Calculate maximum sustainable yield (MSY) reference points by iteratively searching for the fishing mortality that maximises long-run catch.
Usage
get_MSY(
log_F,
logit_h,
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,
SSB0,
catch_like,
rsigma_bias = 0,
match_old_u = 0,
U_ytrf_in = NULL,
min_increase = 0,
search_type = 1,
ssb_lim = 0
)Arguments
- 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
final numbers at end of model
- 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
a
listof data, parameter, and derived value inputs.- legal_ytrsfl
a
listof data, parameter, and derived value inputs.- retained_ytrsfl
a
listof data, parameter, and derived value inputs.- 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.
- SSB0
needed to assess risk but not included in do_dynamics
- 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flag to match outdated version of code exploitation rate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
project U_ytrf
- min_increase
in terms of tons, minimum increase required to increase U
- search_type
default = 1 for exploitation rate, 2 for catch
- ssb_lim
default = 0 to find theoretical MSY, 0.2 to ensure above soft limit