{"id":32440362,"url":"https://github.com/patrickbarks/popmods","last_synced_at":"2026-06-17T16:38:53.134Z","repository":{"id":96005456,"uuid":"136588902","full_name":"patrickbarks/popmods","owner":"patrickbarks","description":"R package to obtain tidy output from continuous-time population models in ecology","archived":false,"fork":false,"pushed_at":"2018-10-12T20:43:16.000Z","size":2076,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-10-26T01:27:52.374Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/patrickbarks.png","metadata":{"files":{"readme":"README.Rmd","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":"2018-06-08T08:17:07.000Z","updated_at":"2019-05-30T09:46:40.000Z","dependencies_parsed_at":"2023-04-01T10:02:18.497Z","dependency_job_id":null,"html_url":"https://github.com/patrickbarks/popmods","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/patrickbarks/popmods","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/patrickbarks%2Fpopmods","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/patrickbarks%2Fpopmods/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/patrickbarks%2Fpopmods/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/patrickbarks%2Fpopmods/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/patrickbarks","download_url":"https://codeload.github.com/patrickbarks/popmods/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/patrickbarks%2Fpopmods/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34455231,"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":"online","status_checked_at":"2026-06-17T02:00:05.408Z","response_time":127,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":[],"created_at":"2025-10-26T01:27:50.866Z","updated_at":"2026-06-17T16:38:53.129Z","avatar_url":"https://github.com/patrickbarks.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/patrickbarks/popmods?branch=master\u0026svg=true)](https://ci.appveyor.com/project/patrickbarks/popmods)\n[![Travis-CI Build Status](https://travis-ci.org/patrickbarks/popmods.svg?branch=master)](https://travis-ci.org/patrickbarks/popmods)\n[![Coverage Status](https://img.shields.io/codecov/c/github/patrickbarks/popmods/master.svg)](https://codecov.io/github/patrickbarks/popmods?branch=master)\n\n```{r, echo = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/img/\",\n  eval=TRUE,\n  dpi = 150,\n  fig.width = 4.5,\n  fig.height = 3\n)\nlibrary(ggplot2)\ntt \u003c- theme_get() +\n  theme(legend.position = c(0.98, 0.97),\n        legend.justification = c(1, 1),\n        text = element_text(size = 9),\n        axis.title = element_text(size = 9.5))\ntheme_set(tt)\n```\n\npopmods\n=========\n\nEasy numerical analysis of continuous-time population models in ecology.\n\nModels currently supported:\n\n- logistic growth\n- delayed-logistic growth\n- Lotka Volterra (predator-prey)\n- Lotka Volterra (two-species competition)\n- rock-paper-scissors intransitive competition\n- rock-paper-scissors-lizard-spock\n- SIR epidemiological model\n\n## Installation\n\nInstall the development version from GitHub with:\n\n```{r, eval=FALSE}\ndevtools::install_github(\"patrickbarks/popmods\")\n#\n# or\n#\ninstall.packages(\"remotes\") # smaller and quicker to install than devtools\nremotes::install_github(\"patrickbarks/popmods\")\n```\n\n## Usage\n\n```{r, message=FALSE}\nlibrary(popmods)\nlibrary(ggplot2)\n\n# vector of time points at which to evaluate models\nt \u003c- seq(0, 50, 0.01)\n```\n\n###### Delayed logistic\n\n```{r Delayed-logistic}\ndf_dl \u003c- logistic_delay(time = t, init_n = 10, r = 1.1, k = 500, tau = 1.12)\n\nggplot(df_dl, aes(time, abundance)) +\n  geom_line(lwd = 1.2)\n```\n\n\n###### Lotka-Volterra predator-prey\n\n```{r Lotka-Volterra-predator-prey}\ndf_lvpp \u003c- lotka_volterra(time = t, init_n = 50, init_p = 30, r = 0.8, c = 0.04,\n                          a = 0.2, m = 0.3)\n\nggplot(df_lvpp, aes(time, abundance, color = population)) +\n  geom_line(lwd = 1.2) +\n  scale_color_brewer(type = 'qual', palette = 6)\n```\n\n###### Rock-paper-scissors-lizard-spock competition\n\n```{r R-P-S-L-K-competition}\ndf_rpslk \u003c- rpslk(time = t, init_r = 0.02, init_p = 0.02, init_s = 0.03,\n                  init_l = 0.9, init_k = 0.03, b = 0.7)\n\nggplot(df_rpslk, aes(time, proportion, color = strategy)) +\n  geom_line(lwd = 1.2) +\n  scale_color_brewer(type = 'qual', palette = 6)\n```\n\n###### SIR epidemiological model\n\n```{r SIR-epidemiological-model}\ndf_sir \u003c- sir(time = t, init_s = 0.9999, init_i = 0.0001, init_r = 0,\n              gamma = 0.6, beta = 0.08)\n\nggplot(df_sir, aes(time, proportion, color = status)) +\n  geom_line(lwd = 1.2) +\n  scale_color_brewer(type = 'qual', palette = 6)\n```\n\n\n## Contributions\n\nAll contributions are welcome. Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpatrickbarks%2Fpopmods","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpatrickbarks%2Fpopmods","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpatrickbarks%2Fpopmods/lists"}