NEWS.md
In salmonMSE: Management Strategy Evaluation for Salmon Species

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

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)

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)

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

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)