Rewetted Peatland_GHG analysis Code: software packages (R and Matlab) for the calculation of greenhouse gas (GHG) fluxes at a rewetted peatland

10.5880/GFZ.1.4.2023.001 Kalhori, Aram Aram Kalhori 0000-0002-0652-8987 GFZ German Research Centre for Geosciences, Potsdam, Germany Wille, Christian Christian Wille 0000-0003-0930-6527 GFZ German Research Centre for Geosciences, Potsdam, Germany Gottschalk, Pia Pia Gottschalk 0000-0003-4842-8893 GFZ German Research Centre for Geosciences, Potsdam, Germany Li, Zhan Zhan Li 0000-0001-6307-5200 GFZ German Research Centre for Geosciences, Potsdam, Germany Hashemi, Josh Josh Hashemi 0000-0002-8660-7406 Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany Kemper, Karl Karl Kemper Department of Geosciences, Institute of Geography, University of Cologne, Cologne, Germany Sachs, Torsten Torsten Sachs 0000-0002-9959-4771 GFZ German Research Centre for Geosciences, Potsdam, Germany Rewetted Peatland_GHG analysis Code: software packages (R and Matlab) for the calculation of greenhouse gas (GHG) fluxes at a rewetted peatland GFZ Data Services 2024 carbon dioxide emission CO2 emission methane emission CH4 emission peatland wetland eddy covariance rewetting emission factor mitigation EARTH SCIENCE > BIOSPHERE > TERRESTRIAL ECOSYSTEMS > WETLANDS > PEATLANDS In Situ Land-based Platforms > GROUND-BASED OBSERVATIONS Kalhori, Aram Aram Kalhori 0000-0002-0652-8987 GFZ German Research Centre for Geosciences, Potsdam, Germany Kalhori, Aram Aram Kalhori 0000-0002-0652-8987 GFZ German Research Centre for Geosciences, Potsdam, Germany Wille, Christian Christian Wille 0000-0003-0930-6527 GFZ German Research Centre for Geosciences, Potsdam, Germany Wille, Christian Christian Wille 0000-0003-0930-6527 GFZ German Research Centre for Geosciences, Potsdam, Germany Wille, Christian Christian Wille 0000-0003-0930-6527 GFZ German Research Centre for Geosciences, Potsdam, Germany Gottschalk, Pia Pia Gottschalk 0000-0003-4842-8893 GFZ German Research Centre for Geosciences, Potsdam, Germany Li, Zhan Zhan Li 0000-0001-6307-5200 GFZ German Research Centre for Geosciences, Potsdam, Germany Hashemi, Josh Josh Hashemi 0000-0002-8660-7406 Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany Kemper, Karl Karl Kemper Department of Geosciences, Institute of Geography, University of Cologne, Cologne, Germany Sachs, Torsten Torsten Sachs 0000-0002-9959-4771 GFZ German Research Centre for Geosciences, Potsdam, Germany Sachs, Torsten Torsten Sachs 0000-0002-9959-4771 GFZ German Research Centre for Geosciences, Potsdam, Germany Kalhori, Aram GFZ German Research Centre for Geosciences Sachs, Torsten GFZ German Research Centre for Geosciences 2023-01-17 2008-01-01/2020-12-31 Software 10.1038/s43247-024-01226-9 https://posit.co/downloads/ 10.5880/GFZ.1.4.2023.004 https://CRAN.R-project.org/package=zyp https://github.com/stekhoven/missForest https://cran.r-project.org/web/packages/REddyProc/index.html 10.1080/01621459.1968.10480934 10.1002/hyp.1095 10.1080/07055900.2000.9649654 10.1093/bioinformatics/btr597 GNU GENERAL PUBLIC LICENSE (Version 3, 29 June 2007), Copyright (C) 2023 Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences, Potsdam, Germany (Aram Kalhori) This publication provides the codes produced for the article "Temporally dynamic carbon dioxide and
methane emission factors for rewetted peatlands. Nature Communications Earth and Environment" by Aram Kalhori, Christian Wille, Pia Gottschalk, Zhan Li, Josh Hashemi, Karl Kemper, and Torsten Sachs (https://doi.org/10.1038/s43247-024-01226-9). In the article, the authors estimate the cumulative GHG emissions of a rewetted peatland in Germany using the long-term ecosystem flux measurements. They observe a source-to-sink transition of annual carbon dioxide (CO2) fluxes and decreasing trend of methane (CH4) emissions.

This software is written in R and MATLAB. Running the codes ([R files and .m files](Code)) and loading the data files ([CSV files and .mat files](Data)) requires the pre-installation of [R and RStudio] (https://posit.co/downloads/) and ([MATLAB]. The RStudio 2022.07.2 Build 576 version has been used for the R scripts. The land cover classification work was performed in QGIS, v.3.16.11-Hannover. Data were analyzed in both MATLAB and R and plots created with R (R Core Development Team 2020) in RStudio®.

The following external packages are required to be incorporated into the codes in order to run the provided codes:

"zyp" package; "missForest" package;"REddyProc" package and explained in detail in the README.

Files: Codes/Kalhori2023_SenSlopes_fig2.r
"zyp" package, Maintainer David Bronaugh <bronaugh@uvic.ca>
Depends R (>= 2.4.0), Kendall
License: LGPL-2.1
https://CRAN.R-project.org/package=zyp

Files: Codes/Kalhori2023_gapfillingMF_validation_figSI1.r
"missForest" package, Maintainer Daniel J. Stekhoven <stekhoven@stat.math.ethz.ch>
Depends randomForest,foreach,itertools
License: GPL (>= 2)
https://www.r-project.org, https://github.com/stekhoven/missForest

Files: Codes/Kalhori2023_NEEpartitioning.r
"REddyProc" package, Maintainer Thomas Wutzler <twutz@bgc-jena.mpg.de>
Depends R (>= 3.0.0), methods
Imports Rcpp, dplyr, purrr, rlang, readr, tibble, magrittr, solartime, bigleaf (>= 0.7)
License: GPL (>= 2)
https://cran.r-project.org/web/packages/REddyProc/index.html

Data are provided as .shp, CSV or text files. The MATLAB scripts for footprint calculation and the R scripts used for gapfilling (missForest) and flux partitioning (REddyProc) are also included.The full description of the data and methods is provided in the manuscript.
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007

Copyright (C) 2023 Helmholtz Centre Potsdam GFZ German Research Centre
for Geosciences, Potsdam, Germany (Aram Kalhori).

Kalhori2023_Rewetted Peatland_GHG Analysis is free software:
you can redistribute it and/or modify
it under the terms of the GNU General Public License as published
by the Free Software Foundation, version 3 of the License.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.

Helmholtz-Zentrum Potsdam - Deutsches GeoForschungsZentrum GFZ http://doi.org/10.13039/501100010956 VH-NG-821 Helmholtz Young Investigators Grant the Helmholtz Association's Initiative and Networking Fund Helmholtz Climate Initiative (HI-CAM)