Changelog

Source: NEWS.md

FLasher 0.6.7

BUG FIXES

  • Ensure max effort input in .Call is numeric.
  • Changed tolerance in solver to match all.equal’s default: 1.5e-8.
  • Getting different spawn seasons to work.
  • Setting to zero rec in seasons < spawn.season.
  • Fix to discards ratio when discards.n is zero.
  • Bug in coertion of FLQuants with iters to fwdControl.
  • Add na.rm argument for discard ratio in stf().
  • sratio now properly applied for either 1 or 2 sex models in bevholtss3.

FLasher 0.6.6

USER-VISIBLE CHANGES

  • Minimum value for ‘f’ or ‘fbar’ targets has been set at sqrt(.Machine$double.eps) ~ 1.5e-08.
  • Added sr as FLQuant argument to fwd(FLStock). The vector by year is converted into a predictModel with rec~a and a yearly value for a.

BUG FIXES

  • Separation of large Jacobian matrix in solver.cpp was operating as in iters were organized target first, but they are iter first.
  • Ensure subset of deviances returns an FLQuants.
  • solver.cpp update to work properly with biols and fisheries with multiple iterations.
  • Bug in coertion of FLQuants with iters to fwdControl.

NEW FEATURES

  • FCB(FLBiols, FLFisheries) method class guessfcb and fcb2nit to return a guess for FCB.
  • stf(FLStocks) simply calls lapply, uses same settings on all elements.
  • partialF method returns the partial Fs by fleet for each FLBiol.

FLasher 0.6.1

NEW FEATURES

  • fwdControl(FLQuant) also accepts extra target arguments (e.g. relYear). # FLasher 0.6.0

NEW FEATURES

  • compare() method draws a comparison between targets in a fwdControl object and the results returned. Available for FLStock at this moment.
  • maxF argument to fwd(FLStock) is implemented through an additional target per timestep with max(fbar) = maxF, rather than by an indirect limit of the effort calculation. It bis not applied for steps with an f/fbar target.
  • Functions are now available for the corresponding ssb and biomass targets used by fwdControl: ssb_end, biomass_end and biomass_spawn

BUG FIXES

  • Calculation of survivors for stocks/biols with age=0 was not correct.

FLasher 0.5.0

NEW FEATURES

  • effort_max argument to fwd() set a maximum valuw for effort. Similar to FLash::maxF, as scale of effort values in fwd(FLStock) is set by fbar.
  • Certain slots in FLStock are checked for NAs in year before projection to avoid R crashing.
  • New stock-recruitment relationship added, survsrr, for low fecundity species (Taylor et al, 2013).
  • Projections are now correct for multiple units, either sex or birth seasons.

USER-VISIBLE CHANGES

  • The residuals argument to fwd() is now called ‘deviances’, and this name is used in all R and C++ code. ‘residuals’ is still accepted, but will be deprecated in the next minor version.

BUG FIXES

  • SRR predictions now work correctly for 2-sex OMs (FLStock or FLBiol).
  • Check for fwdControl rows not being all NA.

FLasher 0.0.4

NEW FEATURES

  • plot(FLStock, fwdControl) will add to the ggplotFL plot of an FLStock a coloured area of the years being projected.

BUG FIXES

  • fwd(FLStock) now returns one more year if quant=‘ssb_flash’ and object has space for it.

USER-VISIBLE CHANGES

  • Added disc.nyears arg to stf() to select years to use for discards ratio calculations.
  • If min and max for the very same target are set in separate rows, they are merged.

FLasher 0.0.3

BUG FIXES

  • Fixed stupid intermittant bug in projection test
  • Added stf to Namespace
  • Fixed bug setting relMinAge etc and added simple projection tests
  • Fixed coerce FLQuant to fwdControl with iters

DOCUMENTATION

  • Edits to mixed fishery vignette and new introductory vignette