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lt_cn_review

This repository contains analysis code for the following publication:

Stocker et al., Empirical evidence and theoretical understanding of ecosystem carbon and nitrogen cycle interactions, (accepted for publication as a Tansley Review in New Phytologist, 6.9.2024)

Author: Benjamin Stocker, Uni Bern

It consists of different analyses, implemented in separate scripts and notebooks:

Workflow

DGVM analysis of land C sink trends

Using TRENDY v8 model outputs for land C sink trend analysis. Done by file vignettes/terr_sink_trends_gcb.Rmd.

Meta-analysis of ecosystem experiments

Using MESI data from eCO2 experiments (all variables): vignettes/analysis_mesi_co2.Rmd (previously vignettes/analysis_mesi.Rmd)

Using MESI + NutNet data from N-fert experiments (subset of variables): vignettes/analysis_mesi_nutnet_nfert.Rmd (previously vignettes/Nfert_merge_MESI_NutNet_eperkowski.Rmd)

Using Liang et al., 2020 data from N-fertilisation experiments (complementary subset of variables): vignettes/analysis_liang_nfert.Rmd

Combine plots for publication figure: vignettes/publication_figures_metaanalysis.Rmd

Field data analysis

Using data from Dong et al., 2022: vignettes/analysis_leafn_vcmax_field.Rmd

CN-model simulations and evaluation

CN-model simulations are done using a the CN-model, available in a separate GitHub repository (stineb/rsofun, branch cnmodel). Get this and build the rsofun R package to run rsofun for analyses in this repository.

Run scripts analysis/exp_co2_cnmodel.R and analysis/exp_nfert_cnmodel.R (both in this repository) to generate model outputs. Adjust the file to which outputs are written by modifying the commit code. The commit code should correspond to the latest commit of the rsofun repository, used for running the cnmodel simulations here. Instead of commit code, may also use tags from the rsofun repository.

Then, make a rough "ballpark comparison" of the outputs against data using vignettes/cnmodel_benchmark_ballpark.Rmd, and finally the model evaluation against MESI data using vignettes/comparison_mesi_cnmodel.Rmd.

Additional analyses

Experiment data by Evan Perkowski on (Vcmax, Jmax) ~ N-fert: vignettes/analysis_vcmaxjmax_nfert.Rmd

C:N by biome

[Not used for publication] Code from Huiying Xu (edited) available by analysis/pre_CN_global.R (loading file data/pre_CN_global.RData obtained by Huiying by email). See also this Notion page (internal-only).

Soil decomposition rate

[Not used for publication] Meta-analysis using data from Van Groenigen et al., 2014, see vignettes/analysis_vangroenigen.Rmd.

Publication figures

All publication figures are in fig_pub/ and are created by the following scripts, provided as RMarkdown files in the vignettes/ folder:

  • Fig. 1: sink_trend_trendy.pdf, Created by terr_sink_trends_gcb.Rmd

  • Fig. 2: diagram_cnreview.pdf, Created "by hand"

  • Fig. 3: combined_metaanalysis.pdf, created by publication_figures_metaanalysis.Rmd

  • Fig. 4: combined_metaanalysis_couplings.pdf, created by publication_figures_metaanalysis.Rmd

  • Fig. 5: coef_bars.pdf, created by analysis_leafn_vcmax_field.Rmd

  • Fig. 6: combined_metaanalysis_cnmodel.pdf, created by comparison_mesi_cnmodel.Rmd

The supporting information notes are created with Latex code (.tex files) in manuscript/.