rxs2tria is an R package to handle Quantitative Wood Anatomy (QWA) data, specifically data generated with the ROXAS or ROXAS AI software. The package includes functionality to prepare, quality check and harmonise a QWA dataset, consisting of QWA images, corresponding cell and ring measurement files and accompanying metadata. The processed dataset may then be submitted to the TRIA database for intra-annual and anatomical tree-ring data.

Note: This package is currently under development and not yet stable nor officially released.

Installation

The package is (not yet) on CRAN. You can install rxs2tria from GitHub:

pak::pak("tria-db/rxs2tria")

# or with another remote package installer, such as:
# devtools::install_github("tria-db/rxs2tria")
# remotes::install_github("tria-db/rxs2tria")

Development version

To get the newest features and bug fixes, you can install the development version:

pak::pak("tria-db/rxs2tria@develop")

Troubleshooting

Ensure that the installer library (pak/devtools/remotes) is properly installed. On Windows OS, you may need to install Rtools to build packages from source. Run pkgbuild::check_build_tool(debug=TRUE) to check for build tools, and restart RStudio/Positron after the installation is completed.

Quick start

The easiest way to get started is to copy the rxs2tria workflow template to your working directory and fill in your dataset-specific paths and settings, then run through each step.

library(rxs2tria)
file.copy(system.file("templates/prepare_rxs_dataset.R", package = "rxs2tria"), ".")

Follow the instructions in the template, or see the workflow vignette for more details.

Contributions

Contributions are welcome! Please feel free to open issues or submit pull requests on the GitHub repository.