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TUBAFsoilFunctions

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. This includes functions for processing data from several laboratory and field instruments used by the soil working group at IBF, TU Bergakademie Freiberg. Roughly, contents of this package 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.