Spatial insurance of distinct ecological functions

Research compendium to reproduce analyses and figures of the following article:

Spatial insurance of distinct ecological functions, by Mouquet N., Mahaut, L., Thuiller, T., Auber, A., Casajus N., Enquist B.J., Gaüzère P., Loiseau N., Mouillot D., Munoz F., Villéger S. & Violle C. Ecology Letters

Content

This repository is structured as follow:

• data/: contains data required to reproduce figures and tables

• analysis/: contains subfolders organized by theme. Each folder contains R scripts to run specific analysis

• results/: follows the structure of analyses. Contains intermediate results and the numeric results used to produce the figures

• outputs/: contains the figures produced for the article

• R/: contains R functions developed for this project

• DESCRIPTION: contains project metadata (author, date, dependencies, etc.)

Workflow

The script analysis/01_Simulations.R compute functional insurance with simulated metacommunities.

The script analysis/02_Divgrass_alps.R compute functional insurance for alpine herbaceous communities.

The script analysis/03_Birds_Global.R compute functional insurance for birds worldwide.

Big files

Some files were not uploaded to GitHub due to their large size. They are available upon request:

- `results/wdpa_I_union.RData`
- `results/wdpa_I_II_union.RData`
- `results/wdpa_I_IV_union.RData`
- `data/BIG_FILES/`

Figures

Figures are stored in outputs/.

The following Figures and Tables can be reproduced with the script indicated in brackets (all in analysis/):

• Figure 1 has been produced with other means.

• Figure 2 has been produced with other means.

• Fig_3, was produced by 01_Simulations.R

• Fig_4b, Fig_4c, Fig_4d were produced by 02_Divgrass_alps.R. Note that the Fig_4a is produced with tmap and pasted into the final figure.

• Fig_5a_1, Fig_5a_2, Fig_5a_3, Fig_5b, Fig_5c were produced by 03_Birds_Global.R.

• Fig_6a, Fig_6b, were produced by 03_Birds_Global.R

• S1_Fig_1 and S1_Fig_2 were produced by 01_Simulations.R

• S2_Fig_1, S2_Fig_2, S2_Fig_3, S2_Fig_4 were produced by 02_Divgrass_alps

• S3_Fig_1, S3_Fig_2,S3_Fig_3,S3_Fig_4, S3_Fig_5, S3_Fig_6, S3_Fig_7 were produced by 03_Birds_Global.R