Utility Functions for the Stox Project Within the Institute of Marine Research, Norway • RstoxUtils

Utility functions for the Stox Project. R package, updated 2026-05-19.

This package contains utility functions for stock assessment and data flow within the Institute of Marine Research (IMR). The package has two purposes: 1) To function as a showcase and developmental platform for functions that may be included in the future releases of the Stox Project. 2) To provide a collection of functions needed in the internal workflow of the Deep-sea species group at IMR.

Installation

The package requires the RstoxData Stox project package to function. These packages can be installed by following the links for each package or using the devtools package. The RstoxUtils package can be installed using devtools once all Stox project packages are installed correctly.

devtools::install_github("DeepWaterIMR/RstoxUtils", upgrade = "never")

The RstoxUtils uses multiple GIS packages developed for R. You may have to update these (Packages -> Update -> Select all -> Install updates in R Studio).

If the installation of a dependency fails, try installing those packages manually (using RStudio or install.packages).

Usage

See the website, function reference and specific articles for the use of the package:

The package also includes functions not covered by the vignettes above: processBioticFile() / processBioticFiles() for reading and merging NMD Biotic XML files into data.table objects; readFdirCodes() for updating the bundled FDIR species and gear code list; read.pos() for reading IMR vessel position tracking files; and extractLogbook() for legacy confidential logbook data from IMR servers. Reference data (cruise series, gear lists, taxa lists) can be refreshed using prepareCruiseSeriesList(), prepareGearList(), and prepareTaxaList(), which delegate to BioticExplorerServer.

Note that the strata functions from this package have been moved to the RstoxStrata package and the entire IMR Biotic database can be accessed using the BioticExplorerServer package.

Citation

When using use the package for stock assessment or scientific articles, please cite it:

citation("RstoxUtils")
#> To cite package 'RstoxUtils' in publications use:
#> 
#>   Vihtakari M (2026). _RstoxUtils: Utility Functions for the Stox
#>   Project Within the Institute of Marine Research, Norway_. R package
#>   version 0.5.0, <https://deepwaterimr.github.io/RstoxUtils>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {RstoxUtils: Utility Functions for the Stox Project Within the Institute of Marine Research, Norway},
#>     author = {Mikko Vihtakari},
#>     year = {2026},
#>     note = {R package version 0.5.0},
#>     url = {https://deepwaterimr.github.io/RstoxUtils},
#>   }

Contributions and contact information

Any contributions to the package are more than welcome. Please contact the package creator Mikko Vihtakari (mikko.vihtakari@hi.no) to discuss your ideas on improving the package or place a request in the issues section.