This repository contains the code for the simulations and analysis for the article by Hagan, Vanschoenwinkel and Gamfeldt

preliminary citation:

We should not necessarily expect positive relationships between biodiversity and ecosystem functioning in observational data (James G. Hagan, Bram Vanschoenwinkel & Lars Gamfeldt, Ecology Letters (accepted))

To reproduce the analysis reported in the paper, start by downloading all the scripts in the repository and running these scripts:

• BIODEPTH_Jena_data_preparation.R
• Jena_data_preparation.R
• LTER_kelp_data_preparation

These scripts directly download the data and output cleaned versions of the data into a newly created folder called: analysis_data

Next, run the script:

• stachova_leps_model_data_preparation.R

This script calls the function from stachova_leps_model.R and runs nine different simulated biodiversity experiments with varying levels of average interspecific competition. The resulting dataset is saved into the analysis_data folder. Note that this is computationally intensive and can take 10-20 minutes to run.

Once these four scripts have been run, you can run the following scripts to create fig. 2, 3 and 5, and fig. S1, S2, S3, S4:

• ms_fig_2_fig_S1_S2_S4_analysis.R
• ms_fig_3_fig_S3_analysis.R
• ms_fig_5_analysis.R

To reproduce fig. 4 and fig. S2, you need to run the script:

• ms_fig_4_fig_S5_analysis.R

This script loads in data from van der Plas (2019)'s systematic review that we added spatial extent information to. The data is downloaded directly from the script via a figshare link from this DOI: https://doi.org/10.6084/m9.figshare.15178248.v1.

For reference, the script called: van_der_plas_review_create_data_template.R was used to take the raw file posted by van der Plas (2019, Biological Reviews) and create a template from which we could add the spatial extent information.

Instruction to download a Github repo

with git

in a Unix Terminal (e.g. bash):

cd path/to/local/folder

(on your computer - the folder were you want the repository to live) command on Windows might differ.

git clone https://github.com/haganjam/bef_experiment_observational.git

This should download the repository directory.

without git

If you don't have git installed, you can download the repository as zip file and save it locally.

• Clone or download (green button top right)
• Download Zip

then save and extract the zip where you want the directory to be saved on your computer.