Multi-Stock Assessment

---

Documentation for package ‘multiSA’ version 0.1.0

• DESCRIPTION file.
• Package NEWS.

Help Pages

calc_eqdist	Equilibrium distribution from movement matrix
calc_F	Newton-Raphson search for fishing mortality
calc_fsel_age	Selectivity at age and length
calc_growth	Calculate von Bertalanffy length-at-age
calc_HSP	Predict the probability of CKMR kinship pairs
calc_index	Calculate index at age
calc_isel_age	Selectivity at age and length
calc_LAK	Length-at-age key
calc_nextN	Project stock abundance to the next time step
calc_NPR	Simple spawners per recruit calculation
calc_phi_project	Equilibrium spawners per recruit by projection
calc_phi_simple	Simple spawners per recruit calculation
calc_POP	Predict the probability of CKMR kinship pairs
calc_population	Multi-fleet, multi-area, multi-stock population dynamics model
calc_recruitment	Calculate recruitment from stock-recruit function
calc_sel_len	Selectivity at age and length
check_data	Check dimensions and inputs in MSAdata object
check_parameters	Make list of parameters for RTMB
CondExpEq	If statements compatible with RTMB
CondExpGe	If statements compatible with RTMB
CondExpGt	If statements compatible with RTMB
CondExpLe	If statements compatible with RTMB
CondExpLt	If statements compatible with RTMB
conv_mov	Calculate movement matrix for all age classes
conv_selpar	Selectivity at age and length
conv_Sigma	Calculate covariance matrix
DCKMR-class	DCKMR S4 object
Dfishery-class	Dfishery S4 object
Dlabel-class	Dlabel S4 object
Dmodel-class	Dmodel S4 object
Dstock-class	Dstock S4 object
Dsurvey-class	Dsurvey S4 object
Dtag-class	Dtag S4 object
fit_MSA	Fit MSA model
get_MSAdata	Retrieve data object used to fit model
get_sdreport	Calculate standard errors
like_CKMR	Likelihood for CKMR
like_comp	Likelihood for composition vectors
make_map	Make list of parameters for RTMB
make_parameters	Make list of parameters for RTMB
MSAassess-class	MSAassess S4 object
MSAdata-class	MSAdata S4 object
plot-MSA-data	Plotting functions for data in MSA model
plot-MSA-state	Plotting functions for fitted MSA model
plot.MSAprof	Profile parameters of MSA model
plot.MSAretro	Retrospective analysis
plot_B	Plotting functions for fitted MSA model
plot_CAA	Plotting functions for data in MSA model
plot_CAL	Plotting functions for data in MSA model
plot_catch	Plotting functions for data in MSA model
plot_Ffleet	Plotting functions for fitted MSA model
plot_Fstock	Plotting functions for fitted MSA model
plot_IAA	Plotting functions for data in MSA model
plot_IAL	Plotting functions for data in MSA model
plot_index	Plotting functions for data in MSA model
plot_mov	Plotting functions for fitted MSA model
plot_N	Plotting functions for fitted MSA model
plot_R	Plotting functions for fitted MSA model
plot_Rdev	Plotting functions for fitted MSA model
plot_recdist	Plotting functions for fitted MSA model
plot_S	Plotting functions for fitted MSA model
plot_SC	Plotting functions for data in MSA model
plot_self	Plotting functions for fitted MSA model
plot_seli	Plotting functions for fitted MSA model
plot_selstock	Plotting functions for fitted MSA model
plot_SRR	Plotting functions for fitted MSA model
plot_tagmov	Plotting functions for data in MSA model
plot_V	Plotting functions for fitted MSA model
posfun	Quadratic penalty function
prior	Priors for MSA model
prior_h	Priors for MSA model
prior_M	Priors for MSA model
prior_q	Priors for MSA model
profile	Profile parameters of MSA model
profile.MSAassess	Profile parameters of MSA model
report	Generate markdown reports
report.MSAassess	Generate markdown reports
report.MSAretro	Retrospective analysis
residuals	Calculate model residuals
residuals.MSAassess	Calculate model residuals
retrospective	Retrospective analysis
simulate	Simulate data
simulate.MSAassess	Simulate data
softmax	Softmax function
summary.MSAretro	Retrospective analysis