Releases: henningte/eb1078
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K.-H. (unpublished).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 (2012), Anzenhofer (2014, unpublished), Mathijssen et al.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).
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Decomposition Records in Three Pristine Ombrotrophic Bogs in Southern
Patagonia.” Biogeosciences 9 (4): 1479–91.
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Environmental Engineering 142 (2): 04015076.
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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.”
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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.
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of Peat Decomposition on
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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,
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.
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Paul H. Glaser, Brittany Verbeke, B. Rose Winkler, et al. 2018.
“Tropical Peatland Carbon Storage Linked to Global Latitudinal Trends in
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