This repository contains the FishGlob database, including the methods to load, clean, and process the public bottom trawl surveys in it. The database is described in the manuscript, "An integrated database of fish biodiversity sampled with scientific bottom trawl surveys" by Aurore A. Maureaud, Juliano Palacios-Abrantes, Zoë Kitchel, Laura Mannocci, Malin L. Pinsky, Alexa Fredston, Esther Beukhof, Daniel L. Forrest, Romain Frelat, Maria L.D. Palomares, Laurene Pecuchet, James T. Thorson, P. Daniël van Denderen, and Bastien Mérigot.
This database is a product of the CESAB working group, FishGlob: Fish biodiversity under global change – a worldwide assessment from scientific trawl surveys.
Main contacts: Aurore A. Maureaud, Juliano Palacios-Abrantes, Zoë J. Kitchel, and Malin L. Pinsky
Anyone interested in reusing this data or its outputs should read this readme as well as our Data Disclaimer in full.
This work is licensed under a Creative Commons Attribution 4.0 International License.
Data processing and cleaning is done on a per survey basis unless formats are similar across a group of surveys. The current repository can process 29 scientific bottom-trawl surveys, according to the following steps.
Steps
Data standardization and flags are done on a per survey basis and per survey_unit basis (integrating seasons and quarters). Flags are performed both on the temporal occurrence of taxa and the spatio-temporal sampling footprint according to the following steps.
Steps
Options Users can either use the single survey data products in outputs/Cleaned_data/ and work with survey .RData files including flags or not (inclusion of flags is specified by XX_std_clean.RData), or generate their own compiled version of the data by running the cleaning_codes/merge.R which will write local versions of the database in outputs/Compiled_data/
Contributors to code
Our full citation policy is described in the Fishglob_data disclaimer. Briefly, users should cite Maureaud et al. 2021, Maureaud et al. 2024, and relevant primary SBTS sources referenced in the FISHGLOB data files and source data tables of the two Maureaud et al. papers. Users integrating multiple surveys are encouraged to cite additional studies on data integration.
5/06/2024: A warning about CSVs Datasets are available for download in outputs/Cleaned_data/ as .Rdata files. We do not recommend saving FishGlob data in .csv format. For at least some surveys, the
haul_id
column is composed of a long string of numerics, which is incorrectly rounded if loaded from a .csv programmatically in R (withread_csv()
orread.csv()
). As documented in issue #49, this leads to errors in thehaul_id
column, and may occur regardless of the "class" assigned to this column. The most robust way to prevent this error is to write to / read from other data types such as .Rdata or .rds. Packages exist for users to import these into Python and other programming languages.23/11/2023: FishGlob_data v2.0
05/09/2023: Norwegian survey is erroneous and will be replaced with a Barents Sea centered survey over 2004-onwards which will change the spatio-temporal coverage of the region (coordinated by Laurene Pecuchet with IMR), see issue #29