This repository contains figures, scripts, and data for the paper:\n\n# Spatial resource heterogeneity creates local hotspots of evolutionary potential\nBy Emily Dolson and Charles Ofria\n\nEuropean Conference on Artificial Life, 2017\n\n![](figs/50065_all_hotspots.png)\n[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)\n[![Paper:10.7551/ecal_a_023](https://img.shields.io/badge/DOI-10.7551%2F978\u0026#8208;0\u0026#8208;262\u0026#8208;33936\u0026#8208;0\u0026#8208;ch071-green.svg)](http://cognet.mit.edu/proceed/10.7551/ecal_a_023)\n## Contents:\n- *hotspots.tex* -  LaTeX file for main paper\n- *alifeconf.sty* - Style file for ECAL\n- *Zotero.bib* - bibliography file for paper\n- *config* - contains all files used to generate daa\n  - *avida* - executable used to generate data\n  - *avida-lineage* - executable used to output lineage trajectories\n  - *avida.cfg* - config file for Avida (not changed from default)\n  - *defaults-heads.org* - starting organism (not changed from default)\n  - *env500XX.cfg* - these files indicate how to build the 8 different environments\n  - *envcontrol.cfg* - file to specify the homogeneous control environment\n  - *events.cfg* - tells Avida what data to output when\n  - *corner_events.cfg* - events file that puts starting organism in oppostie corner\n  - *instset-heads.cfg* - tells avida what instruction set to use (not changed from default)\n  - *lineage_events.cfg* - events file for runs where spatial lineage is being output\n  - *write_events_file.py* - python script to make events file that only prints phenotype grid immediately before a new task is going to evolve (assumes that extract_points.py has already been called to determine when each task will evolve)\n- *data* - contains summary-level data files extracted from raw data (raw data would be too large too include)\n  - *all_task_locs.csv* - the locations where each task first evolved in each run\n  - *control_diversity_ranks.csv* - the percentile of the diversity of the cell where each task first evolved in each replicate of the control condition\n  - *diversity_ranks.csv* - the percentile of the diversity of the cell where each task first evolved in each replicate of the experimental conditions\n  - *qsub_files* - all of the scripts used to submit experiments to MSU's high performance compupting cluster\n- *figs* - figures\n  - *50060_9_paths.png* - all lineage paths for task 9 in environment 50060 (not very useful - there are too many)\n  - *50065_all_hotspots.png* - all hotspots across all environments\n  - *9_50013_density.png* - kernel density map for task 9 in environment 50013\n  - *9_50013_hotspots.png* - hotspot locations for task 9 in environment 50013\n  - *9_50013_k-hat.png* - Ripley's K for task 9 in environment 50013\n  - *9_50013_points.png* - point locations for task 9 in environment 50013\n  - *control_9_paths.png* - 5 example lineage paths for task 9 for each environment\n  - *localdiversity.png* - qqplot comparing diversity ranks to uniform distribution\n  - *statsfig.png* - diagram outlining statsitics pipeline\n  - *statsfig_horizontal_1col.png* - smaller version of the stats pipeline figure that fits in 1 column\n- *scripts* - Python and R scripts for processing and analyzing data\n  - *collect_points.py* - grab data from task_locs.csv files for each rep and summarize them into all_task_locs.csv\n  - *draw_hotspots.py* - can be used to make various figures showing points, hotspots, and lineage paths over an environment\n  - *env500XX.csv* - files generated by extract_env_data.py that indicate distance from each cell in each environment to each resource\n  - *envcontrol.csv* - like above, except it's all 0s\n  - *extract_diversity.py* - generate diversity_ranks.csv file from raw phenotype grids\n  - *extract_env_data.py* - generate csv files indicating the distance from each cell in an environment to each resource\n  - *extract_grids.py* - grab phenotype grids from right before each task evolves out of tar archives\n  - *extract_paths.csv* - convert sequence of ints output by avida-lineage into actual sequences of coordinates and environments that a lineage passed through\n  - *extract_points.csv* - loop through phenotype grids to figure out when each task first appears (generates task_locs.csv)\n  - *kriging.R* - R script that handles all of the regression that we used in an attempt to figure out what causes hotspots\n  - *make_diversity_maps.csv* - makes heat maps of local diversity for updates immediately before tasks evolved\n  - *make_hotspot_figure.py* - variant on draw_hotspots.py, used to make multi-panel hotspot figure in paper\n  - *make_path_figure.py* - variant on draw_hotspots.py used to make multipanel path figure in paper\n  \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Femilydolson%2Fevo_in_space","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Femilydolson%2Fevo_in_space","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Femilydolson%2Fevo_in_space/lists"}