redoxpeat

Compendium URL

https://github.com/henningte/redoxpeat or https://doi.org/10.5281/zenodo.5792970

Authors

Henning Teickner ([email protected]), Chuanyu Gao, Klaus-Holger Knorr

This repository contains the data and code for our paper (Teickner, Gao, and Knorr 2022):

Henning Teickner, Chuanyu Gao, Klaus-Holger Knorr (2022). Electrochemical Properties of Peat Particulate Organic Matter on a Global Scale: Relation to Peat Chemistry and Degree of Decomposition. Global Biochemical Cycles. DOI: 10.1029/2021GB007160.

How to download or install

You can download the compendium as a zip from from this URL: https://doi.org/10.5281/zenodo.5792970

Or you can install this compendium as an R package, redoxpeat, from GitHub with:

remotes::install_github("henningte/redoxpeat")

How to use

Reproduce the analyses

To reproduce the analyses for the paper, open the Rstudio project included in this research compendium and run the Rmarkdown script in analysis/paper/001-paper-main.rmd. To also get the final reference list, run analysis/paper/007-latex.Rmd afterwards.

Running the whole script takes about two hours and occupies additional disk space of ~11 Gb.

Alternatively, the Dockerfile can be used to build a Docker image from which all analyses can be reproduced. The Dockerfile ensures that all required dependencies are installed (e.g. specific R packages; this is managed using the R package renv).

The Dockerfile provides instructions how to build a Docker image from the Dockerfile and how to run the image in a Docker container. It occupies disk space of ~7 Gb.

When the Docker image runs in a container, go to localhost:8787 in your Browser. You will find an RStudio interface where you can log in with username rstudio and password redoxpeat. Here you can find the Rmarkdown scripts (redoxpeat/analysis/paper/001-paper-main.rmd and analysis/paper/007-latex.Rmd) as described above.

Access to the R scripts

All R scripts used to produce the results for the analyses are in folder analysis/paper.

Access to the data

The compendium contains all data used during the analyses of the paper:

General information on peat samples: d
General information on sites: d_sites
Peat electron accepting capacity (EAC) and electron donating capacity (EDC) of suspensions of freeze dried peat: el_t0
Peat iron content and speciation (from acid extraction): fe_t0
Peat elemental contents (C, N) and isotope signatures ((\delta^{13})C, (\delta^{15})N): d_irms
Peat elemental contents from wavelength-dispersive X-ray fluorescence: d_xrf
Peat mid infrared spectra (not preprocessed): d_mir
EAC/EDC data extracted from Aeschbacher et al. (2012): aeschbacher2012
EAC/EDC data extracted from Tan et al. (2017): tan2017
EAC/EDC data extracted from Walpen et al. (2018): walpen2018

There is a full documentation available for each dataset. For example, to read the documentation for el_t0, type:

library(redoxpeat)
?el_t0

Access to models for predicting the EAC/EDC from mid infrared spectra

Functions to get predictions from the fitted models to predict the EAC/EDC from id infrared spectra are available via the R package irpeat (Teickner and Hodgkins 2021).

Detailed overview on the files contained in the compendium

README.md/README.Rmd: Readme for the compendium.
DESCRIPTION: The R package DESCRIPTION file for the compendium.
NAMESPACE: The R package NAMESPACE file for the compendium.
LICENSE.md: Details on the license for the code in the compendium.
CONTRIBUTING.md and CONDUCT.md: Files with information on how to contribute to the compendium.
Dockerfile: Dockerfile to build a Docker image for the compendium.
.Rbuildignore, .gitignore, .dockerignore: Files to ignore during R package building, to ignore by Git, and to ignore while bulding a Docker image, respectively.
configure/configure.win: Files created with rstantools in order to integrate Stan models into the R package.
renv.lock: renv lock file (Lists all R package dependencies and versions and can be used to restore the R package library using renv). renv.lock was created by running renv::snapshot() in the R package directory and it uses the information included in the DESCRIPTION file.
.Rprofile: Code to run upon project start.
R, man, inst, data-raw, data, src: Default folders for making the R package and integration with Stan via rstatools run.
analysis:
- data: Folder with the input data included in the R package (see scripts in data-raw).
- scripts:
  - figures: Folder with figures for the manuscript not derived from data (conceptual figures, etc.).
  - templates: Folder with LaTeX and Rmarkdown templates for the manuscript.
  - paper: Folder with template files and scripts to create the manuscript.
    - 000-preamble.tex: LaTeX setup for the manuscript.
    - 001-paper-main.Rmd: Main Rmarkdown file that represents the body of code and text of the manuscript. Run this to reproduce the manuscript.
    - 002-paper-sites.Rmd: Child Rmarkdown file of 001-paper-main.Rmd to process general information on the sampling sites.
    - 003-regression-elco.Rmd: Child Rmarkdown file of 001-paper-main.Rmd to compute the element ratio-based regression models to predict the EAC_POM and EDC_POM.
    - 004-regression-mirs.Rmd: Child Rmarkdown file of 001-paper-main.Rmd to compute the mid infrared spectra-based regression models to predict the EAC_POM and EDC_POM.
    - 005-paper-abstract-graphical.Rmd: Rmarkdown document used to create parts of the figures for the graphical abstract.
    - 006-paper-supplementary.Rmd: Rmarkdown file to be run from within 001-paper-main.Rmd. This script contains code and text for the supporting information.
    - 007-latex.Rmd: Rmarkdown file to be run after 001-paper-main.Rmd to generate the full reference lists in the rendered pdf file and clean up 006-paper-supplementary.tex.
    - references.bib: Literature references for the manuscript.
    - references_or.bib: Original Literature references for the manuscript. references.bib is created from references_or.bib by 007-latex.Rmd.
    - agujournal2018.cls: The Agu Journal class derived from the rticles package.
    - trackchanges.sty: The trackchanges TeX package needed to run the LaTeX template from rticles.
    - si.aux: Auxiliary file containing the definitions for the supplementary references in 001-paper-main.tex. This file is generated from 007-latex.Rmd.
    - 001-paper-main.tex/001-paper-main.pdf: The LaTeX/PDF document resulting from rendering 001-paper-main.Rmd.
    - 006-paper-supplementary.tex/006-paper-supplementary.pdf: The LaTeX/PDF document resulting from rendering 006-paper-supplementary.Rmd.

Acknowledgements

For their support during sample collection/provision, we would like to thank Svenja Agethen (DE), Werner Borken (SKY I-1, SKY I-6), Tanja Broder (PBR, SKY II, LT, MK), Mariusz Gałka (LT, MK), Liam Heffernan (LP, LB), Norbert Hölzel (KR, ISH), Annkathrain Hömberg (TX, DT), Tim Moore (MB), Sindy Wagner (BB), Tim-Martin Wertebach (KR, ISH), and Zhi-Guo Yu (TX, DT).
Analyses of this study were carried out in the laboratory of the Institute of Landscape Ecology. Svenja Agethen and Michael Sander provided analytical support. The assistance of Ulrike Berning-Mader, Madeleine Supper, Victoria Ratachin, and numerous student assistants is greatly acknowledged. We thank Dr. Hendrik Wetzel, Fraunhofer Institute for Applied Polymer Research, Dept. Starch Modification/Molecular Properties, Potsdam, Germany, for analysis of O and H. The workflow was reproduced by the Reproducible Research Support Service of the University of Münster. We thank two anonymous reviewers whose comments helped to improve the manuscript.
This Study was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) grant no. KN 929/12-1 to Klaus-Holger Knorr; Chuanyu Gao was supported by the Youth Innovation Promotion Association CAS (No. 2020235).

How to cite

Please cite this compendium as:

Henning Teickner, Chuanyu Gao, Klaus-Holger Knorr, (2022). Reproducible research compendium with R code and data for: ‘Electrochemical Properties of Peat Particulate Organic Matter on a Global Scale: Relation to Peat Chemistry and Degree of Decomposition’. Accessed 05 Feb 2022. Online at https://doi.org/10.5281/zenodo.5792970

Licenses

Text and figures: CC BY 4.0

Code: See the DESCRIPTION file

Data: CC-0 attribution requested in reuse

LaTeX templates: The LaTeX templates are derived from the rticles R package.

Contributions

We welcome contributions from everyone. Before you get started, please see our contributor guidelines. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

References/Sources

The format of this research compendium is inspired by Marwick (2017). The Rmarkdown template for the main article is from the rticles package (Allaire et al. 2020).

Aeschbacher, Michael, Cornelia Graf, René P. Schwarzenbach, and Michael Sander. 2012. “Antioxidant properties of humic substances.” Environmental science & technology 46 (9): 4916–25. https://doi.org/10.1021/es300039h.

Allaire, J. J., Yihui Xie, R. Foundation, Hadley Wickham, Journal of Statistical Software, Ramnath Vaidyanathan, Association for Computing Machinery, et al. 2020. “rticles: Article Formats for R Markdown.” https://github.com/rstudio/rticles.

Marwick, Ben. 2017. “Research compendium for the 1989 excavations at Madjedbebe rockshelter, NT, Australia.” figshare. https://doi.org/10.6084/m9.figshare.1297059.

Tan, Wenbing, Beidou Xi, Guoan Wang, Jie Jiang, Xiaosong He, Xuhui Mao, Rutai Gao, et al. 2017. “Increased Electron-Accepting and Decreased Electron-Donating Capacities of Soil Humic Substances in Response to Increasing Temperature.” Environmental science & technology 51 (6): 3176–86. https://doi.org/10.1021/acs.est.6b04131.

Teickner, Henning, Chuanyu Gao, and Klaus-Holger Knorr. 2022. “Electrochemical Properties of Peat Particulate Organic Matter on a Global Scale: Relation to Peat Chemistry and Degree of Decomposition.” Global Biogeochemical Cycles, February. https://doi.org/10.1029/2021GB007160.

Teickner, Henning, and Suzanne B. Hodgkins. 2021. “Irpeat: Simple Functions to Analyze Mid Infrared Spectra of Peat Samples.” Zenodo. https://doi.org/10.5281/ZENODO.5792919.

Walpen, Nicolas, Gordon J. Getzinger, Martin H. Schroth, and Michael Sander. 2018. “Electron-Donating Phenolic and Electron-Accepting Quinone Moieties in Peat Dissolved Organic Matter: Quantities and Redox Transformations in the Context of Peat Biogeochemistry.” Environmental science & technology 52 (9): 5236–45. https://doi.org/10.1021/acs.est.8b00594.

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redoxpeat's Introduction