Laksetap is a R Golem Shiny App for reporting salmon and rainbow trout losses in Norway.
It is published at apps.vetinst.no/laksetap.
The app runs with dummy data locally without the need to be connected to
VI’s server. The dummy data is distributed as part of the package in
inst/extdata. For anyone interested in implementing the
app with their own data, running the app from
dev/run_dev.R will load the app with the dummy data.
The dev folder also contains definitions of the data sets and scripts
to test the visualization functions with the dummy data.
Since the app is built for reporting fish mortality in Norway, it assumes that the species displayed are salmon and rainbow trout. However, the available data for these species may differ in terms of aggregation levels. Additionally, Norway’s geographical areas for displaying this data are also assumed: production area as “Produksjonsområde”, county as “Fylke”, and country.
Because of this, the app has choices (adjustable in the config) for
species and geo_group in mod_top_bar.R and we have implemented a
logic about adjusting the UI when switching between them. This could be
improved, or generalized so any species can be displayed in the app, but
for the time being this remains like so.
The code that produces the dummy data also follows this assumption and does not generate data for other geographical levels than country for rainbow trout.
All of the other inputs are read from the data, such as number of year, areas for which data are available, etc.
The app can be configured and translated to different languages. Files
managing this are passed as golem options in run_app.R.
The inst/app/www/config.json contains paths
to images, favicons, social media previews, and similar. Additional
configuration that lives within the code is the tracking script in
tag_manager in fct_meta.R. This needs to be removed, or adjusted if
you are using the app with your data.
All labels used in the app are in
inst/app/www/labels_nb_no.json. An
English translation of the .json is also provided. The long form text
(i.e. more than a few words) is in separate .md files
inst/app/www/.
The code in fct_data.R also contains a bit of locale specific code,
like for example labeling of data for
"dead", "discarded", "escaped", "other" to
"Døde", "Utkast", "Rømt", "Annet". This could easily be overlooked,
but the idea here is to be able to use the data functions both in the
app, and in an interactive R session. One should be aware of this when
working with the data and app.
We provide a mortality calculator in R and Excel as part of the repository, and downloadable from the app. The calculator itself is not part of the app UI because we don’t want to handle company or farm level data in the app and potentially run into legal or security issues. The calculator uses the same approach to calculate fish mortality that is used in Norwegian Veterinary Institute’s Fish Health Report.
Running the app with docker should work:
docker build -f Dockerfile_base --progress=plain -t laksetap_base .
docker build -f Dockerfile --progress=plain -t laksetap:latest .
docker run -p 80:80 laksetap:latest
# then go to 127.0.0.1:80
To cite package ‘laksetap’ in publications use:
Nakov N, Silva De Oliveira V (2025). laksetap: A Shiny app for reporting salmon and rainbow trout losses in Norway. R package version 1.1.0, https://github.com/NorwegianVeterinaryInstitute/laksetap.
A BibTeX entry for LaTeX users is
@Manual{,
title = {laksetap: A Shiny app for reporting salmon and rainbow trout losses in
Norway},
author = {Novica Nakov and Victor Henrique {Silva De Oliveira}},
year = {2025},
note = {R package version 1.1.0},
url = {https://github.com/NorwegianVeterinaryInstitute/laksetap},
}