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 harmonize 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_githbu("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 libarary (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.
The following creates a file prepare_rxs_dataset.R in
your current directory.
library(rxs2tria)
file.copy(system.file("templates/prepare_rxs_dataset.R",
package = "rxs2tria"), ".")Open the copied file and follow the instructions therein, or see the workflow vignette for more details.