Multi-Stock Assessment
Additional methods for AD types
Equilibrium distribution from movement matrix
Newton-Raphson search for fishing mortality
Calculate von Bertalanffy length-at-age
Calculate index at age
Length-at-age key
Project stock abundance to the next time step
Equilibrium spawners per recruit by projection
Simple spawners per recruit calculation
Predict the probability of CKMR kinship pairs
Multi-fleet, multi-area, multi-stock population dynamics model
Calculate recruitment from stock-recruit function
Check dimensions and inputs in MSAdata object
If statements compatible with RTMB
Calculate movement matrix for all age classes
Selectivity at age and length
Calculate covariance matrix
DCKMR S4 object
Dfishery S4 object
Dlabel S4 object
Dmodel S4 object
Dstock S4 object
Dsurvey S4 object
Dtag S4 object
Fit MSA model
Retrieve data object used to fit model
Calculate standard errors
Likelihood for CKMR
Likelihood for composition vectors
Make list of parameters for RTMB
MSAassess S4 object
MSAdata S4 object
multiSA: Multi-Stock Assessment
Optimize RTMB model
Plotting functions for data in MSA model
Plotting functions for fitted MSA model
Quadratic penalty function
Priors for MSA model
Profile parameters of MSA model
Generate markdown reports
Calculate model residuals
Retrospective analysis
sapply2 function
Simulate data
Softmax function
Implementation of a next-generation, multi-stock age-structured fisheries assessment model. 'multiSA' is intended for use in mixed fisheries where stock composition can not be readily identified in fishery data alone, e.g., from catch and age/length composition. Models can be fitted to genetic data, e.g., stock composition of catches and close-kin pairs, with seasonal stock availability and movement.
Useful links