dia: dia: Atlantic salmon Dam Impact Analysis (DIA) for R
In danStich/dia: R package for Atlantic salmon Dam Impact Analysis (DIA) model
dia R Documentation
dia: Atlantic salmon Dam Impact Analysis (DIA) for R
Description
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_diaThe primary user-facing function used to run the multi-generation DIA model for Atlantic salmon
run_dia_shinyA 'shiny' implementation of 'run_dia()' with graphical user interface
run_one_genRun the DIA model for a single generation
get_dam_passageGet flow-correlated downstream dam passage values and probability of using Stillwater Branch for smolts each year in 'run_one_gen'
make_egg_to_smolt_survivalSimulate survival from egg to smolt stage for naturally produced smolts in 'run_one_gen'
make_eggs_per_femaleSimulate number of eggs per female each year in 'run_one_gen'
make_inriver_sSimulate natural, in-river survival per km for downstream migrating smolts in 'run_one_gen'
make_marine_sSimulate marine survival each year in 'run_one_gen'
run_downstream_passageRun the downstream smolt passage module in 'run_one_gen'
run_inefficiencyRe-distribute adult upstream migrants following failed dam passage in 'run_one_gen'
run_strayingAssign destination production units for adult returns in 'run_one_gen'
run_upstream_passageFunction used to run the upstream passage module for adults in 'run_one_gen'
smolt_stockingFunction used to distribute stocked smolts among production units in 'run_one_gen'
Data
The following built-in datasets are included:
downstream_brownsmillsFlow-correlated estimates of smolt survival through Browns Mills Dam
downstream_frankfortFlow-correlated estimates of smolt survival through Frankfort Dam
downstream_greatworksFlow-correlated estimates of smolt survival through Great Works Dam
downstream_howlandFlow-correlated estimates of smolt survival through Howland Dam
downstream_lowellFlow-correlated estimates of smolt survival through Lowell Dam
downstream_mattaceunkFlow-correlated estimates of smolt survival through Mattaceunk Dam
downstream_medwayFlow-correlated estimates of smolt survival through Medway Dam
downstream_milfordUpdated (2020) flow-correlated estimates of smolt survival through Milford Dam
downstream_milford_oldOriginal (2013) flow-correlated estimates of smolt survival through Milford Dam
downstream_miloFlow-correlated estimates of smolt survival through Milo Dam
downstream_mooseheadFlow-correlated estimates of smolt survival through Moosehead Dam
downstream_oronoUpdated (2020) flow-correlated estimates of smolt survival through Orono Dam
downstream_orono_oldOriginal (2013) flow-correlated estimates of smolt survival through Orono Dam
downstream_sebecFlow-correlated estimates of smolt survival through Sebec Dam
downstream_stillwaterUpdated (2020) flow-correlated estimates of smolt survival through Stillwater Dam
downstream_stillwater_oldOriginal (2013) flow-correlated estimates of smolt survival through Stillwater Dam
downstream_veazieFlow-correlated estimates of smolt survival through Veazie Dam
downstream_westenfieldFlow-correlated estimates of smolt survival through West Enfield Dam
in_river_mCumulative frequency distribution of in-river mortality per km for smolts
life_stage_survivalDistributional parameters for year-specific number of eggs produced per female, egg-to-smolt survival rate, in-river mortality rate, and marine survival rate
n_damsNumber of dams passed by smolts in each production unit and migration route
production_unitsDivision of Penobscot River watershed into sections, or Production Units (PUs)
stillwater_useUpdated (2020) probability of smolts using Stillwater Branch for outmigration given discharge
stillwater_use_oldOriginal (2013) probability of smolts using Stillwater Branch for outmigration given discharge
stocking_defaultDefault stocking proportions of smolts by PU
straying_locationsStraying locations of adult Atlantic salmon based on behavioral patterns
straying_matrixNumeric columns only from 'straying_locations'
upstream_inefficiencyDestination PUs and probabilities for adults that fail to pass dams
inefficiency_matrixColumns 5 through 20 from 'upstream_inefficiency'
Author(s)
Maintainer: Daniel S. Stich daniel.stich@oneonta.edu (ORCID)
Authors:
Julie L. Nieland
Timothy F. Sheehan
See Also
Useful links:
danStich/dia documentation built on Jan. 25, 2025, 4:27 a.m.
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| dia | R Documentation |
dia: Atlantic salmon Dam Impact Analysis (DIA) for R
Description
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_diaThe primary user-facing function used to run the multi-generation DIA model for Atlantic salmon
run_dia_shinyA 'shiny' implementation of 'run_dia()' with graphical user interface
run_one_genRun the DIA model for a single generation
get_dam_passageGet flow-correlated downstream dam passage values and probability of using Stillwater Branch for smolts each year in 'run_one_gen'
make_egg_to_smolt_survivalSimulate survival from egg to smolt stage for naturally produced smolts in 'run_one_gen'
make_eggs_per_femaleSimulate number of eggs per female each year in 'run_one_gen'
make_inriver_sSimulate natural, in-river survival per km for downstream migrating smolts in 'run_one_gen'
make_marine_sSimulate marine survival each year in 'run_one_gen'
run_downstream_passageRun the downstream smolt passage module in 'run_one_gen'
run_inefficiencyRe-distribute adult upstream migrants following failed dam passage in 'run_one_gen'
run_strayingAssign destination production units for adult returns in 'run_one_gen'
run_upstream_passageFunction used to run the upstream passage module for adults in 'run_one_gen'
smolt_stockingFunction used to distribute stocked smolts among production units in 'run_one_gen'
Data
The following built-in datasets are included:
downstream_brownsmillsFlow-correlated estimates of smolt survival through Browns Mills Dam
downstream_frankfortFlow-correlated estimates of smolt survival through Frankfort Dam
downstream_greatworksFlow-correlated estimates of smolt survival through Great Works Dam
downstream_howlandFlow-correlated estimates of smolt survival through Howland Dam
downstream_lowellFlow-correlated estimates of smolt survival through Lowell Dam
downstream_mattaceunkFlow-correlated estimates of smolt survival through Mattaceunk Dam
downstream_medwayFlow-correlated estimates of smolt survival through Medway Dam
downstream_milfordUpdated (2020) flow-correlated estimates of smolt survival through Milford Dam
downstream_milford_oldOriginal (2013) flow-correlated estimates of smolt survival through Milford Dam
downstream_miloFlow-correlated estimates of smolt survival through Milo Dam
downstream_mooseheadFlow-correlated estimates of smolt survival through Moosehead Dam
downstream_oronoUpdated (2020) flow-correlated estimates of smolt survival through Orono Dam
downstream_orono_oldOriginal (2013) flow-correlated estimates of smolt survival through Orono Dam
downstream_sebecFlow-correlated estimates of smolt survival through Sebec Dam
downstream_stillwaterUpdated (2020) flow-correlated estimates of smolt survival through Stillwater Dam
downstream_stillwater_oldOriginal (2013) flow-correlated estimates of smolt survival through Stillwater Dam
downstream_veazieFlow-correlated estimates of smolt survival through Veazie Dam
downstream_westenfieldFlow-correlated estimates of smolt survival through West Enfield Dam
in_river_mCumulative frequency distribution of in-river mortality per km for smolts
life_stage_survivalDistributional parameters for year-specific number of eggs produced per female, egg-to-smolt survival rate, in-river mortality rate, and marine survival rate
n_damsNumber of dams passed by smolts in each production unit and migration route
production_unitsDivision of Penobscot River watershed into sections, or Production Units (PUs)
stillwater_useUpdated (2020) probability of smolts using Stillwater Branch for outmigration given discharge
stillwater_use_oldOriginal (2013) probability of smolts using Stillwater Branch for outmigration given discharge
stocking_defaultDefault stocking proportions of smolts by PU
straying_locationsStraying locations of adult Atlantic salmon based on behavioral patterns
straying_matrixNumeric columns only from 'straying_locations'
upstream_inefficiencyDestination PUs and probabilities for adults that fail to pass dams
inefficiency_matrixColumns 5 through 20 from 'upstream_inefficiency'
Author(s)
Maintainer: Daniel S. Stich daniel.stich@oneonta.edu (ORCID)
Authors:
Julie L. Nieland
Timothy F. Sheehan
See Also
Useful links:
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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