The isobxr package is a set of R tools designed to perform and explore stable isotope box modelling of open or closed systems. It allows users to develop and test isotopic box models of their system of interest, explore the behavior of these systems in both static (e.g., at steady state) or dynamic modes (e.g., in reaction to a perturbation), build complex scenarios, as well as sweep the space of parameters in both static and dynamic modes.

Check the isobxr website for more information on isobxr and introduction to its rationale.

Installation

Released version

The isobxr package is now on the CRAN (Comprehensive R Archive Network) and can be found on its isobxr CRAN page.

It is available as a released package and can be installed directly from CRAN by calling:

Development version

The isobxr package is available as a source package in its development version from the GitHub isobxr master repository.

The isobxr development version can be installed as follows:

  • Download and install/update R and Rstudio.

  • Download and install package devtools as follows:

install.packages("devtools")
  • Download and install isobxr source package.
devtools::install_github("ttacail/isobxr/isobxr", build_vignettes = TRUE) # FALSE if no pandoc/Rstudio 

The full description of installation process can be found here.

Principles and tutorials

The documentation about underlying theory and isobxr use is made fully available to user in the package website.

On this website you can find the following items.

  1. How can I install isobxr and demo files?

  2. What is isobxr?

  3. Box models single runs with run_isobxr: general presentation and tutorial

  4. Box models scenario runs with compose_isobxr: general presentation and tutorial

  5. Sweep parameters at the final state: general presentation

  6. Sweep parameters in response to perturbation: general presentation

  7. Use the shiny offline html app to plot compose_isobxr, sweep_steady and sweep_dyn outputs: general presentation

Cite isobxr

The isobxr should be cited when used in scientific publications. You can retrieve the citation formats by calling:

citation("isobxr")