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Run adult passage inefficiency

run_inefficiency.Rd

Adult inefficiency (homing) routine for Atlantic salmon that fail to pass a dam but that also do not die or return to sea.

Usage

run_inefficiency(n, inefficiency_matrix)

Arguments

n

A vector of length 15 containing total number of fish that failed to pass dams and did not die or return to sea.

inefficiency_matrix

A matrix identical in structure to the built-in inefficiency_matrix dataset (NMFS 2012; Neiland et al. 2013).

References

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). 2012. Biological Opinion regarding effects to the endangered GOM DPS for Atlantic salmon (Salmo salar), endangered shortnose sturgeon (Acipenser brevirostrum), and the threatened and endangered DPSs of Atlantic sturgeon (Acipenser oxyrhynchus oxyrhynchus) from proposed FERC license amendments for Black Bear Hydro Partners’ Hydroelectric Projects on the Penobscot River in Maine. NMFS Greater Atlantic Regional Office, Gloucester, MA.

See also

inefficiency_matrix, upstream_inefficiency

Examples

# Simulate 10,000 starting fish at each dam and
# randomly sample number of failures for each PU (15 of these)

failures = sample(1e4, 15, replace = TRUE)

# Use run_inefficiency to simulate where these 
# failed migrants end up in the watershed based on the 
# default inefficiency_matrix in dia.

run_inefficiency(failures, dia::inefficiency_matrix)
#>  [1]     0  8513 12112     0     0     0  5120 21781     0 15318     0     0
#> [13]     0   280 38808