R Under development (unstable) (2026-01-10 r89298 ucrt) -- "Unsuffered Consequences"
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> if (!interactive()) options(warn=2, error = function() { sink(stderr()) ; traceback(3) ; q(status = 1) })
> library(unittest)
> 
> library(gadget3)
> 
> # Core years the model will run for
> year_range <- 1975:1990
> 
> areas <- g3_areas(c('1', '2', '3'))
> 
> actions_time <- list(
+   g3a_time(start_year = min(year_range), end_year = max(year_range))
+ )
> 
> ### Configure stocks & stock dynamics
> #########################################
> 
> stocks <- list(
+   imm = g3_stock(c(species = 'bli', maturity = 'imm'), 1:100) |>
+     g3s_age(minage = 0, maxage = 8) |>
+     g3s_livesonareas(areas[c('1', '2', '3')])
+ )
> 
> actions_time <- list(
+   g3a_time(
+     start_year = min(year_range),
+     end_year = max(year_range),
+     step_lengths = rep(3L, 4)
+   )
+ )
> 
> # Define actions for immature stocks
> actions_imm <- list(
+   g3a_initialconditions_normalcv(
+     stocks$imm,
+     cv_f = g3_parameterized('lencv', by_stock = stocks, by_age = TRUE),
+     mean_f = g3a_renewal_vonb_t0(
+         Linf = g3_parameterized('Linf', value = 1, by_stock = TRUE, by_area = TRUE),
+         by_stock = stocks ),
+     by_stock = stocks
+   ),
+   g3a_naturalmortality(stocks$imm, g3a_naturalmortality_exp(by_stock = stocks)),
+   g3a_age(stocks$imm),
+   g3a_growmature(
+     stocks$imm,
+     impl_f = g3a_grow_impl_bbinom(
+       maxlengthgroupgrowth = 10,
+       delta_len_f = g3a_grow_lengthvbsimple(
+           linf_f = g3_parameterized('Linf', by_stock = TRUE, by_area = TRUE),
+           by_stock = stocks ),
+       by_stock = stocks
+     )
+   ),
+   g3a_renewal_normalcv(stocks$imm,
+     mean_f = g3a_renewal_vonb_t0(
+         Linf = g3_parameterized('Linf', value = 1, by_stock = TRUE, by_area = TRUE),
+         by_stock = stocks ),
+      by_stock = stocks)
+ )
> 
> actions <- c(
+   actions_time,
+   actions_imm,
+   # NB: Only required for testing
+   gadget3:::g3l_test_dummy_likelihood()
+ )
> model_fn <- g3_to_r(c(
+   actions,
+   list(
+     g3a_report_detail(actions),
+     g3l_bounds_penalty(actions)
+   )
+ ))
> model_cpp <- g3_to_tmb(c(
+   actions,
+   list(
+     g3a_report_detail(actions),
+     g3l_bounds_penalty(actions)
+   )
+ ))
> 
> params.in.base <-
+   attr(model_fn, 'parameter_template') |>
+ 
+   # Recruitment and initial conditions
+   g3_init_val("recage", 2) |>
+   g3_init_val('*.rec.#', 2) |>
+   g3_init_val('*.init.#', 0.01) |>
+   g3_init_val('*.rec.scalar', 50) |>
+   g3_init_val('*.init.scalar', 0) |>
+   g3_init_val('*.lencv.#', 0.01) |>
+ 
+   # Growth
+   g3_init_val('*.K', 0.05) |>
+   g3_init_val('*.t0', -.5) |>
+   g3_init_val('*.bbin', 100) |>
+   g3_init_val('*.M.#', 0.15) |>
+ 
+   # Weight-length relationship
+   g3_init_val('*.walpha', 8.511e-07) |>
+   g3_init_val('*.wbeta', 3.3264) |>
+ 
+   identity()
> 
> params.in <-
+   params.in.base |>
+   # TODO: We're muddling integer area numbers and names for the parameter table, this needs fixing
+   g3_init_val('*.Linf.1', 40) |>
+   g3_init_val('*.Linf.2', 60) |>
+   g3_init_val('*.Linf.3', 100) |>
+   identity()
> r <- attributes(model_fn(params.in))
> ok(ut_cmp_equal(
+   as.vector(g3_array_agg(r$dstart_bli_imm__num, c("area"), agg = "length_mean", year = 1990, step = 2, age = 8)),
+   c(17.35107, 25.58539, 42.64214),
+   tolerance = 1e-6), "Longest fish in area 3")
ok - Longest fish in area 3
> gadget3:::ut_tmb_r_compare2(model_fn, model_cpp, params.in)
# skip: not running TMB tests 0  <  1
NULL
>   
> params.in <-
+   params.in.base |>
+   # TODO: We're muddling integer area numbers and names for the parameter table, this needs fixing
+   g3_init_val('*.Linf.1', 40) |>
+   g3_init_val('*.Linf.2', 100) |>
+   g3_init_val('*.Linf.3', 40) |>
+   identity()
> r <- attributes(model_fn(params.in))
> ok(ut_cmp_equal(
+   as.vector(g3_array_agg(r$dstart_bli_imm__num, c("area"), agg = "length_mean", year = 1990, step = 2, age = 8)),
+   c(17.35107, 42.64214, 17.35107),
+   tolerance = 1e-6 ), "Longest fish in area 2")
ok - Longest fish in area 2
> gadget3:::ut_tmb_r_compare2(model_fn, model_cpp, params.in)
# skip: not running TMB tests 0  <  1
NULL
>   
> 
> proc.time()
   user  system elapsed 
   8.57    0.37    8.93 
1..2
# Looks like you passed all 2 tests.