NEWS.md

In iagomosqueira/FLasher: Projection and Forecasting of Fish Populations, Stocks and Fleets

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

iagomosqueira/FLasher documentation built on Jan. 11, 2024, 12:58 a.m.