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@brianstock-NOAA brianstock-NOAA released this 03 May 18:31
· 409 commits to master since this release
v1.0.4
e1ea8f2

WHAM description + simulation test paper published: https://doi.org/10.1016/j.fishres.2021.105967

Major improvements

  • New ability to plot results from multiple ASAP3 and WHAM models together for comparison. Thanks to @liz-brooks for contributing read_asap3_fit! See ?compare_wham_models and new vignette 8.

Minor improvements

  • New save.sdrep = F option to only save summary(sdreport) instead of sdreport. Can make saved models MUCH smaller (e.g. 2 MB vs. 150 MB). (2f8875).
  • Added proj.opts$percentFXSPR option, percent of F_XSPR to use for calculating catch in projections. For example, GOM cod uses F = 75% F_XSPR, so proj.opts$percentFXSPR = 75.
  • Added proj.opts$useFMSY and proj.opts$percentFMSY options, to project population and catches at (a percentage of) F_MSY. (467532)
  • Allow peels to be projected so can do retrospective predictions, as in Fig. 4 of Xu et al. 2018. See new vignette 9. (e1e00c)

Bug fixes

  • Broken links in vignettes (thanks to @tcarruth)
  • Plotting issue with Ecov OSA residuals and peels (thanks to @h-du-pontavice, 1163df)
  • Double logistic selectivity setup in prepare_wham_input (thanks to @tcarruth, f270dd)
  • tryCatch error assignment issues (9d5c87)
  • Remove error in default projection options (percentSPR)
  • Setting up projections with multiple Ecovs (again thanks to @h-du-pontavice, 42a6a4)
  • Selectivity parameter initial values set to middle of range if unspecified in prepare_wham_input
  • Fixed fit_tmb to make $final_gradient reported by wham equivalent to sdreport()$gradient.fixed. Issue was that the model$env$last.par.best is not updated by the newton steps after optimization so model$opt$par was slightly different (10^(-7) or smaller). e20bd8
  • Factor order problem caused indices to be out of order when > 9 indices present. 9e0141
  • Fixed default determination of age corresponding to fully selected (total) fishing mortality. Now which_F_age is a vector of annual values (including projection years) and the values are reassigned after fitting before reporting. (189b6c)
  • Added check for F_XSPR to verify percent of SPR0 is correct and, in projections, catch at F from catch is verified. Initial values for these algorithms can be specified by the user. (189b6c)
  • If ecov years differ from model years, peel to same year in fit_peel (e1e00c)
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