Flexible cycle threshold modelling

Flexible piecewise modelling of cycle thresholds with adjustment for varying intercepts and linear scales.

Installation

Installing the package

Install the unstable development from GitHub using the following,

remotes::install_github("seabbs/epict", dependencies = TRUE)

Installing CmdStan

If you don’t already have CmdStan installed then, in addition to installing epict, it is also necessary to install CmdStan using CmdStanR’s install_cmdstan() function to enable model fitting in epict. A suitable C++ toolchain is also required. Instructions are provided in the Getting started with CmdStanR vignette. See the CmdStanR documentation for further details and support.

cmdstanr::install_cmdstan()

Quick start

Package

As well as epict this quick start makes use of data.table and ggplot2 which are both installed when epict is installed.

library(epict)
library(data.table)
library(ggplot2)

Data

Data preprocessing and model specification

Model fitting

Results

Citation

If using epict in your work please consider citing it using the following,

#> 
#> To cite epict in publications use:
#> 
#>   Sam Abbott, Timothy Russell, Joel Hellewell (2022). epict: Cycle
#>   threshold modelling, DOI:
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {epict: Cycle threshold modelling},
#>     author = {Sam Abbott and Timothy Russell and Joel Hellewell},
#>     journal = {Zenodo},
#>     year = {2022},
#>   }

How to make a bug report or feature request

Please briefly describe your problem and what output you expect in an issue. If you have a question, please don’t open an issue. Instead, ask on our Q and A page.

Contributing

We welcome contributions and new contributors! We particularly appreciate help on priority problems in the issues. Please check and add to the issues, and/or add a pull request.

If interested in expanding the functionality of the underlying model note that epict allows users to pass in their own models meaning that alternative parameterisations may be easily tested within the package infrastructure. Once this testing has been done alterations that increase the flexibility of the package model and improves its defaults are very welcome via pull request or other communication with the package authors.

Code of Conduct

Please note that the epict project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

seabbs / epict