Compendium of R code and data for "Estimation of the Degree of Decomposition of Peat and Past Net Primary Production from Mid-Infrared Spectra"

Compendium of R code and data for "Estimation of the Degree of Decomposition of Peat and Past Net Primary Production from Mid-Infrared Spectra" This repository contains the data and code for our manuscript: Teickner, Henning, Julien Arsenault, Mariusz Gałka, and Klaus-Holger Knorr. 2025. "Estimation of the Degree of Decomposition of Peat and Past Net Primary Production from Mid-Infrared Spectra." (unpublished). How to cite Please cite this compendium as: Teickner, Henning, Julien Arsenault, Mariusz Gałka, and Klaus-Holger Knorr, (2025). Compendium of R code and data for "Estimation of the Degree of Decomposition of Peat and Past Net Primary Production from Mid-Infrared Spectra." Accessed 26 Sep 2025. https://github.com/henningte/eb1149 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, their licenses, 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: :file_folder: 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. :file_folder: ecy2462-sup-0005-npp_moss.csv: This is one of the csv files contained in the Peatland Decomposition and Productivity Database (Bona et al. 2018). The reproduction is a copy of an official work that is published by Natural Resources Canada (NRCan) and has not been produced in affiliation with, or with the endorsement of, NRCan. Commercial reproduction and distribution are prohibited except with written permission from NRCan. For more information, contact NRCan at copyright.droitdauteur@nrcan-rncan.gc.ca. The full copyright statement is: © Her Majesty the Queen in Right of Canada, 2018. Information contained in this publication or product may be reproduced, in part or in whole, and by any means, for personal or public noncommercial purposes, without charge or further permission, unless otherwise specified. You are asked to exercise due diligence in ensuring the accuracy of the materials reproduced; indicate the complete title of the materials reproduced, and the name of the author organization; and indicate that the reproduction is a copy of an official work that is published by Natural Resources Canada (NRCan) and that the reproduction has not been produced in affiliation with, or with the endorsement of, NRCan. Commercial reproduction and distribution are prohibited except with written permission from NRCan. For more information, contact NRCan at copyright.droitdauteur@nrcan-rncan.gc.ca. See Bona et al. (2018) (https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecy.2462) for details. :file_folder: Bengtsson_etal_sph_holarctic_growth.csv: csv file from Bengtsson et al. (2020) (these data are described in more detail in Bengtsson et al. (2021)). License: CC-0. See http://datadryad.org/stash/dataset/doi:10.5061/dryad.1ns1rn8rm for details. :file_folder: d88_2.rds, d89_2.rds, d90_1.rds: These are average testate amoebae-reconstructed water table depth for the peat cores analyzed in our manuscript, digitized from figures in the original publications (Gałka, Diaconu, et al. 2022; Gałka, Hölzer, et al. 2022; Diaconu et al. 2020). License: CC-0 :file_folder: pangaea_metadata_reuter2019.rds: rds file with the metadata from Reuter et al. (2019), extracted from the Pangaea repository using the pangaear R package (Chamberlain et al. 2025). License: CC-BY-4.0. For details, see https://doi.pangaea.de/10.1594/PANGAEA.902181. :file_folder: eb1064: Folder with preprocessed data from Arsenault et al. (2024a) (the contents of the folder were not directly derived from Arsenault et al. (2024a), but processed from the same original raw data files) and containing in addition the mid-infrared spectra for the samples in Arsenault et al. (2024a) (for an overview on the data, see Arsenault et al. (2024b)). Contributions We welcome contributions from everyone. Please note that the eb1149 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 Arsenault, Julien, Julie Talbot, Tim R. Moore, Klaus-Holger Knorr, Henning Teickner, and Jean-François Lapierre. 2024a. “Patterns and Drivers of Organic Matter Decomposition in Peatland Open-Water Pools.” Zenodo. https://doi.org/10.5281/ZENODO.10581235. ———. 2024b. “Patterns and Drivers of Organic Matter Decomposition in Peatland Open-Water Pools.” Biogeosciences 21 (15): 3491–3507. https://doi.org/10.5194/bg-21-3491-2024. Bengtsson, Fia, Håkan Rydin, Jennifer L. Baltzer, Luca Bragazza, Zhao-Jun Bu, Simon J. M. Caporn, Ellen Dorrepaal, et al. 2021. “Environmental Drivers of Sphagnum Growth in Peatlands Across the Holarctic Region.” Edited by Rien Aerts. Journal of Ecology 109 (1): 417–31. https://doi.org/10.1111/1365-2745.13499. Bengtsson, Fia, Håkan Rydin, Jennifer Baltzer, Luca Bragazza, Zhao-Jun Bu, Simon Caporn, Ellen Dorrepaal, et al. 2020. “Environmental Drivers of Sphagnum Growth in Peatlands Across the Holarctic Region.” Dryad. https://doi.org/10.5061/DRYAD.1NS1RN8RM. Bona, Kelly Ann, Arlene Hilger, Magdalena Burgess, Nicole Wozney, and Cindy Shaw. 2018. “A Peatland Productivity and Decomposition Parameter Database.” Ecology 99 (10): 2406–6. https://doi.org/10.1002/ecy.2462. Chamberlain, Scott, Kara Woo, Andrew MacDonald, Naupaka Zimmerman, and Gavin Simpson. 2025. pangaear: Client for the ’Pangaea’ Database. Manual. Diaconu, Andrei-Cosmin, Ioan Tanţău, Klaus-Holger Knorr, Werner Borken, Angelica Feurdean, Andrei Panait, and Mariusz Gałka. 2020. “A Multi-Proxy Analysis of Hydroclimate Trends in an Ombrotrophic Bog over the Last Millennium in the Eastern Carpathians of Romania.” Palaeogeography, Palaeoclimatology, Palaeoecology 538 (January): 109390. https://doi.org/10.1016/j.palaeo.2019.109390. Gałka, Mariusz, Andrei-Cosmin Diaconu, Angelica Feurdean, Julie Loisel, Henning Teickner, Tanja Broder, and Klaus-Holger Knorr. 2022. “Relations of Fire, Palaeohydrology, Vegetation Succession, and Carbon Accumulation, as Reconstructed from a Mountain Bog in the Harz Mountains (Germany) During the Last 6200 Years.” Geoderma 424 (October): 115991. https://doi.org/10.1016/j.geoderma.2022.115991. Gałka, Mariusz, Adam Hölzer, Angelica Feurdean, Julie Loisel, Henning Teickner, Andrei-Cosmin Diaconu, Marta Szal, Tanja Broder, and Klaus-Holger Knorr. 2022. “Insight into the Factors of Mountain Bog and Forest Development in the Schwarzwald Mts.: Implications for Ecological Restoration.” Ecological Indicators 140 (July): 109039. https://doi.org/10.1016/j.ecolind.2022.109039. Reuter, Hendrik, Julia Gensel, Marcus Elvert, and Dominik Zak. 2019. “FTIR, CuO Lignin, and Bulk Decomposition Data of a 75-Day Anoxic Phragmites Australis Litter Decomposition Experiment in Soil Substrates from Three Northeast German Wetlands.” PANGAEA. https://doi.org/10.1594/PANGAEA.902181.

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