Obtain the initial numbers at length and the run the annual model dynamics over all years.
Usage
do_dynamics(
n_newton = 3,
log_F = 0,
logit_h = qlogis(0.99),
R0,
recruitment_size_sl,
Rdev_yr,
Rsigma,
numbers_rsl,
growth_ytrsll,
M_ytrsl,
catch_ytrf,
selectivity_ytrsfl,
legal_ytrsfl,
retained_ytrsfl,
handling_mortality_y,
weight_ytrsl,
maturity_ytrsl,
catch_like = -1,
rsigma_bias = 0,
match_old_u = 0,
U_ytrf_in = NULL
)Arguments
- n_newton
number of Newton-Rhapson iterations when solving the catch equation.
- log_F
a
listof data, parameter, and derived value inputs.- logit_h
a
listof data, parameter, and derived value inputs.- R0
average recruitment \(R_0\).
- recruitment_size_sl
size at recruitment.
- Rdev_yr
recruitment deviations.
- Rsigma
recruitment standard deviation \(\sigma_R\).
- numbers_rsl
initial numbers by region, sex, and length prior to running dynamics
- growth_ytrsll
growth matrix.
- M_ytrsl
natural mortality (M) by year, season, region, sex, and length.
- catch_ytrf
the catch (tonnes) by year, season, region, and fishery.
- selectivity_ytrsfl
selectivity array by year, season, region, sex, fishery, and length.
- legal_ytrsfl
proportion legal array by year, season, region, sex, fishery, and length.
- retained_ytrsfl
proportion retained array by year, season, region, sex, fishery, and length.
- handling_mortality_y
the handling mortality rate by year.
- weight_ytrsl
the average weight (tonnes) by year, season, region, sex, and length.
- maturity_ytrsl
the proportion of the population mature by year, season, region, sex, and length.
- catch_like
the type of catch likelihood.
- rsigma_bias
flag to turn on bias adjustment rdevs
- match_old_u
flag to match outdated version of code exploitation rate
- U_ytrf_in
projected exploitation rate array.