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")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. |
A good way to start working with DATRASextra is the tutorial vignette. You can access it with:
vignette("tutorial")The tutorial and other vignettes guide you through the full workflow: from downloading the complete DATRAS database (or selected subsets), through processing and cleaning the data following recommended good-practice guidelines, to calculating swept-area indices and biomass estimates per species and haul.
All functions in DATRASextra are documented and include example code.
You can access the help pages with help(function_name) or
?function_name, for example:
?check_lengthsThe package also includes several vignettes and articles that demonstrate common workflows and show how to use DATRAS data for your own research questions. To see all available vignettes, use:
browseVignettes("DATRASextra")An overview of pkgdown articles is available at: 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: https://github.com/tokami/DATRASextra/issues
To see how to cite DATRASextra in your work, run:
citation("DATRASextra")The foundation of DATRASextra is the R package DATRAS, which provides the core tools for downloading and pre-processing DATRAS data.
An alternative R package for working with the DATRAS database is icesDatras, maintained by ICES.
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.
