The current version of salmonMSE package is available on CRAN.

Version 3.0.0

• salmonMSE no longer uses openMSE as a dependency. ProjectSOM() is now the primary internal function that organizes the projection. Various internal functions have been replaced and updated.
• Parallel processing by individual operating model is now supported with the ncores argument to salmonMSE().
• Check for NAs in start values for fit_CM.
• Update .CM_MSY() and .CM_Sgen() functions for parallel computation.
• MSY calculations and catch calculations use adult equivalents (AEQs) for preterminal fisheries.
• Add new slot Hatchery@p_female_brood for sex-selective brood.
• SMSE output object reports brood numbers and catch with age dimension. Harvest rates and exploitation rates are aggregated over age classes.
• Add custom catch function (for harvest control rules, etc.)
• Add simple_SOM class and simple_salmonMSE() function for modeling recruits-spawners

Version 2.1.0

• Update terminal year escapement, brood, and egg production calculations for multiple release strategies and life cycle groups
• Fix typos in smolt_func() and compare_statevar_ts()
• Broodtake optimization uses uniroot() with tolerance to machine precision (need this when population is very large and broodtake is small)
• plot_tradeoff can plot x1 as a continuous variable (numerics were previously coerced to factors)

Version 2.0.0

• Add example objects
• New arguments in Hatchery object to determine if hatchery releases compete with natural-origin juveniles
• plot_tradeoff() can create panels with scenario rows and columns
• plot_decision_table2() allows more control of colour scheme. Add examples as well in documentation
• Update units of Ricker Smax to be units of spawners, tau argument convert to Emax (corresponding egg production)
• Projection now reports terminal year escapement, brood, and egg production (long-standing issue)

Version 1.0.0

salmonMSE projections

• SOM@Bio@p_female parameter can now be age-specific. Intended for cases where older spawners are predominantly female.
• Fix markdown reporting for projections
• If release target is exceeded in custom brood rule, projection will proportionally reduce broodtake to return to target
• Fix calculation in freshwater survival when habitat features are used
• Hard code in openMSE historical period to 2 real years. Historical reconstruction no longer supported.
• M vector now reduce to length maxage-1
• Allow NO removals at the spawning grounds (facilitates in-river fishery operations)
• Add compare function to generate markdown report to compare several model runs

Conditioning model

• Allow NAs in target population escapement time series in likelihood
• Conditioning model reports realized productivity (adults/spawner) annually with time-varying maturity and M
• Add initial hatchery production assumption
• Add likelihood for observed pHOS (by calendar year or brood year)
• Export CM plotting functions
• Allow estimation of finitPT and finitT (initial fishing mortality), but likely slows down MCMC convergence
• Allow initial population to be specified by spawn_init (total spawners) and pHOS_init (fraction hatchery-origin)

Other

• Decision tables and tradeoff figures can now be a grid
• Remove stats::uniroot import for compatibility with RTMB 1.9

Version 0.1.0

• Initial CRAN release