This document descibes the source code and data in the repository related to:
Seibold et al (2021): Deadwood decomposition mediated by insects influences global carbon fluxes.
The folder contains RMarkdown files (.Rmd) and also the generated (“knitted”) .html files. In addition, necessary data (mostly GIS grids) are located in the data folder. During processing of the markdown files data products are stored in the products folder.
Statistical analysis of the experimental data. The file includes the data set from the experiment inline.
Includes the steps for the upscaling of results and the global estimates for C effects of deadwood decomposition. The auxiliary_calculations.R includes code we used for data preprocessing. However, it is not necessary to run this code to replicate the main results.
This scripts includes the sensitivity analysis reported in the paper.
The easiest way to work with the data set is to use RStudio, but the base R command prompt is possible too. We use markdown to provide both the code and results in a easy-to-read report format.
To execute the scripts, hit the “Knit” button in RStudio, or use the render function:
# run the script and produce Seibold_et_2021.html
rmarkdown::render("Seibold_et_al_2021.Rmd")Seibold_et_al_2021.rmd. This runs the statistical analysis of the experiment, and creates two output files data/ret_natural.rda and data/ret_dowel.rda (see Seibold_et_al_2021 for a detailed description)Seibold_et_al_2021_global_estimates.Rmd. This script uses the aforementioned files in order to create global predictions. The script uses GIS data sets located in the data folder. Running the script takes some minutes and produces output raster files (see below).Seibold_et_al__2021_sensitivity_analysis.Rmd. The script comprises the sensitivity analysis which uses data created in the previous steps. Note: Running the script takes a while (~ 3 hours).The processing steps for the evaluation of our model against independent empirical data from Harmon et al (2020) are shown in evaluation_dataset.R. The (edited) raw file in Excel format is in the data folder (13021_2019_136_MOESM2_ESM_edited.xlsx).
data/ret_natural.rda and data/ret_dowel.rda: R data file including the ret_n and ret_d dataframes.products/total_deadwood_2cm_tha.tif: Deadwood carbon pools (>2cm, Mg C/ha, 5 arc minute resolution)products/total_bl_2cm_tha.tif: Deadwood carbon pools, angiosperms (>2cm, Mg C/ha, 5 arc minute resolution)products/total_con_2cm_tha.tif: Deadwood carbon pools, gymnosperms (>2cm, Mg C/ha, 5 arc minute resolution)products/total_flux_t_ha.tif: Annual dead wood carbon loss (Mg C/ha, 5 arc minute resolution)products/total_uc_t_ha.tif: contribution of insects(Mg C/ha, 5 arc minute resolution, delta between uncaged and closed treatments)