brownag/labtaxa repository overview

⁠labtaxa

The goal of {labtaxa} is to provide ‘Lab Data Mart’ (https://ncsslabdatamart.sc.egov.usda.gov/⁠) database snapshots for use in R. This repository is an R package used to download and cache the contents of the Lab Data Mart GeoPackage database.

This repository is built automatically via a GitHub Action. Find the source on GitHub: https://github.com/brownag/labtaxa⁠

⁠Docker

To get up and running quickly you can use the Docker container. The labtaxa container is based on "rocker/rstudio:latest"⁠. In addition to the standard RStudio tools, the container has the cached Lab Data Mart GeoPackage (containing lab and spatial data) and the companion morphologic database (derived from NASIS pedon descriptions) pre-downloaded. Also, the results of soilDB::fetchLDM() called on the LDM GeoPackage data source are cached as an R object file (.rds). Finally, a variety of useful R packages are pre-installed. All can be accessed via an RStudio Server web browser interface.

From Docker Hub:

docker pull brownag/labtaxa:latest

Or from GitHub:

docker pull ghcr.io/brownag/labtaxa:latest

Once you have a local copy of the labtaxa container you can run:

docker run -d -p 8787:8787 -e PASSWORD=mypassword -v ~/Documents:/home/rstudio/Documents -e ROOT=TRUE brownag/labtaxa

Then open your web browser and navigate to http://localhost:8787. The default username is rstudio and the default password is mypassword.

⁠R package usage

When you start up {labtaxa} in the Docker container you will have the latest database and the first-step data object (as if you ran the {soilDB} functions) readily available for post-processing for answering specific questions. See demo.R in the container home folder to get started.