SRJPEdata

This data package contains Juvenile, Adult and environmental data for each of the watersheds within the Spring Run Juvenile Production Estimate (SRJPE) Forecast model (Battle Creek, Butte Creek, Clear Creek, Deer Creek, Feather River, Mill Creek, Sacramento River, and the Yuba River). Historical data are used to train the model and seasonal updates are used to Forecast the JPE of a given season.

This data has been compiled from monitoring programs and gages and is stored in the SRJPE model database on Microsoft Azure. Biweekly, automated scripts update the database, pulling new datasets from CDEC & USGS gages and from EDI monitoring data packages. RST data is updated biweekly throughout the trapping season and Adult data is updated annual at the end of the adult monitoring season.

This data package will be updated in annually after adult datasets are finalized and then biweekly through the RST motioning season (Nov - June).

Installation 

# install.packages("remotes")
remotes::install_github("SRJPE/SRJPEdata")

Usage

This package provides datasets to the SRJPEmodelpackage.

# datasets within the package
data(package = 'SRJPEdata')

# explore package documentation
?SRJPEdata

Update Instructions

A GitHub Action (to run on a biweekly trigger) is currently in development. In the interim, data are updated by:

  • Check out a branch off of dev called data-update-month-year-number (e.g. data-update-jan-2027-1)
  • Run update_data.R
  • Run data-qc-visual-inspection.qmd for visual data checks
  • Update NEWS.md to include the appropriate version and add a description of the data added. New year of data is considered a major release.
  • Create PR to merge branch into dev branch which will trigger automated validation checks. Resolve any issues and merge to dev.
  • Submit a PR to merge branch to main which will also trigger automated validation checks.
  • Merge to main and tag as the appropriate data release (this should correspond to the package version)

Data Sources

Spring Run Monitoring Datasets

Adult and Juvenile monitoring datasets from 7 systems are compiled within this data package. All data can be found on the Environmental Data Initiatives Data Portal by searching “SR JPE.”

Acoustic Tagging Survival Data

NOAA collects acoustic tagging data as part of the Central Valley Enhanced Acoustic Tagging Project. This data package queries tagging data from many studies using the ERDDAP data server. We processed data, aggregating detection sites into 3 distinct locations and processing fish detection data to create a capture history for each fish.

Genetics Data

Genetics monitoring data is also included in this data package to prepare data inputs for a probabilistic length at date (PLAD) model. Genetics data is pulled directly from the SR JPE genetics database into this data package.

Explore datasets

Explore model datasets on the SRJPEdashboard shiny app. (Add link)