1 - Install isobxr

Théo Tacail

2023-09-01

Source: vignettes/vgn_01_Installation.Rmd

Full documentation and tutorials can be found on the isobxr website.

The isobxr package is a set of R tools designed to perform and explore stable isotope box modelling of open or closed systems. It provides a ready-to-use tool allowing users to develop and test isotopic box models of their system of interest. It allows the user to 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, and sweep the space of parameters in both static and dynamic modes.

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

Load isobxr

You can load the isobxr package in R as follows:

Here is the package description of the current version, where you can find the required minimal versions of dependencies:

You can locally browse the vignettes as follows:

browseVignettes("isobxr")

Download templates and tutorials

The tutorial can be run using the tutorial files embedded in the package extdata. The tutorial files are then called by setting the workdir argument as follows:

workdir <- "/Users/username/Documents/1_ABC_tutorial"
# or
workdir <- "use_isobxr_demonstration_files"
Note
The tutorial mode will prevent you from saving the run outputs to a local working directory.

Alternatively, the user is encouraged to download and browse the input files:

  1. Download xlsx templates. These files provide the user with formatted master files, used as arguments to isobxr functions, as explained in vignettes and on the isobxr website.

  2. Download tutorial files. These files provide the user with all master files and R commands used throughout tutorials, as shown on the isobxr website.