Fall Chinook Salmon Reorienting to Recovery Model

This model is adapted from the CVPIA SIT Fall Run Model for use in the Reorienting to Recovery Structured Decision Making process.

License

CC BY-NC-SA 4.0

IP-117068

Usage

Package Installation

The fallRunDSM package depends on a number of packages developed by the Reorienting to Recovery Organization. To install fallRunDSM and additional CVPIA-OSC packages use the remotes::install_github() function.

# install.packages("remotes")
remotes::install_github("reorienting-to-recovery/fallRunDSM")
remotes::install_github("reorienting-to-recovery/R2Rscenarios")

# optional - need if wanting to explore or modify flow, habitat, and temperature inputs
remotes::install_github("reorienting-to-recovery/DSMflow")
remotes::install_github("reorienting-to-recovery/DSMhabitat")
remotes::install_github("reorienting-to-recovery/DSMtemperature")

Run Model

The fall_run_model() is a Fall Run Chinook life cycle model used for Reorienting to Recovery Structured Decision Making Process. Running the model simulates Fall Run Chinook population dynamics across 31 watersheds in California over a 20 year period.

The following code runs the fall run model:

# seed the model
fall_run_seeds <- fall_run_model(mode = "seed")

# run the 20 year simulation
results <- fall_run_model(mode = "simulate",
                          seeds = fall_run_seeds)

Details on Supporting Data

Dependencies

The fallRunDSM package uses data from several other packages within the Reorienting to Recovery Organization. These relationships are visualized in the dependency graph below.

Flow, Habitat, and Temperature Data

All data used in the fallRunDSM is passed in as a argument to fall_run_model() from a fallRunDSM::r_to_r_baseline_params data list that is composed of data objects from the following packages:

  • Flow Data: View detailed documentation of flow data inputs at DSMflow. Flow inputs to the fallRunDSM are generated using CalSim II and CalSim 3 data.
  • Habitat Data: View detailed documentation of habitat data inputs at DSMhabitat. Modeling details for each stream can be viewed here.
  • Temperature Data: View detailed documentation of temperature data inputs at DSMtemperature. Modeling details for each stream can be viewed here.

Calibration Data

This model is calibrated using methodology and calibration data prepared for the CVPIA SIT model in the DSMCalibration package:

  1. GrandTab estimated escapement data for the years 1998-2017. The GrandTab data is prepared as DSMCalibrationData::grandtab_observed and is used to measure the difference between model predictions and observed escapements. Grandtab data is additionally prepared as DSMCalibrationData::grandtab_imputed and is used to calculate the number of juveniles during the 20 year simulation.

  2. Proxy years are used to select Habitat, Flow, and Temperature data for 1998-2017 to correspond with the years of GrandTab escapement data. The data inputs to the DSM are for years 1980-1999. We selected proxy years for 1998-2017 from the 1980-1999 model inputs by comparing the DWR water year indices.

For a detailed overview of the calibration process see the calibration markdown.