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Changelog

Source: NEWS.md

Version 3.0.0

CRAN release: 2026-08-20

  • 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

CRAN release: 2026-04-25

  • 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

CRAN release: 2026-04-16

  • 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

CRAN release: 2026-03-20

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

CRAN release: 2025-09-23

  • Initial CRAN release