Makes working with ICES DATRAS extra easy!
DATRASextra is an R package that extends the functionality of the ICES DATRAS database and the DTU Aqua DATRAS R package, providing practical tools for downloading, cleaning, standardising, analysing, and visualising bottom-trawl survey data.
Key features include:
- Streamlined workflows for downloading, cleaning, and preparing DATRAS data
- Calculation and visualisation of swept area, catch rates, biomass, and numbers-at-length for custom length classes
- Support for reproducing key components of the FishGlob data-processing workflow
- Tools for species harmonisation, taxonomic standardisation, and exploratory diagnostics
DATRASextra is currently under active
development and some functions or workflows may change in future
versions. Please report bugs, issues, or feature requests here:
https://github.com/tokami/DATRASextra/issues
DATRASextra can be installed from GitHub:
## Install the package
remotes::install_github("tokami/DATRASextra")Or the development version:
## Install the package
remotes::install_github("tokami/DATRASextra", ref = "dev")Note that if you want to install vignettes locally, you have to use an extra argument:
## Install the package with vignettes
remotes::install_github("tokami/DATRASextra", build_vignettes = TRUE)DATRASextra provides a set of powerful functions that guide you through a typical workflow with the ICES DATRAS database: from discovering available surveys, to downloading, cleaning and checking the data, and finally making quick plots of survey coverage and hauls. The table below summarises the main user-facing functions.
| Function | Description |
|---|---|
list_surveys() |
List available surveys in the ICES DATRAS database. |
plot_datras_overview() |
Plot haul locations |
download_datras() |
Download the full or filtered subset of the DATRAS database. |
read_datras() |
Read DATRAS data into R. |
clean_datras() |
Clean and harmonise DATRAS data. |
check_outliers() |
Flag (and remove) hauls with invalid or extreme values. |
prune_datras() |
Prune DATRAS data by removing or filtering problematic records. |
add_swept_area() |
Calculate swept area per haul using gear-specific median values by gear type. |
check_lengths() |
Check length information and identify suspicious length distributions. |
add_numbers_at_length() |
Calculate the numbers by specified length classes and add it to the HH data set. |
add_total_numbers_by_haul() |
Calculate total numbers by haul and add it to the HH data set. |
check_weights() |
Check weight information and length–weight consistency. |
add_weight_at_length() |
Convert the numbers at length classes to weight at length classes and add it to the HH data set. |
add_total_weight_by_haul() |
Calculate total weight by haul and add it to the HH data set. |
The best introduction to DATRASextra is the tutorial vignette, which walks through a complete workflow: downloading data from the DATRAS database, performing recommended quality checks and data processing steps, and transforming survey observations into standardised numbers and biomass by species, haul, and length class for use in abundance and biomass index calculations.
The tutorial is available on the package website under Articles → Getting started: https://tokami.github.io/DATRASextra/articles/datrasextra-tutorial.html
If you installed the package with build_vignettes = TRUE, you can also
open the tutorial directly from R:
vignette("datrasextra-tutorial")All functions in DATRASextra are documented and include examples. Help
pages can be accessed using help() or ?, for example:
?check_lengthsAdditional tutorials and worked examples are available on the package website, demonstrating common workflows and applications of DATRAS survey data: https://tokami.github.io/DATRASextra/
If your question is not answered by the package documentation or the
pkgdown site, you are welcome to contact the maintainer, Tobias
Mildenberger. If you find a bug or
would like to request a feature, please open an issue on GitHub with:
https://github.com/tokami/DATRASextra/issues/new/choose
To see how to cite DATRASextra in your work, run:
citation("DATRASextra")DATRASextra was originally developed to extend the functionality of the R package DATRAS, which provides tools for accessing and working with ICES DATRAS survey data. While DATRASextra continues to build on some of this functionality, it has evolved into a broader framework for downloading, managing, processing, and analysing DATRAS data, with an increasing share of functionality implemented directly within the package.
An alternative R package for accessing DATRAS data is icesDatras, which is maintained by ICES and provides a direct interface to the DATRAS database.
The development of DATRASextra was funded by the European Maritime and Fisheries Fund (EMFF) through the project: FISHMAP - FISH distribution and its role in fisheries Management Advice and marine spatial Planning (EFMVB-23-0031), which is co-financed by the EU through the Danish Maritime, Fisheries and Aquaculture Fund.
