R Under development (unstable) (2024-07-02 r86866 ucrt) -- "Unsuffered Consequences"
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> library(unittest)
> 
> library(gadget3)
> 
> 
> # Stratified sumofsquares
> prey_a <- g3_stock('prey_a', seq(1, 5, by = 1)) |> g3s_livesonareas(1) |> g3s_age(1,5)
> prey_a__init <- g3_stock_instance(prey_a)
> prey_a__init[] <- rep(10000, length(prey_a__init))
> 
> obsdata <- expand.grid(
+     year = 2000:2005,
+     age = 2:5)  # NB: Only report age 2,5
> obsdata$number <- runif(nrow(obsdata)) * 10000
> 
> actions <- list(
+     g3a_time(2000, 2005, c(6L, 6L)),
+     g3a_initialconditions(
+         prey_a,
+         num_f = g3_formula(stock_ss(prey_a__init), prey_a__init = prey_a__init),
+         wgt_f = 10),
+     g3a_naturalmortality(prey_a),
+     g3a_spawn(
+         prey_a,
+         g3a_spawn_recruitment_bevertonholt(10, 10),
+         output_stocks = list(prey_a)),
+     g3a_age(prey_a),
+     g3l_abundancedistribution("adist",
+         obsdata,
+         function_f = g3l_distribution_surveyindices_linear(alpha = NULL, beta = 1.8),
+         stocks = list(prey_a),
+         report = TRUE))
> actions <- c(actions, list(g3a_report_detail(actions)))
> model_fn <- g3_to_r(actions)
> model_cpp <- g3_to_tmb(actions)
> 
> params <- attr(model_fn, 'parameter_template')
> params['report_detail'] <- 1
> 
> r <- model_fn(params)
> modeldata <- attr(r, 'prey_a__num')
> 
> exp_nll <- 0
> for (age in unique(obsdata$age)) {
+     ok_group(paste0("age = ", age))
+     N <- colSums(attr(r, 'detail_prey_a__num')[,,age = age,], 2)
+     N <- colSums(array(N, dim=c(2,length(N) / 2)))  # Group timestep by year
+     I <- obsdata[obsdata$age == age, 'number']
+     alpha <- mean(I) - 1.8 * mean(N)
+     exp_nll <- exp_nll + sum((alpha + 1.8 * N - I)**2)
+ 
+     # NB:  __params is a bit broken from a reporting perspective. Should be giving all params, not just the final
+     if (age == max(obsdata$age)) ok(ut_cmp_equal(
+         attr(r, 'adist_surveyindices_linear_adist_model__params'),
+         c(alpha, 1.8)), "__params: Linear regression matches expected")
+ }
# age = 2
# age = 3
# age = 4
# age = 5
ok - __params: Linear regression matches expected
> ok(ut_cmp_equal(as.vector(r), exp_nll), "Total nll matches expected")
ok - Total nll matches expected
> 
> if (Sys.getenv('G3_TEST_TMB') == "2") {
+     #model_cpp <- edit(model_cpp)
+     #writeLines(TMB::gdbsource(g3_tmb_adfun(model_cpp, compile_flags = "-g", output_script = TRUE)))
+     model_tmb <- g3_tmb_adfun(model_cpp, trace = TRUE, parameters = params, compile_flags = c("-O0", "-g"))
+     gadget3:::ut_tmb_r_compare(model_fn, model_tmb, params, model_cpp = model_cpp)
+ }
> 
> proc.time()
   user  system elapsed 
   1.04    0.12    1.17 
# Looks like you passed all 2 tests.