README.md

In nmouquet/RLS_AESTHE: Research Compendium

RLS_AESTHE

Research compendium to reproduce analyses and figures of the article:

Langlois J, Guilhaumon F, Baletaud F, Casajus N, De Almeida Braga C, Fleure V, Kulbicki K, Loiseau N, Mouillot D, Renoult JP, Stahl A, Stuart Smith RD, Tribot AS & N, Mouquet (2022) The aesthetic value of reef fishes is globally mismatched to their conservation priorities. PLoS Biol 20(6): e3001640. doi:10.1371/journal.pbio.3001640

http://nicolasmouquet.free.fr/pdf/Langlois_et_al_2022_Plos_Biology.htm

General

This repository is structured as follow:

• data/: contains data required to reproduce figures and tables
• R/: contains R functions developed for this project
• analyses/: contains folders 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.

Storage

Not all fish images are free of copyrights. We thus provide an example sample of images in data/example_images/. The codes calling all images will show errors but you can use the example images set to run them. See Extended Table 1 (provided as a supplementary information) for copyrights.

The script analyses/elo/01_group_effect.R normally generates and use a large file: 01_first_model.RData. It takes several days to generate this file but you can instead download it from https://zenodo.org/record/6325532#.YiDG99_jLoA (see lines 257-258 of script).

File with all results

The file results/conservation/01_sptable_all.csv contains all the information used and produced in this study at the species level for the 2,415 species concerned. You are welcome to use it by citing properly our work, but even more welcome to contact us ([e-mail]) if you want to collaborate :smiley:

Figures and Tables

Figures and Tables will be stored in figures_tables/.

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

• Figure 1b (deep/06_prediction_performances.R)
• Figure 2a (features/features_analysis.R)
• Figure 2b (features/features_analysis.R)
• Figure 3 (biodiversity/01_phylogeny.R must be run to have data for panel a and biodiversity/02_functional_div.R generates data for panel b and the entire figure)
• Figure 4 (biodiversity/01_phylogeny.R produces the tree)
• Figure 5 (conservation/01_iucn_status.R)
• Figure S1 A (features/cluster.R)
• Figure S1 B (features/cluster.R)
• Figure S1 C modified from Wikipedia source (see legend)
• Figure S1 D (features/momocs.R)
• Figure S1 E (features/features_analysis.R)
• Figure S1 G (elo/01_group_effect.R)
• Figure S1 H (elo/01_group_effect.R)
• Figure S1 I (elo/02_elo_scores.R)
• Figure S1 J (elo/02_elo_scores.R)
• Figure S1 K (deep/05_size_effect.R)
• Figure S1 M (deep/06_prediction_performances.R)
• Figure S1 N (biodiversity/01_phylogeny.R)
• Figure S1 O (biodiversity/01_phylogeny.R)
• Figure S1 P (biodiversity/02_functional_div.R)
• Figure S1 Q (deep/03_aggregate_species_level.R)
• Figure S1 R (deep/03_aggregate_species_level.R)
• Figure S1 S (biodiversity/02_functional_div.R)

• Figure S1 T (conservation/01_conservation_status.R)

• Table S1 A (elo/01_group_effect.R)

• Table S1 B (biodiversity/01_phylogeny.R)

• Table S1 D (biodiversity/02_functional_div.R)

• Extended Table 2 (deep/03_aggregate_species_level.R)

Usage

Clone the repository and run this command in R/RStudio:

source("make.R")

All required packages will be installed (if necessary) and loaded.

:boom: WARNING: running make.R calls all the scripts and takes days so if you want to work on one or a few scripts, you should run lines 17-42 of make.R and then go to the other script.

Enjoy!

nmouquet/RLS_AESTHE documentation built on May 9, 2023, 5:45 p.m.