R: Multi-Stock Assessment

# Multi-Stock Assessment

## Documentation for package ‘multiSA’ version 0.1.1

- DESCRIPTION file
- Package NEWS
- Package README

## 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-method | Profile parameters of MSA model
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-method | Profile parameters of MSA model
profile.MSAassess | Profile parameters of MSA model
report | Generate markdown reports
report-method | Generate markdown reports
report.MSAassess | Generate markdown reports
report.MSAretro | Retrospective analysis
residuals | Calculate model residuals
residuals-method | Calculate model residuals
retrospective | Retrospective analysis
simulate | Simulate data
simulate-method | Simulate data
simulate.MSAassess | Simulate data
softmax | Softmax function
summary | Summarize MSA model output
summary-method | Summarize MSA model output
summary.MSAretro | Retrospective analysis