CondExpLt               If statements compatible with RTMB
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
MSAassess-class         MSAassess S4 object
MSAdata-class           MSAdata S4 object
calc_F                  Newton-Raphson search for fishing mortality
calc_LAK                Length-at-age key
calc_POP                Predict the probability of CKMR kinship pairs
calc_eqdist             Equilibrium distribution from movement matrix
calc_growth             Calculate von Bertalanffy length-at-age
calc_index              Calculate index at age
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_population         Multi-fleet, multi-area, multi-stock population
                        dynamics model
calc_recruitment        Calculate recruitment from stock-recruit
                        function
check_data              Check dimensions and inputs in MSAdata object
conv_Sigma              Calculate covariance matrix
conv_mov                Calculate movement matrix for all age classes
conv_selpar             Selectivity at age and length
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
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
simulate                Simulate data
softmax                 Softmax function
summary                 Summarize MSA model output
