{"id":19769707,"url":"https://github.com/mlysy/subdiff","last_synced_at":"2026-01-03T00:03:31.248Z","repository":{"id":101356746,"uuid":"98570209","full_name":"mlysy/subdiff","owner":"mlysy","description":"R package for subdiffusive particles tracking","archived":false,"fork":false,"pushed_at":"2024-09-06T13:24:55.000Z","size":2404,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2024-11-12T04:44:30.826Z","etag":null,"topics":["particle-tracking","r-package","subdiffusion"],"latest_commit_sha":null,"homepage":"https://mlysy.github.io/subdiff/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mlysy.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":null,"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":"2017-07-27T18:51:43.000Z","updated_at":"2024-10-26T18:54:24.000Z","dependencies_parsed_at":null,"dependency_job_id":"ac075b1c-ba19-4f8e-bdb1-b476822a2eec","html_url":"https://github.com/mlysy/subdiff","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mlysy%2Fsubdiff","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mlysy%2Fsubdiff/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mlysy%2Fsubdiff/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mlysy%2Fsubdiff/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mlysy","download_url":"https://codeload.github.com/mlysy/subdiff/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":233426114,"owners_count":18674551,"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":["particle-tracking","r-package","subdiffusion"],"created_at":"2024-11-12T04:44:36.362Z","updated_at":"2025-09-17T21:32:51.396Z","avatar_url":"https://github.com/mlysy.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# subdiff: Subdiffusive Modeling in Passive Particle-Tracking Microrheology\n\n*Martin Lysy, Yun Ling*\n\n\u003c!-- badges: start --\u003e\n[![R-CMD-check](https://github.com/mlysy/subdiff/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/mlysy/subdiff/actions/workflows/R-CMD-check.yaml)\n\u003c!-- badges: end --\u003e\n\n---\n\n### Description\n\nTools for implementing various models for particle subdiffusion in biological fluids.  In addition to the well-known semiparametric least-squares estimator based on the mean square displacement (MSD), the package provides functions for simulation, inference, and goodness-of-fit for two fully-parametric subdiffusion models: fractional Brownian motion and the generalized Langevin equation (GLE) model with Rouse memory kernel.  A generic model class allows users to easily implement custom subdiffusion models, with a ready-made framework for drift, high-frequency error correction, and efficient maximum likelihood estimation.\n\n### Installation\n\n1.  Install the [**Rcpp**](https://CRAN.R-project.org/package=Rcpp) package.  To do this properly you will also need to install a C++ compiler.  Instructions for this are available [here](https://teuder.github.io/rcpp4everyone_en/020_install.html).  \n\n    To test that this step is done correctly, quit + restart R, then run the following command:\n\t\n    ```r\n    Rcpp::evalCpp(\"2 + 2\")\n    ```\n\n    If the output is `4` then **Rcpp** is installed correctly.\n\n2.  Install the [**devtools**](https://CRAN.R-project.org/package=devtools) package.\n\n3.  In an R session run the following commands:\n\n    ```r\n    devtools::install_github(\"mlysy/subdiff\",\n                             force = TRUE, INSTALL_opts = \"--install-tests\")\n    ```\n\n4.  Once the packages are installed, you can test that everything works correctly by first quitting + restarting R, then running the command:\n\n    ```r\n    testthat::test_package(\"subdiff\", reporter = \"progress\")\n    ```\n\t\n\tOccasionally due to random chance a few of the tests may fail.  However, if everything is installed correctly, then rerunning this a few times will eventually produce zero test failures.  \n\n### Usage\n\nPlease see the package vignette: `vignette(\"subdiff\")`.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmlysy%2Fsubdiff","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmlysy%2Fsubdiff","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmlysy%2Fsubdiff/lists"}