inseasonDashR

inseasonDashR is an internal AFSC R package that provides a standardized, reusable framework for launching and running an in-season fisheries monitoring dashboard. The package wraps a Shiny application used to explore Alaska fisheries catch, composition, and CPUE data during the fishing year.

This repository is maintained under afsc-assessments/inseasonDashR and is intended for internal NOAA/AFSC analytical use.

⚠️ Data Access Notice
This package connects to password-protected AFSC and AKFIN databases. It is not intended for public deployment.

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What this package does

• Provides a single launch function (launch_inseason()) to start the in-season dashboard
• Encapsulates a Shiny app for:
  • Observer and EM catch maps (confidential and gridded)
  • Length-frequency visualization
  • Cumulative council catch tracking
  • Observer CPUE (weight and number)
• Handles secure database credentials via keyring
• Designed for local analyst use, not a centralized Shiny server

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Installation

From GitHub (internal use)

install.packages("remotes")
remotes::install_github("afsc-assessments/inseasonDashR")

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Running the dashboard

Once installed, launch the dashboard with:

library(inseasonDashboard)
launch_inseason()

This will start the Shiny application in your local R session.

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Credentials and database access

The dashboard requires access to the AFSC and AKFIN databases.

• Credentials are managed using the keyring package
• On first use, if credentials are not found, the app will prompt you to enter them
• Credentials are stored securely in your system credential store (not in the repository)

Required keyring services:

• afsc
• akfin

No passwords are written to disk or saved in plaintext.

Checking your keyring

You can verify which credentials are currently stored on your system using:

keyring::key_list("afsc")
keyring::key_list("akfin")

These commands list the usernames associated with each service without revealing passwords.
If nothing is returned, no credentials are stored for that service.

Adding credentials

If the required credentials are not found, the dashboard will prompt you to enter them when needed.
You may also add credentials manually in advance:

keyring::key_set_with_values(service="afsc", username = "<your_afsc_username>", password = "<your_afsc_password>")
keyring::key_set_with_values("akfin", username = "<your_akfin_username>", password = "<your_akfin_password>")

You will be prompted securely for the password, which will then be stored in your system keychain.

Removing or resetting credentials

If you need to remove stored credentials (for example, if a password has changed or the wrong username was saved), you can delete them explicitly.

To delete a specific credential:

keyring::key_delete("afsc",  "<your_afsc_username>")
keyring::key_delete("akfin", "<your_akfin_username>")

To remove all stored credentials for a service:

keyring::key_list("afsc")$username |>
  lapply(function(u) keyring::key_delete("afsc", u))

keyring::key_list("akfin")$username |>
  lapply(function(u) keyring::key_delete("akfin", u))

After deletion, the next dashboard run will prompt you to re-enter credentials.

Notes

• Credentials are stored per-user and per-machine
• Different analysts can use different database accounts without conflict
• Passwords are never printed, logged, or cached by the application

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Requirements

R packages

Core dependencies:

    data.table
    DBI
    odbc
    bslib
    keyring
    dplyr
    ggplot2
    scales
    shiny 
    stat
    rnaturalearth
    rnaturalearthdata

Optional (recommended):

shinycssloaders   # loading spinners

Install missing packages with:

install.packages(c(
  "shiny", "ggplot2", "bslib", "dplyr", "lubridate",
  "keyring", "shinycssloaders"
))

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Intended workflow

1. Install and load the package
2. Run launch_inseason()
3. Set species, dates, region, and gear filters
4. Click Pull data only to query databases
5. Click Render plots to generate visualizations
6. Use tabbed panels to explore results

This separation avoids unnecessary recomputation and supports iterative in-season analysis.

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Package structure (high level)

• R/ – helper functions for data access and plotting
• inst/shiny/ – Shiny application code
• launch_inseason() – wrapper to start the app

The Shiny app is intentionally bundled inside the package to ensure consistent behavior across analysts.

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Security and data sensitivity

• Point-level catch maps are considered confidential
• This package should only be used on approved systems
• Do not deploy to public Shiny servers without removing sensitive data access

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Disclaimer

This software is provided as-is for internal scientific and management support.
It is not an official NOAA product and carries no warranty or guarantee of support.

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Maintainer

Steve Barbeaux
Steve.barbeaux@noaa.gov

Questions, issues, or enhancements should be coordinated within the AFSC assessment community.