Compendium of R code and data for "Peatland Mid-Infrared Database 1.0.0"

Compendium of R code and data for "Peatland Mid-Infrared Database 1.0.0" This repository contains the data and code for our manuscript: Teickner, H., Agethen, S., Berger, S., Boelsen, R. I., Borken, W., Bragazza, L., Broder, T., De La Cruz, F. B., Diaconu, A.-C., Dise, N. B., Drollinger, S., Estop-Aragonés, C., Gałka, M., Martí, M., Glatzel, S., Groß, J., Harris, L., Heffernan, L., Hodgkins, S. B., … Knorr, K.-H. (unpublished). Peatland mid-infrared database (1.0.0). How to cite Please cite this compendium as: Henning Teickner (2025). Compendium of R code and data for "Peatland Mid-Infrared Database 1.0.0". Accessed 25 Sep 2025. https://github.com/henningte/eb1078 Contents R: directory with R functions for the manuscript. data/raw_data/mir_quality_results.rds: RDS file with information on spectral quality of the spectra in the pmird database. pmird-paper.Rmd: R Markdown script that represents the main manuscript file. pmird-supporting-info.Rmd: R Markdown script that represents the supporting information for the manuscript. To reproduce the manuscripts, run the 'targets' workflow by executing run.R in above folders. Please note that you also have to set up the pmird database (Teickner et al. 2025), as described in the Zenodo repository. 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 the pmird database were derived from the following sources: De la Cruz, Osborne, and Barlaz (2016), Hodgkins et al. (2018), Knierzinger et al. (2020), Knierzinger (2020), Münchberger (2019), Münchberger et al. (2019), Schuster et al. (2022), Drollinger, Kuzyakov, and Glatzel (2019), Drollinger et al. (2020), Agethen and Knorr (2018), Kendall (2020), L. I. Harris et al. (2023), L. Harris and Olefeldt (2023), Pelletier et al. (2017), Teickner, Gao, and Knorr (2021), Teickner, Gao, and Knorr (2022), Heffernan (2019), Heffernan et al. (2020), Broder et al. (2012), Anzenhofer (2014, unpublished), Mathijssen et al. (2019), Wagner (2013), Hömberg (2014), Berger et al. (2017), Berger et al. (2018), T. R. Moore et al. (2019), Diaconu et al. (2020), Gałka, Hölzer, et al. (2022), Gałka, Diaconu, et al. (2022), L. I. Harris et al. (2018), L. I. Harris et al. (2019), Boothroyd et al. (2021), Worrall (2021), Reuter et al. (2019b), Reuter et al. (2019a), Reuter et al. (2020), Liu and Lennartz (2019), T. Moore et al. (2005), Turunen et al. (2004). Contributions We welcome contributions from everyone. Please note that the eb1078 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 Agethen, Svenja, and Klaus-Holger Knorr. 2018. “Juncus Effusus Mono-Stands in Restored Cutover Peat Bogs – Analysis of Litter Quality, Controls of Anaerobic Decomposition, and the Risk of Secondary Carbon Loss.” Soil Biology and Biochemistry 117: 139–52. https://doi.org/10.1016/j.soilbio.2017.11.020. Anzenhofer, Regina. 2014, unpublished. “Biogeochemical Characterization of Peat Profiles Along a Vegetation Gradient in an Ombrotrophic Bog, Patagonia.” Master’s thesis. Berger, Sina, Gerhard Gebauer, Christian Blodau, and Klaus-Holger Knorr. 2017. “Peatlands in a Eutrophic World – Assessing the State of a Poor Fen-Bog Transition in Southern Ontario, Canada, After Long Term Nutrient Input and Altered Hydrological Conditions.” Soil Biology and Biochemistry 114 (November): 131–44. https://doi.org/10.1016/j.soilbio.2017.07.011. Berger, Sina, Leandra S. E. Praetzel, Marie Goebel, Christian Blodau, and Klaus-Holger Knorr. 2018. “Differential Response of Carbon Cycling to Long-Term Nutrient Input and Altered Hydrological Conditions in a Continental Canadian Peatland.” Biogeosciences 15 (3): 885–903. https://doi.org/10.5194/bg-15-885-2018. Boothroyd, I. M., F. Worrall, C. S. Moody, G. D. Clay, G. D. Abbott, and R. Rose. 2021. “Sulfur Constraints on the Carbon Cycle of a Blanket Bog Peatland.” Journal of Geophysical Research: Biogeosciences 126 (8). https://doi.org/10.1029/2021JG006435. Broder, T., C. Blodau, H. Biester, and K. H. Knorr. 2012. “Peat Decomposition Records in Three Pristine Ombrotrophic Bogs in Southern Patagonia.” Biogeosciences 9 (4): 1479–91. https://doi.org/10.5194/bg-9-1479-2012. De la Cruz, Florentino B., Jason Osborne, and Morton A. Barlaz. 2016. “Determination of Sources of Organic Matter in Solid Waste by Analysis of Phenolic Copper Oxide Oxidation Products of Lignin.” Journal of Environmental Engineering 142 (2): 04015076. https://doi.org/10.1061/(ASCE)EE.1943-7870.0001038. 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. Drollinger, Simon, Klaus-Holger Knorr, Wolfgang Knierzinger, and Stephan Glatzel. 2020. “Peat Decomposition Proxies of Alpine Bogs Along a Degradation Gradient.” Geoderma 369 (June): 114331. https://doi.org/10.1016/j.geoderma.2020.114331. Drollinger, Simon, Yakov Kuzyakov, and Stephan Glatzel. 2019. “Effects of Peat Decomposition on δ 13C and δ 15N Depth Profiles of Alpine Bogs.” CATENA 178 (July): 1–10. https://doi.org/10.1016/j.catena.2019.02.027. 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. Harris, Lorna I., Tim R. Moore, Nigel T. Roulet, and Andrew J. Pinsonneault. 2018. “Lichens: A Limit to Peat Growth?” Edited by John Lee. Journal of Ecology 106 (6): 2301–19. https://doi.org/10.1111/1365-2745.12975. ———. 2019. “Data from: Lichens: A Limit to Peat Growth?” Data. https://doi.org/10.5061/dryad.s136dc8. Harris, Lorna I., David Olefeldt, Nicolas Pelletier, Christian Blodau, Klaus-Holger Knorr, Julie Talbot, Liam Heffernan, and Merritt Turetsky. 2023. “Permafrost Thaw Causes Large Carbon Loss in Boreal Peatlands While Changes to Peat Quality Are Limited.” Global Change Biology, August, gcb.16894. https://doi.org/10.1111/gcb.16894. Harris, Lorna, and David Olefeldt. 2023. “Permafrost Thaw Causes Large Carbon Loss in Boreal Peatlands While Changes to Peat Quality Are Limited.” Dryad. https://doi.org/10.5061/DRYAD.47D7WM3KK. Heffernan, Liam. 2019. “Peat Carbon, δ 14C, Macrofossil, and Humification Data from a Thawing Permafrost Peatland in Western Canada.” UAL Dataverse. https://doi.org/10.7939/DVN/MKM0ZE. Heffernan, Liam, Cristian Estop-Aragonés, Klaus-Holger Knorr, Julie Talbot, and David Olefeldt. 2020. “Long-Term Impacts of Permafrost Thaw on Carbon Storage in Peatlands: Deep Losses Offset by Surficial Accumulation.” Journal of Geophysical Research: Biogeosciences 125 (3). https://doi.org/10.1029/2019JG005501. Hodgkins, Suzanne B., Curtis J. Richardson, René Dommain, Hongjun Wang, Paul H. Glaser, Brittany Verbeke, B. Rose Winkler, et al. 2018. “Tropical Peatland Carbon Storage Linked to Global Latitudinal Trends in Peat Recalcitrance.” Nature Communications 9 (1): 3640. https://doi.org/10.1038/s41467-018-06050-2. Hömberg, Annkathrin. 2014. “Geochemische Charakterisierung von Mooren der Changbai Mountains.” {Bachelor thesis}, Münster: Münster. Kendall, Rachel Anne. 2020. “Microbial and Substrate Decomposition Factors in Commercially Extracted Peatlands in Canada.” Master’s thesis, Montréal: McGill University. Knierzinger, Wolfgang. 2020. “(Bio)geochemical Data Pürgschachen Moor.” Pangaea. Knierzinger, Wolfgang, Ruth Drescher-Schneider, Klaus-Holger Knorr, Simon Drollinger, Andreas Limbeck, Lukas Brunnbauer, Felix Horak, Daniela Festi, and Michael Wagreich. 2020. “Anthropogenic and Climate Signals in Late-Holocene Peat Layers of an Ombrotrophic Bog in the Styrian Enns Valley (Austrian Alps).” E&G Quaternary Science Journal 69 (2): 121–37. https://doi.org/10.5194/egqsj-69-121-2020. Liu, Haojie, and Bernd Lennartz. 2019. “Hydraulic Properties of Peat Soils Along a Bulk Density Gradient-A Meta Study.” Hydrological Processes 33 (1): 101–14. https://doi.org/10.1002/hyp.13314. Mathijssen, Paul J. H., Mariusz Gałka, Werner Borken, and Klaus-Holger Knorr. 2019. “Plant Communities Control Long Term Carbon Accumulation and Biogeochemical Gradients in a Patagonian Bog.” Science of The Total Environment 684 (September): 670–81. https://doi.org/10.1016/j.scitotenv.2019.05.310. Moore, Tim R., Klaus-Holger Knorr, Lauren Thompson, Cameron Roy, and Jill L. Bubier. 2019. “The Effect of Long-Term Fertilization on Peat in an Ombrotrophic Bog.” Geoderma 343 (June): 176–86. https://doi.org/10.1016/j.geoderma.2019.02.034. Moore, Tim, Christian Blodau, Jukka Turunen, Nigel T. Roulet, and Pierre J. H. Richard. 2005. “Patterns of Nitrogen and Sulfur Accumulation and Retention in Ombrotrophic Bogs, Eastern Canada.”

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