The current version of salmonMSE package is available on CRAN.

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

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)