Compendium of R code and data for “Prediction of Peat Properties from Transmission Mid-Infrared Spectra”

This repository contains the data and code for our manuscript:

Teickner, H. & Knorr, K.-H. (2025). “Prediction of peat Properties from transmission mid-infrared spectra”. (unpublished).

How to cite

Please cite this compendium as:

Henning Teickner and Klaus-Holger Knorr, (2025). Compendium of R code and data for “Prediction of peat Properties from transmission mid-infrared spectra”. Accessed 26 Sep 2025. https://github.com/henningte/eb1079

How to use

Instructions how to set up the Docker containers to reproduce the computations are available from the Dockerfile. The Dockerfile also provides instructions to run the targets workflow to reproduce all computations and eventually the manuscript and supporting information.

Licenses

Text and figures : CC-BY-4.0

Code : GPL-3

Data : CC-0 attribution requested in reuse. See the sources section for licenses for data derived from external sources and how to give credit to the original author(s) and the source.

Sources

Data in folder data/raw_data are derived from different sources. To use these data and give credit to data authors, please follow the following information:

• 📁 d9.rds: This file contains data values (porosity and bulk density of organic shales) extracted from Fig. 4 in Wang et al. (2015).
• 📁 caldat-wittington2024: This folder contains data values (bulk density, porosity, saturated hydraulic conductivity) extracted from Fig. 1 and 3 from Whittington and Koiter (2024).
• 📁 CHNOSZ: This folder contains additional data for P$_4$O$_10$ to be included in the ‘OBIGT’ database from the R package ‘CHNOSZ’ (Dick 2019). These additional data values are derived from https://webbook.nist.gov/cgi/cbook.cgi?ID=C16752606&Mask=6F (Linstrom 1997).
• 📁 dry_thermal_conductivity: This folder contains corrected versions of the supporting data from O’Connor et al. (2020) which I received via email from Prof. Cardenas.
• 📁 pmird: This is a template folder in which the folder pmird_prepared_data from the pmird database needs to be stored to reproduce the computations. This folder is available from https://doi.org/10.5281/zenodo.17092587.
• 📁 specific_heat_capacity: This folder contains the supporting data from Gnatowski et al. (2022).

Contributions

We welcome contributions from everyone. Please note that the eb1079 project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Funding

This study was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) grant no. KN 929/23-1 to Klaus-Holger Knorr and grant no. PE 1632/18-1 to Edzer Pebesma.

References

Dick, Jeffrey M. 2019. “CHNOSZ: Thermodynamic Calculations and Diagrams for Geochemistry.” Frontiers in Earth Science 7 (July): 180. https://doi.org/10.3389/feart.2019.00180.

Gnatowski, Tomasz, Ewa Ostrowska-Ligęza, Cedric Kechavarzi, Grzegorz Kurzawski, and Jan Szatyłowicz. 2022. “Heat Capacity of Drained Peat Soils.” Applied Sciences 12 (3): 1579. https://doi.org/10.3390/app12031579.

Linstrom, Peter. 1997. “NIST Chemistry WebBook, NIST Standard Reference Database 69.” National Institute of Standards and Technology. https://doi.org/10.18434/T4D303.

O’Connor, Michael T., M. Bayani Cardenas, Stephen B. Ferencz, Yue Wu, Bethany T. Neilson, Jingyi Chen, and George W. Kling. 2020. “Empirical Models for Predicting Water and Heat Flow Properties of Permafrost Soils.” Geophysical Research Letters 47 (11): e2020GL087646. https://doi.org/10.1029/2020GL087646.

Wang, Guochang, Yiwen Ju, Zhifeng Yan, and Qingguang Li. 2015. “Pore Structure Characteristics of Coal-Bearing Shale Using Fluid Invasion Methods: A Case Study in the Huainan–Huaibei Coalfield in China.” Marine and Petroleum Geology 62 (April): 1–13. https://doi.org/10.1016/j.marpetgeo.2015.01.001.

Whittington, Pete, and Alex Koiter. 2024. “Evaluation of Hydro-Physical Properties Along a Northern Boreal Bog Peatland Transect.” https://doi.org/10.21203/rs.3.rs-4650224/v1.