NEWS

gadget3 0.12-1-999

All-zero lengthgroups in initialconditions / > 1 maturity ratios no longer result in NaN #187 #182

The stock column in likelihood data can now contain name parts as well as full stock names
g3_to_r-produced model functions will accept both a list & data.frame parameter template
g3_to_r models can include arbitary R functions, see vignettes/writing_actions #194
Add g3_array_agg #193
Add surplus production model action g3a_spmodel #209

Split likelihood distribution by predator_length / predator_age / predator_tag #154
Predation support, see ?g3a_predate / ?g3a_predate_catchability_predator #29
g3a_otherfood, g3a_otherfood_normalparam, g3a_otherfood_normalcv #155
Support length transform_fs in g3l_catchdistribution #95

g3_to_r() output can be debugged in R-Studio
Unknown stock names in likelihood data now an error
g3l_distribution_surveyindices_*() can now be broken down by age without error

Add g3_parameterized('x', by_year = 1998:2099) to override year range for parameters
Add g3a_initialconditions_normalcv for initialconditions driven by a lencv parameter
Add g3a_renewal_normalcv for initialconditions driven by a lencv parameter
by_predator parameter for g3_parameterized
Defaults for g3_suitability_exponentiall50
Support cut() formatted character columns as well as factor columns in likelihood observation data.
Add g3_init_val() helper, to replace gadgetutils::g3_init_guess()
Add g3_areas() helper to create numbered area vectors
Add g3_distribution_preview() helper to see how observatation data will be converted to array
period now optional for g3l_random_walk(), g3l_random_dnorm()
g3l_bounds_penalty() can now generate bounds from actions which update automatically

g3l_distribution_surveyindices_* now default to beta = 1, set beta = NULL to restore previous behaviour.
stock_param() & stock_param_table() replaced with stock_prepend()
Remove unused g3_to_tmb(adreport_re) option #60
Naturalmortality M now by-age by default #113
g3_suitability_andersenfleet() now uses by_predator = TRUE by default #133

Add g3_parameterized('x', by_step = TRUE) for seasonal parameters #115
Support R factor levels as well as MFDB-style attributes for likelihood observation data. This means dplyr group_by(length = cut(...)) can be used as well as MFDB for groupings #112
Parameterised defaults for g3l_understocking(), g3a_naturalmortality(), g3a_renewal_normalparam()
Add g3a_renewal_vonb_t0() & g3a_renewal_vonb_recl(), with g3a_renewal_vonb() being an alias to the latter

Remove scale = 0.001 from default K parameters in g3a_grow, g3a_renew_*
g3a_renewal_vonb_t0() is now the default mean_f for *_normalparam()
g3a_initialconditions_normalparam() now offsets any age in mean_f (i.e. the VonB formula) by cur_step_size, in effect running at step -1.

g3_suitability_andersen() now produces sensible values - https://github.com/gadget-framework/gadget3/issues/108
g3a_age() now supports stocks with a single age (i.e. minage == maxage)

Add recage parameter to g3a_renewal_vonb / g3a_renewal_initabund
Add g3_suitability_andersenfleet(), a fleet-specialised andsersen suitability function.
Make g3_is_stock() public
g3_eval(), to evaluate snippets of a gadget3 model.

g3l_distribution_*(transform_fs = ...) now happens before aggregation, not after. Any matrix used now has to be expressed in terms of the stock, not aggregated age.
g3_param_table() now returns NaN (and warns) on a missing value, instead of aborting.
optim(g3_tmb_par(...)) is now an error. When optimising, always use obj.fun$par.

Support as.vector(array) in TMB formulas, so arrays can be used with TMB vectorized functions, e.g. pnorm(as.vector(ar[,1])).