{"id":18621302,"url":"https://github.com/4ment/skyplotr","last_synced_at":"2025-10-07T04:56:35.973Z","repository":{"id":232546824,"uuid":"768898157","full_name":"4ment/skyplotr","owner":"4ment","description":null,"archived":false,"fork":false,"pushed_at":"2025-02-21T01:32:59.000Z","size":732,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-08T21:44:29.353Z","etag":null,"topics":["beast","coalescent","ggplot2","mcmc","visualization"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/4ment.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}},"created_at":"2024-03-07T23:51:43.000Z","updated_at":"2025-02-21T03:24:25.000Z","dependencies_parsed_at":"2024-04-10T08:29:35.700Z","dependency_job_id":"01afd716-9600-418e-9eec-13b6c9b59ee1","html_url":"https://github.com/4ment/skyplotr","commit_stats":null,"previous_names":["4ment/skyplotr"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/4ment/skyplotr","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fskyplotr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fskyplotr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fskyplotr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fskyplotr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/4ment","download_url":"https://codeload.github.com/4ment/skyplotr/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/4ment%2Fskyplotr/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278722763,"owners_count":26034461,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-07T02:00:06.786Z","response_time":59,"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":["beast","coalescent","ggplot2","mcmc","visualization"],"created_at":"2024-11-07T04:10:24.585Z","updated_at":"2025-10-07T04:56:35.967Z","avatar_url":"https://github.com/4ment.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# skyplotr\n\n[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n\n### Overview\n\n**skyplotr** is an R package providing functions for plotting the population size trajectory across time. The plots created by **skyplotr** are ggplot objects, which means that after a plot is created it can be further customized using various functions from the **ggplot2** package.\n\n### Installation\n\n* Install the latest development version from GitHub (requires [devtools](https://github.com/hadley/devtools) package):\n\n```r\ndevtools::install_github(\"4ment/skyplotr\")\n```\n\n### Example\n\n`HCV.tsv` contains 1000 MCMC samples obtained from BEAST. This analysis involves a nucleotide alignment of Hepatitis C Virus (HCV), utilizing the piecewise-constant coalescent model (aka skygrid). This model comprises 75 epochs with a cutoff set at 400.\n\n```r\nlibrary(dplyr)\nlibrary(ggplot2)\nlibrary(skyplotr)\n\nsamples \u003c- read.csv(\"data-raw/HCV-skygrid.tsv\", sep = \"\\t\")\n\nroot_height \u003c- samples$treeModel.rootHeight\nlog_pop_size \u003c- select(samples, starts_with(\"skygrid.logPopSize\"))\ncutoff \u003c- samples$skygrid.cutOff[1]\nskygrid \u003c- prepare_skygrid(root_height, log_pop_size, cutoff, age_of_youngest=1994)\nskygrid \u003c-  mutate(skygrid, across(all_of(c(\"trajectory\", \"trajectory_low\", \"trajectory_high\")), exp))\n\nplot_title \u003c- ggtitle(\"Population size trajectory\",\n                      \"with median and 95% intervals\")\n\nskyplot(skygrid, fill=\"darkcyan\") + plot_title + ylab(\"Effective population size\")\n```\n\n![HCV-skygrid](images/HCV-skygrid.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Fskyplotr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2F4ment%2Fskyplotr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2F4ment%2Fskyplotr/lists"}