{"id":17844826,"url":"https://github.com/dombennett/om..partitionfinder","last_synced_at":"2025-10-12T20:39:58.396Z","repository":{"id":68566948,"uuid":"201453145","full_name":"DomBennett/om..partitionfinder","owner":"DomBennett","description":"outsider-module: partitionfinder","archived":false,"fork":false,"pushed_at":"2020-01-16T10:37:39.000Z","size":36,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-06-20T06:03:26.687Z","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/DomBennett.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}},"created_at":"2019-08-09T11:17:27.000Z","updated_at":"2020-01-16T10:37:41.000Z","dependencies_parsed_at":null,"dependency_job_id":"7cb1dfa5-59c9-427d-a4d5-6798b7d1f06f","html_url":"https://github.com/DomBennett/om..partitionfinder","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/DomBennett/om..partitionfinder","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2Fom..partitionfinder","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2Fom..partitionfinder/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2Fom..partitionfinder/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2Fom..partitionfinder/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DomBennett","download_url":"https://codeload.github.com/DomBennett/om..partitionfinder/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2Fom..partitionfinder/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":260891058,"owners_count":23077904,"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","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":"2024-10-27T21:33:09.933Z","updated_at":"2025-10-12T20:39:53.362Z","avatar_url":"https://github.com/DomBennett.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\u003c!--\nThe README should be used to describe the program. It acts like the homepage of\nyour module.\n\nEdit README.Rmd not README.md. The .Rmd file can be knitted to parse real-code\nexamples and show their output in the .md file.\n\nTo knit, use devtools::build_readme() or outsider.devtools::build()\n\nEdit the template to describe your program: how to install, import and run;\nrun exemplary, small demonstrations; present key arguments; provide links and\nreferences to the program that the module wraps.\n\nLearn more about markdown and Rmarkdown:\nhttps://daringfireball.net/projects/markdown/syntax\nhttps://rmarkdown.rstudio.com/\n--\u003e\n\n```{r, echo = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"README-\"\n)\n```\n\n# Run [`partitionfinder`](http://www.robertlanfear.com/partitionfinder/) with `outsider` in R\n\n[![Build Status](https://travis-ci.org/dombennett/om..partitionfinder.svg?branch=master)](https://travis-ci.org/dombennett/om..partitionfinder)\n\n\u003e Select best-fit partitioning schemes and models of molecular evolution for\nphylogenetic analyses.\n\n\u003c!-- Install information --\u003e\n## Install and look up help\n\n```{r install-snippet, eval=TRUE, include=TRUE}\nlibrary(outsider)\nmodule_install(repo = \"dombennett/om..partitionfinder\")\n# module_help(repo = \"dombennett/om..partitionfinder\")\n```\n\n\u003c!-- Detailed examples --\u003e\n## Examples\n\nThe module comes with three functions for each program comprising the\n\"PartitionFinder2\" software.\n\n* `PartitionFinder` - For nucleotide data\n* `PartitionFinderMorphology` - For morphological data\n* `PartitionFinderProtein` - For protein data\n\nThe module ships with example datasets. These data can be accessed by using the\n`example_fetch` function.\n\nAt a minimum all that is required is to provide a input folder containing the\nconfiguration file and the data. In the arguments, there is no need to\ncall python, this is done by the module. For example, on the command-line if you\nwrote `python PartitionFinder.py example` where \"example\" is the name of the\ninput folder, in R this would be `partitionfinder(\"example\")`.\n\nIf required, additional arguments can be provided as a character vector. E.g.\n\n```\npython PartitionFinder.py --raxml example/\n```\n\nIn R becomes ...\n\n```r\npartitionfinder(c('--raxml', 'example/'))\n```\n\nEach argument must be a separate charcter in the argument list vector.\n\n### DNA\n\n```{r n-example, eval=TRUE, include=TRUE}\nlibrary(outsider)\nPartitionFinder \u003c- module_import('PartitionFinder',\n                                 repo = 'dombennett/om..partitionfinder')\n# show help\nPartitionFinder('-h')\n\n# data\nexample_fetch \u003c- module_import('example_fetch',\n                               repo = 'dombennett/om..partitionfinder')\nexample_fetch(type = 'nucleotide')\n\n# run on the \"nucleotide\" example folder\nPartitionFinder(arglist = 'nucleotide')\n```\n\n### Morphology\n\n```{r m-example, eval=TRUE, include=TRUE}\nlibrary(outsider)\nPartitionFinderMorphology \u003c- module_import('PartitionFinderMorphology',\n                                 repo = 'dombennett/om..partitionfinder')\nexample_fetch \u003c- module_import('example_fetch',\n                               repo = 'dombennett/om..partitionfinder')\n# bring PartitionFinder examples to working directory\nexample_fetch(type = 'morphology')\n# run on the \"morphology\" example folder\nPartitionFinderMorphology(arglist = c('--raxml', 'morphology'))\n```\n\n### Protein\n\n```{r p-example, eval=TRUE, include=TRUE}\nlibrary(outsider)\nPartitionFinderProtein \u003c- module_import('PartitionFinderProtein',\n                                        repo = 'dombennett/om..partitionfinder')\nexample_fetch \u003c- module_import('example_fetch',\n                               repo = 'dombennett/om..partitionfinder')\n# bring PartitionFinder examples to working directory\nexample_fetch(type = 'aminoacid')\n# run on the \"aminoacid\" example folder\nPartitionFinderProtein(arglist = 'aminoacid')\n```\n\n\u003c!-- Remove module after running above example --\u003e\n```{r uninstall-snippet, eval=TRUE, include=FALSE}\nfor (fldr in c('nucleotide', 'morphology', 'aminoacid')) {\n  if (fldr %in% ls() \u0026\u0026 dir.exists(wd)) {\n    unlink(x = fldr, recursive = TRUE, force = TRUE)\n  }\n}\nmodule_uninstall(repo = \"dombennett/om..partitionfinder\")\n```\n\n## Links\n\nFind out more by visiting the\n[PartitionFinder's homepage](www.robertlanfear.com/partitionfinder/).\n\n## Please cite\n\n* Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T., Calcott, B. 2016\nPartitionFinder 2: new methods for selecting partitioned models of evolution\nfor molecular and morphological phylogenetic analyses. Molecular biology and\nevolution. DOI: dx.doi.org/10.1093/molbev/msw260\n* Bennett et al. (2020). outsider: Install and run programs, outside of R,\ninside of R. *Journal of Open Source Software*, In review\n\n\n\u003c!-- Footer --\u003e\n---\n\n\u003cimg align=\"left\" width=\"120\" height=\"125\" src=\"https://raw.githubusercontent.com/ropensci/outsider/master/logo.png\"\u003e\n\n**An `outsider` module**\n\nLearn more at [outsider website](https://docs.ropensci.org/outsider/).\nWant to build your own module? Check out [`outsider.devtools` website](https://docs.ropensci.org/outsider.devtools/).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fom..partitionfinder","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdombennett%2Fom..partitionfinder","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fom..partitionfinder/lists"}