R2Rscenario

This package provides tools for creating valid scenario input data to run with the fallRunDSM, winterRunDSM, or springRunDSM life cycle models.

Installation

This package can be installed using the following commands:

# install.packages("remotes")
remotes::install_github("Reorienting-to-Recovery/DSMscenario")

Usage

Building a scenario

Scenarios can be defined within a dataframe and built using the load_scenario function. Each row within the dataframe represents one unique scenario action for a given watershed, for a period of years and number of units of effort.

Actions are defined below:

Habitat

First define flow-to-habitat relationship:

  • 1: Baseline Habitat
  • 2: Theoretical Max Habitat
  • 3: Healthy Rivers & Landscapes (HRL) habitat

Layer on additional actions

  • 4: Add Rice Lands Salmon Rearing Practice Standard
  • 5: Increase prey density
  • 6: Decrease predation (scale contact points by 1/3)
  • 7: Add 20,000 acres of fish food production (HRL)
  • 8: Remove predation contact points (HRL)
  • 27: Add effects of spring run weir on fall run
  • 28: Add effects of above-dam spring run habitat on fall run
  • 29: Add San Joaquin floodplain habitat

Harvest

  • 10: Baseline Harvest
  • 11: Tribal harvest only
  • 12: In river harvest only
  • 13: Ocean harvest only
  • 14: Intelligent CRR harvest
  • 15: Intelligent habitat harvest
  • 16: Harvest only hatchery fish (ocean)
  • 17: Harvest only hatchery fish (tributary)
  • 25: No harvest of dry year cohort

Hatchery

  • 18: Baseline hatchery
  • 19: Only terminal hatchery / outplanting
  • 20: Phased hatcheries
  • 26: Install weir at hatchery

Hydrology

  • 22: Use 2019 BiOp hydrology
  • 23: Use Functional Flow (FF) hydrology
  • 24: Use HRL hydrology

Customizing actions

Some actions allow the user to specify the watershed and/or year for which you want the action to be implemented. Please refer to the more in-depth action documentation to see where this is possible:

Example: Kitchen Sink (Blended Scenario)

For more information run ?load_scenario in the console.

The following example builds the kitchen sink scenario:

Habitat

  • 2: Theoretical Max Habitat in all locations
  • 5: Increase prey density in all locations

Harvest

  • 14: Intelligent CRR harvest
  • 16: Harvest only hatchery fish (ocean)

Hatchery

  • 19: Only terminal hatchery / outplanting

Hydrology

  • 23: Use FF hydrology on the Sacramento River
scenario_df <- data.frame(
  watershed = c(rep("All", 6), "Sacramento River"),
  action = c(2, 5, 6, 14, 16, 19, 23),
  years =  rep("All", 7))

scenario <- load_scenario(scenario = scenario_df,
                          species = R2Rscenario::species$FALL_RUN,
                          params = fallRunDSM::r_to_r_baseline_params)

Helper Datasets

See reference, datasets, for a full list of helper datasets.

For a list of proper watershed labels see: R2Rscenario::watershed_labels

The minimum decay rates for each watershed are stored in R2Rscenario::spawn_decay_rate and R2Rscenario::rear_decay_rate

Regulated watersheds are stored in DSMscenario::regulated_watersheds and SIT watershed groupings are stored in R2Rscenario::watershed_groups

Dependencies

The R2Rscenario package uses data from several packages within the Reorienting To Recovery Organization. These relationships are visualized in the dependency graph below.