v2.2.7.6

Changes in MULTIFAN-CL version : 2.2.7.6

• Added the orthogonal-polynomial coefficients to the indepvar.rpt.
• Tags inform movement - reinstated the grouped case.
• Estimation of the size composition self-scaling multinomial likelihood with random-effects (SSMULT-AUAU) - instated estimation of the variance exponent multiplier coefficient parameter.
• New report "fishmort2" with headers and indices for the fish_mort output.
• CPUE likelihood extended to the multi-species/sexes case - entails accommodating fishery data, specifically catches and survey fishery indices, that are aggregated among species/sexes, and to apportion them according to the model predicted sex-ratios of vulnerable numbers at age for deriving the Newton-Raphson solution for fishing mortality and the predicted CPUE indices.
• Catch-conditioned operating model projections with all projection fisheries being effort-conditioned - requires employing the predictions of the catchability regression for all projection time periods.
• Reconciled the action of age_flags(177) for initial equilibrium population calculations when the orthogonal-polynomial recruitment parameterisation is active.
• New output files needed for reproducing the original input survey fishery indices are output from the final model evaluation for reporting: "cpue_obs_mls" and "cpue_pred_mlv".
• Implementation of the Richards growth curve - mean_length correction, and gamma parameter input from .ini file version 1005; added gamma to the indepvar.rpt.
• Extensions to multi-sex case:
  • correction for movement coefficients input via a file
  • assignments of sex-specific Lorenzen natural mortality as estimated
  • indexed sex-specific fisheries to the input of conditional age-length observations
  • shared selectivity at length includes the estimated independent von Bertalanffy growth offsets
• Extensions to length-based selectivity:
  • implementation of fish_flags(75) case - young ages have selectivity = 0
  • implementation of case: fish_flags(57)=0 and fish_flags(3)< maximum age; older age classes have selectivity = 0
  • implementation of case: fish_flags(57)=0 and fish_flags(16)= 1; non-decreasing selectivity
• Initial equilibrium survival rate - scalar of natural mortality is assigned from age_flags(128)/100 to allow finer resolution; WARNING - not yet backwardly compatible for solutions obtained with versions < 2.2.7.5.
• Independent control of the ests.rep and *.fit output file generation.
• Upgrades to the input .ini file:
  • version 1005 - input of the Richards growth gamma parameter
  • version 1006 - input of the intital total population scalar parameter value
  • version 1007 - input of the tag_flags assignments with warnings relating to implausible tag mixing assumptions
• Upgraded screen output error messages to be more informative.

Fixes

• Correction to length-based selectivity estimation for models without weight frequency data.