Reef Life Survey and Human Interest

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

Low human interest for the most at-risk reef fishes worldwide, by Mouquet N., Langlois J., Casajus C., Auber A., Flandrin U.,Guilhaumon F., Loiseau N., McLean M., Receveur A., Stuart Smith R.D. & Mouillot, D. submitted to Science Advances in July 2023.

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

• tables_figures/: contains the figures and tables produced for the article

• R/: contains R functions developed for this project

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

• make.R: main R script to run the entire project by calling each R script stored in the analyses/ folder

Workflow

Build species list

The script analysis/01_build_species_list/species_raw_list.R

• uses the species list from Langlois et al. (2022), checks the names and the presence on Fishbase
• creates the results/01_build_table/all_accepted_syn.csv table that contains all the accepted synonyms for the species.

Note: this table is created by combining the information recorded in the folder results/02_scrap/wta/ (not uploaded on GitHub). Contact us (nicolas.mouquet@cnrs.fr) to access these data.

Get data from Flickr, Wikipedia, NCBI, WOS & Scopus

The script analysis/02_scrap/Scrap_them_all.R retrieves data from different databases.

FLICKR

Queries were performed on species accepted name and synonyms.

We used the Flickr API in R with the R package httr. The time frame was 2010-01-01 to 2023-02-31.

WIKIPEDIA

Queries were performed on species accepted names only.

We recorded views for the 10 most-viewed languages (English, German, Spanish, Russian, Japanese, French, Polish, Dutch, Italian, and Portuguese) accounted for 81.3% of page views (Mittermeier et al. 2021).

We used the Wikimedia API with the R package pageviews. The time frame was 2015-10-01 2022-12-31.

NCBI

Queries were performed on species accepted name and synonyms.

We used the Entrez NCBI API for nucleotide and protein sequences with the R package rentrez.

WOS & SCOPUS

Queries were performed on species accepted name and synonyms.

We used the WOS Lite API with the R package rwoslite to retrieve number of references in Web of Science for each species and the metadata of each reference (titles, journal, etc.). When the title of the article was indexed in Scopus, we could get the number of citations for each article and the ASJC field code of the journal with the script analysis/02_scrap/scopus_refsall.R.

Get data from Twitter

The script analysis/02_scrap/twitter.R was used to retrieved data from Twitter.

Queries were performed on species accepted name and synonyms.

The scrap has been performed in 2019 with the built-in function get_twitter_intel(). Note that this function use the R package RSelenium but because Twitter often changes its credential, there is no guaranty that the function is still working.

Get data from FishBase

The script analysis/02_scrap/fishbase.R was used to retrieved data from FishBase.

Queries were performed on species accepted names only.

This script uses the functions species() and stocks() from the R package rfishbase.

Get data from GBIF

Scripts in analysis/03_gbif_homerange/ were used to 1) retrieve GBIF data using the R package rgbif and 2) compute species home range.

Get species evolutionary data

The script analysis/04_phylo/species_evol.R was used to retrieve species classification, phylogenetic tree and to compute evolutionary age.

Combine data

The script analysis/05_assemble_knowInt/assemble_knoint.R combines all human interest metrics and species attributes in a single file (results/05_assemlble_knowInt/05_Human_Interest_final_table.csv).

It produces the Figure S1

It computes the two dimensions of knowledge (academic knowledge and public interest) and produces the Figure 2A and the Figure 2B.

Analysis

The script analysis/06_main_analysis/main_analysis.R run the main analysis of this study. Details can be found in the section methods of the associated article.

It produces Figures 3-6, Figure S2 and tables results/06_main_analysis/pagel_acad.csv and results/06_main_analysis/pagel_public.csv.

Results

The file results/05_assemlble_knowInt/05_Human_Interest_final_table.csv contains all the information used in this study. You are welcome to use it by citing properly our work, but even more welcome to contact us (nicolas.mouquet@cnrs.fr) if you want to collaborate :smiley:

Some files were not uploaded on GitHub as they were too big. They can be provided on demand:

• results/02_scrap/wta/
• results/03_gbif/gbif/
• results/03_scrap/scholar/rawdata/

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 analysis/):

• Figure 1 has been produced with other means.

• Figures 2A, 2B were produced by 05_assemble_knowint/assemble_knoint.R

• Figures 3A, 3B were produced by 06_main_analysis/main_analysis.R

• Figure 4 was produced by 06_main_analysis/main_analysis.R. Note that the final figure was produced by other means.

• Figure 5 was produced by 06_main_analysis/main_analysis.R

• Figure 6 was produced by 06_main_analysis/main_analysis.R

• Table 1 has been produced by other means.

• Figure S1 was produced by 05_assemble_knowint/assemble_knoint.R

• Figure S2 was produced by 06_main_analysis/main_analysis.R

Credits

Drawings of fishes used in the figures were created with the platform DreamStudio using several images of each species as a baseline for training and using the keyword Fish, a stretch of 70% and 35 steps of variations. Resulting images are licensed under CC0 1.0). They are stored in data/images/.

References

Langlois J, Guilhaumon F, Baletaud F, Casajus N, de Almeida Braga C, Fleur V, Kulbicki M, Loiseau N, Mouillot D, Renoult JP, Stahl A, Stuart-Smith RD, Tribot A-S & Mouquet N (2022) The aesthetic value of reef fishes is globally mismatched to their conservation priorities. PLoS Biology, 20, e3001640. DOI: 10.1371/journal.pbio.3001640.

Mittermeier JC, Correia R, Grenyer R, Toivonen T & Roll U (2021) Using Wikipedia to measure public interest in biodiversity and conservation Conservation Biology, 35, 412-423. DOI: 10.1111/cobi.13702