dia: Atlantic salmon Dam Impact Analysis (DIA) for R

The dia package is a collection of functions and datasets used to run the Dam Impact Analysis (DIA) for Atlantic salmon in the Penobscot River, Maine, USA.

Details

Additional examples and descriptions of the primary user-facing functions (run_dia() and run_dia_shiny()) can be found on the GitHub repository for the `dia` package: https://github.com/danStich/dia.

Functions called directly

The following functions can be called directly from dia.

run_dia: The primary user-facing function used to run the multi-generation DIA model for Atlantic salmon
run_dia_shiny: A `shiny` implementation of `run_dia()` with graphical user interface
run_one_gen: Run the DIA model for a single generation
get_dam_passage: Get flow-correlated downstream dam passage values and probability of using Stillwater Branch for smolts each year in `run_one_gen`
make_egg_to_smolt_survival: Simulate survival from egg to smolt stage for naturally produced smolts in `run_one_gen`
make_eggs_per_female: Simulate number of eggs per female each year in `run_one_gen`
make_inriver_s: Simulate natural, in-river survival per km for downstream migrating smolts in `run_one_gen`
make_marine_s: Simulate marine survival each year in `run_one_gen`
run_downstream_passage: Run the downstream smolt passage module in `run_one_gen`
run_inefficiency: Re-distribute adult upstream migrants following failed dam passage in `run_one_gen`
run_straying: Assign destination production units for adult returns in `run_one_gen`
run_upstream_passage: Function used to run the upstream passage module for adults in `run_one_gen`
smolt_stocking: Function used to distribute stocked smolts among production units in `run_one_gen`

Data

The following built-in datasets are included:

downstream_brownsmills: Flow-correlated estimates of smolt survival through Browns Mills Dam
downstream_frankfort: Flow-correlated estimates of smolt survival through Frankfort Dam
downstream_greatworks: Flow-correlated estimates of smolt survival through Great Works Dam
downstream_howland: Flow-correlated estimates of smolt survival through Howland Dam
downstream_lowell: Flow-correlated estimates of smolt survival through Lowell Dam
downstream_mattaceunk: Flow-correlated estimates of smolt survival through Mattaceunk Dam
downstream_medway: Flow-correlated estimates of smolt survival through Medway Dam
downstream_milford: Updated (2020) flow-correlated estimates of smolt survival through Milford Dam
downstream_milford_old: Original (2013) flow-correlated estimates of smolt survival through Milford Dam
downstream_milo: Flow-correlated estimates of smolt survival through Milo Dam
downstream_moosehead: Flow-correlated estimates of smolt survival through Moosehead Dam
downstream_orono: Updated (2020) flow-correlated estimates of smolt survival through Orono Dam
downstream_orono_old: Original (2013) flow-correlated estimates of smolt survival through Orono Dam
downstream_sebec: Flow-correlated estimates of smolt survival through Sebec Dam
downstream_stillwater: Updated (2020) flow-correlated estimates of smolt survival through Stillwater Dam
downstream_stillwater_old: Original (2013) flow-correlated estimates of smolt survival through Stillwater Dam
downstream_veazie: Flow-correlated estimates of smolt survival through Veazie Dam
downstream_westenfield: Flow-correlated estimates of smolt survival through West Enfield Dam
in_river_m: Cumulative frequency distribution of in-river mortality per km for smolts
life_stage_survival: Distributional parameters for year-specific number of eggs produced per female, egg-to-smolt survival rate, in-river mortality rate, and marine survival rate
n_dams: Number of dams passed by smolts in each production unit and migration route
production_units: Division of Penobscot River watershed into sections, or Production Units (PUs)
stillwater_use: Updated (2020) probability of smolts using Stillwater Branch for outmigration given discharge
stillwater_use_old: Original (2013) probability of smolts using Stillwater Branch for outmigration given discharge
stocking_default: Default stocking proportions of smolts by PU
straying_locations: Straying locations of adult Atlantic salmon based on behavioral patterns
straying_matrix: Numeric columns only from `straying_locations`
upstream_inefficiency: Destination PUs and probabilities for adults that fail to pass dams
inefficiency_matrix: Columns 5 through 20 from `upstream_inefficiency`

Author

Maintainer: Daniel S. Stich daniel.stich@oneonta.edu (ORCID)

Authors:

Julie L. Nieland
Timothy F. Sheehan

dia: Atlantic salmon Dam Impact Analysis (DIA) for R

Details

Functions called directly

Data

See also

Author