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("CVPIA-OSC/DSMscenario")Usage
Full Scenario Example
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:
- 1: Do nothing
- 2: Add 1 acre of spawning habitat
- 3: Add 2 acres of inchannel rearing habitat
- 4: Add 3 acres of floodplain rearing habitat
- 5: Increase rearing survival by 5%
For more information run ?load_scenario in the console.
The following example builds a scenario of adding inchannel rearing to the following watersheds for the fall run life cycle model:
- 2 units of effort (4 acres) applied in Upper Sacramento River for the years 1980-1989
- 1 unit of effort (2 acres) applied in Upper Sacramento River for the years 1990-1999
- 1 unit of effort (2 acres) applied in American River for the years 1980-1989
- 1 unit of effort (2 acres) applied in Feather River for the years 1980-1989
- 1 unit of effort (2 acres) applied in Lower-mid Sacramento River for the years 1980-1989
- 1 unit of effort (2 acres) applied in Battle Creek for the years 1990-1999
- 1 unit of effort (2 acres) applied in Butte Creek for the years 1990-1999
- 1 unit of effort (2 acres) applied in Deer Creek for the years 1990-1999
- 1 unit of effort (2 acres) applied in Stanislaus River for the years 1990-1999
habitats <- list(
spawning_habitat = fallRunDSM::params$spawning_habitat,
inchannel_habitat_fry = fallRunDSM::params$inchannel_habitat_fry,
inchannel_habitat_juvenile = fallRunDSM::params$inchannel_habitat_juvenile,
floodplain_habitat = fallRunDSM::params$floodplain_habitat,
weeks_flooded = fallRunDSM::params$weeks_flooded
)
scenario_df <- data.frame(
watershed = c("Upper Sacramento River", "Upper Sacramento River",
"American River", "Feather River", "Lower-mid Sacramento River",
"Battle Creek", "Butte Creek", "Deer Creek", "Stanislaus River"),
action = c(3, 3, 3, 3, 3, 3, 3, 3, 3),
start_year = c(1980, 1990, 1980, 1980, 1980, 1990, 1990, 1990, 1990),
end_year = c(1989, 1999, 1989, 1989, 1989, 1999, 1999, 1999, 1999),
units_of_effort = c(2, 1, 1, 1, 1, 1, 1, 1, 1))
scenario <- get_action_matrices(scenario_df)
scenario <- load_scenario(scenario = scenario,
species = DSMscenario::species$FALL_RUN,
habitat_inputs = habitats)Helper Datasets
For a full list of proper watershed labels see: DSMscenario::watershed_labels
The list DSMscenario::species can be used to provide appropriate values to the species argument to the load_scenario function. For example, DSMscenario::species$FALL_RUN.
The minimum decay rates for each watershed are stored in DSMscenario::spawn_decay_rate and DSMscenario::rear_decay_rate
Regulated watersheds are stored in DSMscenario::regulated_watersheds and SIT watershed groupings are stored in DSMscenario::watershed_groups
Dependencies
The DSMscenario package uses data from several other packages within the CVPIA Open Science Collaborative. These relationships are visualized in the dependency graph below.
