https://github.com/mlysy/subdiff

R package for subdiffusive particles tracking
https://github.com/mlysy/subdiff

particle-tracking r-package subdiffusion

Last synced: 10 days ago
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R package for subdiffusive particles tracking

• Host: GitHub
• URL: https://github.com/mlysy/subdiff
• Owner: mlysy
• Created: 2017-07-27T18:51:43.000Z (over 7 years ago)
• Default Branch: main
• Last Pushed: 2024-09-06T13:24:55.000Z (5 months ago)
• Last Synced: 2024-11-12T04:44:30.826Z (2 months ago)
• Topics: particle-tracking, r-package, subdiffusion
• Language: R
• Homepage: https://mlysy.github.io/subdiff/
• Size: 2.29 MB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS.md

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README

        
# subdiff: Subdiffusive Modeling in Passive Particle-Tracking Microrheology

*Martin Lysy, Yun Ling*

[![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)

---

### Description

Tools 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.

### Installation

1.  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).  

    To test that this step is done correctly, quit + restart R, then run the following command:

	

    ```r

    Rcpp::evalCpp("2 + 2")

    ```

    If the output is `4` then **Rcpp** is installed correctly.

2.  Install the [**devtools**](https://CRAN.R-project.org/package=devtools) package.

3.  In an R session run the following commands:

    ```r

    devtools::install_github("mlysy/subdiff",

                             force = TRUE, INSTALL_opts = "--install-tests")

    ```

4.  Once the packages are installed, you can test that everything works correctly by first quitting + restarting R, then running the command:

    ```r

    testthat::test_package("subdiff", reporter = "progress")

    ```

	

	Occasionally 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.  

### Usage

Please see the package vignette: `vignette("subdiff")`.