Skip to content

v2.0.0

Latest
Latest
Compare
Choose a tag to compare
@timjmiller timjmiller released this 04 Feb 18:50
v2.0.0
c9983ff

Major improvements

Many new features have been developed previously on the lab and devel branch and not attributed to a specific commit, but are now included as the main version of WHAM

  • Large changes in structure of input data, parameters, and reported output may require editing workflows for previous versions.
  • 1 or more stocks and regions can now be modeled with movement among regions.
  • User can define seasonal intervals within years (possibly varying in length).
  • Seasonal operation of fleets.
  • Movement parameters are stock, season, and region-to-region specific.
  • Movement parameters can incorporate time and age varying random effects and effects of environmental covariates much like natural mortality.
  • Priors for mean movement parameters are allowed because it is currently not possible to include tagging data observations.
  • Exported functions for components of model (e.g., set_NAA, set_catch, set_M, set_move) can be used build model input sequentially or to modify a previously created input.
  • Greatly increased options to functions to allow user to specify initial parameter values and mapping of parameter estimation.
  • Random effects options for initial abundance at age.
  • Functions to perform jittering (jitter_wham) and self tests (self_test).
  • Functions to add reference point estimation (do_reference_points), TMB::sdreport objects (do_sdrep), and retrospective peels (do_retro_peels), and OSA residuals (make_osa_residuals) to a previously fitted model.
  • New Rmarkdown based generation of html by plot_wham_output that is self-contained (can be opened from any location).

Minor improvements

  • Can now specify fleet-specific catch or F in projection years. f2a298e
  • add some more input options for M, catch, indices. d50acc7

Bug fixes

  • fix bugs in reporting of NAA re cor parameters in table of estimates and bug in setting covariate effect maps. 0ab78d8
  • fix mapping of selectivity RE when selectivity block does not span all years, correct marginal variance used for basic_info$bias_correct_BRPs=TRUE in the SSB/R and Y/R calculations when there is AR1 correlation of NAA RE, and correct dimension of recruitment random effects for projection of SCAA models. b031806
  • fix bug in use of user-defined waa, maturity in projection years. 24dd1ab
  • fix some indexing errors for retros with Ecovs or selectivity RE, fix some setup problems for movement. 2371fc3
  • fix specification of initial/fixed M when input M is both age and time varying. 1d637e3
  • fix specification of shared fleet selectivity blocks provided by ASAP input. fcbdfca
Assets 2
Loading