prepare_wham_input
(ecov$logsigma
) a3328a9.plot_wham_output
13094c6.prepare_wham_input
introduced in 1.0.5 when not all index data in .dat
are used (aggregate or proportion-at-age, all years or a subset) 12abdefTMBhelper::check_estimability
is now internal issue 47which_F_age
(fix error when projecting a peel doing retrospective predictions, ex9)opt
element when do.fit = FALSE.plot_wham_output
now removes any existing plot files in the directories where plots are saved before writing files so that any orphaned files from previous fits are not included in the results and html rendering.plot_wham_output
now creates .png
output by default because of 1) issues opening the .html
in Firefox on Windows, and 2) it was annoying to close dozens of browser tabs during testing. issues 42 and 50, thanks to @ejosymart and @JDeroba.set_catch
bug when catch age comp data exist for some years and not othersprepare_wham_input
is now modularized and can take a "basic_info" argument or generate a dummy input for fit_wham without an asap3 object. This provides better organization and helps fix the operating model/MSE features that have been broken since version 1.0.0. Options have been added to NAA_re argument to configure how initial numbers at age and recruitment are treated. Including initial parameter values. A tenth example and vignette illustrate the usage to generate an assessment model without an asap3 file and a simple management strategy evaluation 9bc161d. ecov$ages
, allows user to specify that an ecov only affects a subset of ages e6518f Ecov_re
padding in projections with multiple ecovs that have different lags a57f3bWHAM description + simulation test paper published: https://doi.org/10.1016/j.fishres.2021.105967
read_asap3_fit
! See ?compare_wham_models
and new vignette 8.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).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
.proj.opts$useFMSY
and proj.opts$percentFMSY
options, to project population and catches at (a percentage of) F_MSY. (467532)prepare_wham_input
(thanks to @tcarruth, f270dd)tryCatch
error assignment issues (9d5c87)percentSPR
)prepare_wham_input
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). e20bd8which_F_age
is a vector of annual values (including projection years) and the values are reassigned after fitting before reporting. (189b6c)fit_peel
(e1e00c)sessioninfo
package (within devtools
).exp(10)
). This approximates ASAP + AgePro, allows for simulating projected recruitment according to the ECDF.err
object) 53f5ec6tau
) by effective sample size (Neff
) for option 7 4c133311e-15
to predicted proportions to make age composition likelihoods robust to 0 predictions when selAA is fixed at 0. This affects the multinomial, Dirichlet, and Dirichlet-multinomial (options 1-3), since the logistic normal (options 4-7) already did this. 88f15d4age_comp
argument to prepare_wham_input
. See ?prepare_wham_input
for details. fd94b3drun_all_examples.R
script to test all examples worktidyr::gather
to tidyr::pivot_longer
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