run_upstream_passage: Run upstream migration routine

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

Run upstream migration routine

Description

Run the upstream migration routine for adult Atlantic salmon in the Dam Impact Analysis (DIA) model v67 during year 6. Not intended to be called directly.

Usage

run_upstream_passage(
  hatchery_returns,
  hatchery_proportions,
  wild_returns,
  wild_proportions,
  upstream_passage,
  straying_matrix,
  p_mainstem_up,
  stocking,
  n_broodstock,
  inefficiency_matrix
)

Arguments

hatchery_returns	Total number of hatchery smolts exiting river in year 4.
hatchery_proportions	Proportion of individuals attempting to return to each production unit (PU in the river). Within the 'run_dia()' function, these values are passed as output from 'run_downstream_migration()'.
wild_returns	Number of wild-reared smolts exiting river in year 4.
wild_proportions	Proportion of individuals attempting to return to each production unit (PU in the river). Within the 'run_dia()' function, these values are passed as output from 'run_downstream_migration()'.
upstream_passage	Numeric vector with length = 15 corresponding to dam passage efficiencies at each of 15 dams in the watershed that are used to delineate PUs. Default usage is to inherit these values from the link{run_dia} function's 'upstream_passage' argument using default values based on NMFS (2013) prescriptions as implemented in Nieland and Sheehan (2020).
straying_matrix	A dataframe identical in structure to the built-in straying_locations dataset.
p_mainstem_up	Probability that fish use the mainstem Penobscot River (and not Stillwater Branch) for upstream migration around Marsh Island.
stocking	Number indicating whether hatchery stocking is on ('1') or off ('0'). Will be a vector corresponding to 'n_generations' at some point.
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.
inefficiency_matrix	A matrix identical in structure to the built-in inefficiency_matrix dataset.

References

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.

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.

See Also

run_dia, run_downstream_passage

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