leafnp

This repository contains R code for all analyses and modelling used for the following article:

Di Tian, Zhengbing Yan, Bernhard Schmid, Jens Kattge, Jingyun Fang, Benjamin D. Stocker: Environmental versus phylogenetic controls on leaf nitrogen and phosphorous concentrations of terrestrial plants. (in review)

Preparation

The analysis uses the published dataset of leaf N, P, and N:P concentrations by Tian et al (2019), complemented with environmental covariate data for the present analysis. The complemented dataset and code for generating it in contained in the dataset repository leafnp_data.

Download the file and adjust the paths to your local copy of the data file in vignettes (vignettes/*.Rmd) of this repository.

Workflow

To reproduce the analysis, obtain the data file from above-mentioned source. Then, run code contained in the following files

1. Data preparation
   • Code: vignettes/prepare_data.Rmd.
   • Reads local file leafnp_data_covariates_20210702.csv (not in this repository).
   • Writes file data/dfs_leafnp_20210729.rds.
2. Feature elimination: The (computationally costly) job is performed in a High Performance Computing environment.
   • Code: src/submit_feature_elimination_leafnp.sh and analysis/feature_elimination_leafnp.R run and evaluate jobs.
   • Outputs from jobs are collected, analysed and visualised by vignettes/feature_elimination_leafnp.Rmd.
   • "Intermediate data files" created by the feature elimination and used in vignettes/feature_elimination_leafnp.Rmd are contained in this repository.
   • Model coefficients from LMMs, shown Fig. 2 (d,e,f) are created in vignettes/model_fitting.Rmd.
3. Model fitting:
   • Code: vignettes/model_fitting.Rmd
   • Outputs:
     • Fig. 3 in Tian et al. The figure file is contained in this repository (fig/bars_model_fitting.pdf).
     • Fig. 2 in Tian et al. The figure file is contained in this repository (fig/bars_fe_tvals.pdf). This requires vignettes/feature_elimination_leafnp.Rmd to be run first.
4. Trait gradient analysis:
   • Code: vignettes/traitgradient.Rmd
   • Outputs: Fig. 4 in Tian et al. The figure file is contained in this repository (fig/tga_log_all.pdf).
5. Demo of trait gradient analysis
   • Code: vignettes/tga_hypotheses.qmd
   • Outputs: vignettes/tga_hypotheses.pdf. This document is submitted as supplementary information to the article Tian et al. (in review).
6. Linear mixed effects model fitting explorations
   • Code: vignettes/leafnp_fitting_order.Rmd
   • Outputs: a html document showing results of the explorations. Results were used in the discussion of the article Tian et al. (in review).

Note: Published figures can be re-created directly using intermediate data objects stored in data/data_published_figures.

Repository structure

Folder analysis

Contains scripts that can be ignored.

Folder data

Contains data files produced by code of this repository.

Folder vignettes

Contains implementations of analyses used for the study Tian et al. (in review).

References

Tian, D., Kattge, J., Chen, Y., Han, W., Luo, Y., He, J., Hu, H., Tang, Z., Ma, S., Yan, Z., Lin, Q., Schmid, B., and Fang, J.: A global database of paired leaf nitrogen and phosphorus concentrations of terrestrial plants, Ecology, 100, e02812, https://doi.org/10.1002/ecy.2812, 2019.

Di Tian, Zhengbing Yan, Bernhard Schmid, Jens Kattge, Jingyun Fang, Benjamin D. Stocker: Environmental versus phylogenetic controls on leaf nitrogen and phosphorous concentrations of terrestrial plants. (in review)