run_one_year: Run one year in penPass model

In danStich/penPass: R package for Atlantic salmon PenPass model

Run one year in penPass model

Description

Function used to simulate downstream migration in a single year for available timeseries (1970 - 2020). A wrapper for the 'sample()' function for resampling the empirical cumulative distribution function included in the mort_per_km data set.

Usage

run_one_year(
  year = 2017,
  downstream = list(seeboomook = NA, ripogenus = NA, north_twin = NA, quakish = NA,
    dolby = NA, east_millinocket = NA, medway = NA, matagamon = 1, guilford = NA,
    moosehead = NA, browns_mills = NA, howland = NA, mattaseunk = NA, west_enfield = NA,
    milford = NA, great_works = NA, gilman_falls = NA, stillwater = NA, orono = NA,
    veazie = NA, bangor_waterworks = 1),
  km_surv = NULL,
  prod = c(WPN_prod = 3, EPN_prod = 3, Matt_prod = 3, PISC_prod = 3, PN_prod = 3),
  sat = c(WPN_sat = 0, EPN_sat = 0, Matt_sat = 0, PISC_sat = 0, PN_sat = 0),
  p_stillwater = NA
)

Arguments

year	Year used for simulation. Must be 1970 - 2010.
downstream	Downstream dam passage survival rates for smolts
km_surv	Natural downstream survival of smolts per kilometer
prod	Habitat productivity in smolts produced per 100 m2 of wetted habitat area (Stevens et al. 2019).
sat	Habitat saturation for wild fish as the proportion of habitat filled
p_stillwater	Probability of smolts using Stillwater Branch Penobscot River for downstream migration. By default sampled from stillwater_splits based on simulated value of flow at West Enfield Dam.

References

Stevens, JR, JF Kocik, and TF Sheehan. 2019. Modeling the impacts of dams and stocking practices on an endangered Atlantic salmon (Salmo salar) population in the Penobscot River, Maine, USA. Canadian Journal of Fisheries and Aquatic Sciences 76:1795-1807.

danStich/penPass documentation built on July 1, 2023, 9:31 a.m.