run_dia: Run the Dam Impact Analysis

In danStich/dia: R package for Atlantic salmon Dam Impact Analysis (DIA) model

Run the Dam Impact Analysis

Description

Use functions from dia to simulate multiple generations of 2 sea-winter female Atlantic salmon through time using data and inputs from Nieland et al. (2013, 2015) and Nieland and Sheehan (2020) as implemented in '@Risk' add-in for 'Excel'. This function is a wrapper for run_one_gen that uses output from one generation as the seed for user-specified number of subsequent generations.

Usage

run_dia(
  n_generations = 15,
  n_wild = 31,
  n_hatchery = 306,
  stocking = 1,
  n_stocked = rep(545000, 15),
  upstream = list(medway = 0, mattaceunk = 0.9, west_enfield = 0.95, upper_dover = 0.92,
    browns_mills = 0.92, sebec = 0, milo = 0, howland = 0.95, lowel = 0.92, stillwater =
    0, milford = 0.95, great_works = 1, orono = 0, veazie = 1, frankfort = 1),
  downstream = list(medway = 0, mattaceunk = 1, west_enfield = 0.96, upper_dover =
    0.9215, browns_mills = NA, sebec = NA, milo = NA, howland = 1, lowell = NA,
    stillwater = 0.96, milford = 0.96, great_works = 1, orono = 0.96, veazie = 1,
    frankfort = NA),
  in_river_s = NA,
  mattaceunk_impoundment_mortality = 0.072,
  p_stillwater = NA,
  indirect_latent_mortality = 0.06,
  p_female = 0.6,
  new_or_old = "new",
  marine_s_hatchery = NA,
  marine_s_wild = NA,
  straying_matrix = NULL,
  p_mainstem_up = 1,
  n_broodstock = 150
)

Arguments

n_generations	Number of generations to simulate. One complete generation from egg to returning adult is six years.
n_wild	Number of starting wild, adult Atlantic salmon.
n_hatchery	Number of starting hatchery adult Atlantic salmon.
stocking	Numeric indicating whether hatchery stocking is on ('1') or off ('0'). If hatchery stocking is on, then hatchery smolts are stocked into production units based on the proportion_stocked column in the built-in stocking_default dataset.
n_stocked	A numeric vector corresponding to 'n_generations' in length with the number of stocked hatchery smolts per generation.
upstream	Upstream passage efficiency of adult Atlantic salmon through dams. Default values are based on NMFS (2013) prescriptions as implemented in Nieland and Sheehan (2020). Any numeric value between zero and 1, inclusive, can be specified for any dam by the user.
downstream	Downstream survival of Atlantic salmon smolts through dams. The default values are based on the most recent values used by Nieland et al. (2020) based on standards established in the the NOAA Species Protection Plan following implementation of the Penobscot River Restoration Project. The default 'NA' randomly samples correlated survival rates of smolts for each dam based on cumulative flow probabilities and associated empirical survival rates (Nieland et al. 2013, Nieland and Sheehan 2020), and can also be used for dams that have a default value other than NA.
in_river_s	In-river survival per kilometer for downstream migrating smolts. The default 'NA' value simulates from a cumulative distribution function using values in in_river_m. This value is the same for hatchery stocked and wild smolts.
mattaceunk_impoundment_mortality	Mortality incurred by Atlantic salmon smolts during migration through the Mattaceunk (Weldon) Dam impoundment. The default value is based on Nieland and Sheehan (2020), who used results of Holbrook et al. (2011) and Stich et al. (2015a).
p_stillwater	Probability that fish use the Stillwater Branch for downstream migration. The default (NULL) draws flow-correlated probability of using the Stillwater Branch from a cumulative distribution of flows with paired estimates of p_stillwater used by Nieland and Sheehan (2020), based on empirical results in Holbrook et al. (2006), Stich et al. (2014), and Stich et al. (2015a).
indirect_latent_mortality	Indirect, latent mortality incurred by Atlantic salmon smolts at each dam passed. The default value of 0.06 is what was used in Nieland and Sheehan (2020), derived from estimates in Stich et al. (2015b).
p_female	Proportion of females in population. Any value between zero and one, inclusive, is allowable.
new_or_old	A character string indicating whether to use "new" (Nieland and Sheehan 2020) or "old" (Nieland et al. 2013, 2015) flow-correlated probabilities of p_stillwater as well as flow-correlated survival at milford, orono, and stillwater dams.
marine_s_hatchery	Numeric indicating marine survival rate for post-smolt to adult survival of hatchery outmigrants. The default ('NA') simulates values from a truncated normal distribution using hatchery smolt survival estimates from the Penobscot River, ME, USA.
marine_s_wild	Numeric indicating marine survival rate for post-smolt to adult survival of wild outmigrants during two winters at sea. The default ('NA') simulates values from a truncated normal distribution using wild smolt survival estimates from the Narraguagus River, ME, USA.
straying_matrix	A dataframe identical in structure to the built-in straying_locations dataset. By default, uses the built-in data set to parameterize straying probabilities to destination PUs from starting PUs.
p_mainstem_up	Probability that fish use the mainstem Penobscot River (and not Stillwater Branch) for upstream migration around Marsh Island. The default value '1' was used by Nieland and Sheehan (2020).
n_broodstock	Target number of adult returns collected at Milford Dam for spawning at US Fish and Wildlife Service Craig Brook National Fish Hatchery each year. Broodstock are collected upstream of Milford Dam in run_upstream_passage and removed from the population for that generation, as is the case in reality.

Value

A dataframe with four variables corresponding to each generation of the simulation. Variables correspond to output from run_one_gen.

production_unit Production unit

generation Generation number from simulation

origin Fish origin (hatchery or wild)

abundance Fish abundance within production units, generations, and origin

References

Holbrook CM, Kinnison MT, Zydlewski J. 2011. Survival of migrating Atlantic salmon smolts through the Penobscot River, Maine: a prerestoration assessment. Transactions of the American Fisheries Society 140:1255-1268.

Holbrook CM, Zydlewski J, Gorsky D, Shepard SL, Kinnison MT. 2009. Movements of prespawn adult Atlantic salmon near hydroelectric dams in the lower Penobscot River, Maine. North American Journal of Fisheries Management 29:495-505.

Nieland JL, Sheehan TF. 2020. Quantifying the Effects of Dams on Atlantic Salmon in the Penobscot River Watershed, with a Focus on Weldon Dam. US Department of Commerce, Northeast Fisheries Science Center Reference Document 19-16, Woods Hole, MA.

Nieland JL, Sheehan TF, Saunders R. 2015. Assessing demographic effects of dams on diadromous fish: a case study for Atlantic salmon in the Penobscot River, Maine. ICES Journal of Marine Science 72:2423-2437.

Nieland JL, Sheehan TF, Saunders R, Murphy JS, Trinko Lake TR, Stevens JR. 2013. Dam Impact Analysis model for Atlantic salmon in the Penobscot River, Maine. US Department of Commerce, Northeast Fisheries Science Center Reference Document 13-09, Woods Hole, MA.

NMFS (National Marine Fisheries Service). 2013. Endangered Species Act Biological Opinion: FERC amendment of license for the Mattaceunk Project (Interim Species Protection Plan). NMFS Greater Atlantic Regional Office, NER-2013-9640, Gloucester, MA.

Stich DS, Bailey MM, Holbrook CM, Kinnison MT, Zydlewski JD. 2015a. Catchment-wide survival of wild- and hatchery-reared Atlantic salmon smolts in a changing system. Canadian Journal of Fisheries and Aquatic Sciences 72:1352-1365.

Stich DS, Bailey MM, Zydlewski JD. 2014. Survival of Atlantic salmon Salmo salar smolts through a hydropower complex. Journal of Fish Biology 85:1074-1096.

Stich DS, Kinnison MT, Kocik JF, Zydlewski JD. 2015b. Initiation of migration and movement rates of Atlantic salmon smolts in fresh water. Canadian Journal of Fisheries and Aquatic Sciences 72:1339-1351.

Examples

# Additional examples, including parallel implementation can be found in the
# readme file for the GitHub repository for this package: 
# https://github.com/danStich/dia.

# 1. Run dia model with defaults for 15 generations ----

result <- run_dia(n_generations = 15)

# 2. Run dia model with user-specified dam passage ----

run_dia(
  n_generations = 15,
  upstream = list(
    medway = 0, 
    mattaceunk = 0.9, 
    west_enfield = 0.95, 
    upper_dover = 0.92, 
    browns_mills = 0.92, 
    sebec = 0, 
    milo = 0, 
    howland = 0.95, 
    lowel = 0.92,
    stillwater = 0, 
    milford = 0.95, 
    great_works = 1, 
    orono = 0, 
    veazie = 1, 
    frankfort = 1),
  downstream = list(
  medway = 0, 
  mattaceunk = 1, 
  west_enfield = 0.96, 
  upper_dover = 0.9215, 
  browns_mills = 1, 
  sebec = 1, 
  milo = 1, 
  howland = 1, 
  lowell = 1,
  stillwater = 0.96, 
  milford = 0.96, 
  great_works = 1, 
  orono = 0.96, 
  veazie = 1,
  frankfort = 1))

danStich/dia documentation built on Jan. 25, 2025, 4:27 a.m.