Man pages for multiSA
Multi-Stock Assessment

AD	Additional methods for AD types
calc_eqdist	Equilibrium distribution from movement matrix
calc_F	Newton-Raphson search for fishing mortality
calc_growth	Calculate von Bertalanffy length-at-age
calc_index	Calculate index at age
calc_LAK	Length-at-age key
calc_nextN	Project stock abundance to the next time step
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...
calc_recruitment	Calculate recruitment from stock-recruit function
check_data	Check dimensions and inputs in MSAdata object
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_parameters	Make list of parameters for RTMB
MSAassess-class	MSAassess S4 object
MSAdata-class	MSAdata S4 object
multiSA-package	multiSA: Multi-Stock Assessment
optimize_RTMB	Optimize RTMB model
plot-MSA-data	Plotting functions for data in MSA model
plot-MSA-state	Plotting functions for fitted MSA model
posfun	Quadratic penalty function
prior	Priors for MSA model
profile	Profile parameters of MSA model
report	Generate markdown reports
residuals	Calculate model residuals
retrospective	Retrospective analysis
sapply2	'sapply2' function
simulate	Simulate data
softmax	Softmax function
summary	Summarize MSA model output