Internal function that predicts the natural origin or hatchery origin smolt production from the escapement, and saves state variables to salmonMSE_env.
smolt_func() is the population dynamics function
makeRel_smolt() generates a list for openMSE to use in the simulations
smolt_func(
Nage_NOS,
Nage_HOS,
Nage_stray,
x = -1,
y,
output = c("natural", "hatchery"),
s_enroute,
p_female,
fec,
SRRpars,
hatchery_args,
fitness_args,
habitat_args,
stray_args,
s,
g,
prop_LHG,
r
)makeRel_smolt(
p_smolt = 1,
s = 1,
p_natural,
p_hatchery = NULL,
p_stray = NULL,
maxage,
output = c("natural", "hatchery"),
s_enroute,
p_female,
fec,
SRRpars,
hatchery_args,
fitness_args,
habitat_args,
stray_args,
g,
prop_LHG,
r
)
smolt_func() returns a numeric for the ratio of the realized smolt production vs. the hypothetical value if there were no
hatchery, en route mortality, or habitat improvement
makeRel_smolt() returns a list that is passed to openMSE as a inter-population relationship
Matrix [n_age, n_g] of natural escapement from openMSE. n_g is the number of life history groups (sub groups within cohorts)
that contribute to spawning.
Matrix [n_age, n_r] of hatchery escapement from openMSE. n_r is the number of release strategies (sub groups within cohorts)
that contribute to spawning.
Matrix [nage, n_stray] of hatchery escapement from donor populations that will stray to the recipient population. stray_args$stray_matrix
determines the proportions of the donor escapement that will move to the recipient population.
Integer, simulation number from openMSE
Integer, simulation year (including historical years)
Character, whether to predict the natural origin or hatchery origin smolt production
Numeric, en route survival of the escapement to the spawning grounds
Numeric, proportion female for calculating the egg production.
Array [nsim, maxage, nyears+proyears]. The fecundity at age schedule of spawners
Data frame containing stock recruit parameters for natural smolt production from egg production. Column names include: SRrel, kappa, capacity, Smax, phi
Named list containing various arguments controlling broodtake and hatchery production. See details below.
Named list containing various arguments controlling population fitness from hatchery production. Names include: fitness_type, omega2, theta, fitness_variance, heritability, zbar_start, fitness_floor, rel_loss
Named list with arguments sontrolling freshwater life stage survival. Names include: use_habitat (logical), Habitat (Habitat object)
Named list with arguments controlling strays in and out of the local population Names include:
Integer, salmonMSE population index. Used to report variables to salmonMSE_env.
Integer for the life history group of natural origin fish to pass the parameter back to openMSE (if output = "natural")
Numeric vector, proportion of the egg production assign to life history groups (sums up to one) (only used if output = "natural")
Integer for the release strategy of hatchery origin fish to pass the parameter back to openMSE (if output = "hatchery")
Integer, the population index for the smolt production in the openMSE model, corresponding to output
Integer vector, the population index for the natural origin escapement in the openMSE model. Can be more than one if spawning is from multiple life history groups
Integer vector, the population index for the hatchery origin escapement in the openMSE model. Can be more than one
if there are multiple release strategies. Set to NULL for no hatchery production
Integer vector, population index for the hatchery strays in multi-system models
Hatchery control parameters are included in a named list with the following arguments:
egg_target Numeric, target egg production for hatchery. Set to zero for no hatchery production.
ptarget_NOB Numeric, the target proportion of the natural origin broodtake relative to the overall broodtake
pmax_NOB Numeric, the maximum proportion of the natural origin escapement to be used as broodtake
fec_brood Array [nsim, maxage, nyears+proyears]. the fecundity at age schedule of broodtake to calculate the total hatchery egg production
s_yearling Numeric, the survival of eggs to the smolt life stage (for yearling release)
s_subyearling Numeric. the survival of eggs to subyearling life stage (for subyearling release)
p_yearling Numeric, the proportion of annual releases at the yearling life stage (vs. subyearling)
phatchery Numeric, the proportion of the hatchery origin escapement that return to the hatchery,
for example, by removal from spawning grounds or swim-in facilities. These fish are available for broodtake.
premove_HOS Numeric, the proportion of the hatchery origin escapement to be removed from the spawning
grounds (in order to ensure a high proportion of NOS). These fish are not available for broodtake.
For example, a value less than one can represent imperfect implementation of weir removal.
s_prespawn Numeric, the survival of broodtake prior to egg production. 1 - s_prespawn is the proportion of fish
not used for hatchery purposes, e.g., mortality or other resesarch purposes. Used to back-calculate the broodtake.
gamma Numeric, the relative reproductive success of hatchery origin spawners (relative to natural origin spawners)
m Numeric, mark rate for selective broodtake