TUBAFsoilFunctions

General description

This package contains an assortment of functions used in the soil working group at IBF, TU Bergakademie Freiberg.

Installation

Install using remotes::install_github("seanadamhdh/TUBAFsoilFunctions").

Currently, packages are loaded lazy with (import?)... instead of (importFrom?).... If you are running on a deprecated version of R, try skipping. It is planned to implement proper import handling at some point, though, for now, you should be fine with R>4.3 and package versions from 2023 or newer. If you use legacy versions of the r-packages used by this package, or R itself, you should be careful, as a) Updates could break code written in older versions of R or use legacy versions of package, and b) it might take quite a wile to update everything. You might want to consider setting up a renv environment.

Contents

This package contains an assortment of functions that I wrote during my doctorate. Roughly, they can be grouped into the following categories:

  • Loading, processing, and cleaning of Elementar soliTOCcube data

  • Loading, processing, and cleaning of Bruker Alpha DRIFTS data (heavily relying on Baumann (2020), Stevens and Ramirez-Lopez (2022), and Ramirez-Lopez et al. (2023))

  • Loading, processing and cleaning of Spectrolyzer UV-Vis spectra

  • Chemometric modelling with the caret Kuhn (2008) framework, including calibration, validation and application of models for midDRIFTS and UV-Vis data

  • Loading, processing and cleaning (CO2) respiration data collected with SEMACHv3 chamber systems (also see seanadamhdh/SEMACHv3 for a python single-file exe) and PriEco Pri8800 incubator data

  • Assorted additional functions and helpers for smaller tasks, i.e., for soil profile data homogenisation, or sample label generator.

Baumann, Philipp. 2020. “Simplerspec: Soil and Plant Spectroscopic Model Building and Prediction.” https://github.com/philipp-baumann/simplerspec.
Kuhn, Max. 2008. “Building Predictive Models in r Using the Caret Package.” Journal of Statistical Software 28 (5). https://doi.org/10.18637/jss.v028.i05.
Ramirez-Lopez, Leonardo, Antoine Stevens, Claudio Orellano, Raphael Viscarra Rossel, Zefang Shen, Alex Wadoux, and Timo Breure. 2023. “Resemble: Regression and Similarity Evaluation for Memory-Based Learning in Spectral Chemometrics.” https://cran.r-project.org/web/packages/resemble/index.html.
Stevens, Antoine, and Leonardo Ramirez-Lopez. 2022. “An Introduction to the Prospectr Package.” https://cran.r-project.org/web/packages/prospectr/index.html.