R Under development (unstable) (2024-03-18 r86148 ucrt) -- "Unsuffered Consequences"
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> library(magrittr)
> library(unittest)
> 
> library(gadget3)
> 
> actions <- list(
+     g3a_time(
+         start_year = 1990,
+         end_year = 1994,
+         c(3,3,3,3)),
+     g3l_random_dnorm('dnorm_log',
+         ~g3_param('dnorm_log', value = 0, random = TRUE),
+         mean_f = ~g3_param('dnorm_log_mean', value = 0, optimise = FALSE),
+         sigma_f = ~g3_param('dnorm_log_sigma', value = 1, optimise = FALSE),
+         weight = ~g3_param('dnorm_log_enabled', value = 0, optimise = FALSE)),
+     g3l_random_dnorm('dnorm_lin',
+         ~g3_param('dnorm_lin', value = 0, random = TRUE),
+         mean_f = ~g3_param('dnorm_lin_mean', value = 0, optimise = FALSE),
+         sigma_f = ~g3_param('dnorm_lin_sigma', value = 1, optimise = FALSE),
+         log_f = FALSE,
+         weight = ~g3_param('dnorm_lin_enabled', value = 0, optimise = FALSE)),
+     g3l_random_walk('walk_year',
+         ~g3_param_table('walk_year', expand.grid(cur_year = seq(start_year,  end_year)), value = 0, random = TRUE),
+         sigma_f = ~g3_param('walk_year_sigma', value = 1, optimise = FALSE),
+         weight = ~g3_param('walk_year_enabled', value = 0, optimise = FALSE)),
+     g3l_random_walk('walk_step',
+         ~g3_param_table('walk_step', expand.grid(
+             cur_year = seq(start_year,  end_year),
+             cur_step = 1:4), value = 0, random = TRUE),
+         sigma_f = ~g3_param('walk_step_sigma', value = 1, optimise = FALSE),
+         weight = ~g3_param('walk_step_enabled', value = 0, optimise = FALSE)),
+     list('999' = ~{}))
> 
> model_fn <- g3_to_r(actions)
> # model_fn <- edit(model_fn)
> if (nzchar(Sys.getenv('G3_TEST_TMB'))) {
+     model_cpp <- g3_to_tmb(actions, trace = FALSE)
+     # model_cpp <- edit(model_cpp)
+     model_tmb <- g3_tmb_adfun(model_cpp, compile_flags = c("-O0", "-g"))
+ } else {
+     writeLines("# skip: not compiling TMB model")
+     model_cpp <- c()
+ }
# skip: not compiling TMB model
> 
> ok_group('g3l_random_dnorm', {
+     params <- attr(model_fn, 'parameter_template')
+     params['dnorm_log'] <- runif(1, 0, 10)
+     params['dnorm_log_mean'] <- runif(1, 0, 10)
+     params['dnorm_log_sigma'] <- runif(1, 0, 10)
+     params['dnorm_log_enabled'] <- 1
+     params['dnorm_lin'] <- runif(1, 0, 10)
+     params['dnorm_lin_mean'] <- runif(1, 0, 10)
+     params['dnorm_lin_sigma'] <- runif(1, 0, 10)
+     params['dnorm_lin_enabled'] <- 1
+     result <- model_fn(params)
+ 
+     ok(ut_cmp_equal(
+         as.vector(attr(result, "nll_random_dnorm_dnorm_log__dnorm")),
+         -dnorm(params$dnorm_log, params$dnorm_log_mean, params$dnorm_log_sigma, TRUE),
+         tolerance = 1e-7), "dnorm_log matches dnorm")
+     ok(ut_cmp_equal(
+         as.vector(attr(result, "nll_random_dnorm_dnorm_lin__dnorm")),
+         dnorm(params$dnorm_lin, params$dnorm_lin_mean, params$dnorm_lin_sigma, FALSE),
+         tolerance = 1e-7), "dnorm_lin matches dnorm")
+     ok(ut_cmp_equal(
+         as.vector(result),
+         sum(c(
+             -dnorm(params$dnorm_log, params$dnorm_log_mean, params$dnorm_log_sigma, TRUE),
+             dnorm(params$dnorm_lin, params$dnorm_lin_mean, params$dnorm_lin_sigma, FALSE),
+             0)),
+         tolerance = 1e-7), "nll matches both (and has been included only once)")
+ 
+     if (nzchar(Sys.getenv('G3_TEST_TMB'))) {
+         param_template <- attr(model_cpp, "parameter_template")
+         param_template$value <- params[param_template$switch]
+         # Reproduce model to include any unoptimised parameters
+         model_tmb <- g3_tmb_adfun(model_cpp, param_template, compile_flags = c("-O0", "-g"))
+         ok(ut_cmp_identical(names(model_tmb$env$last.par)[model_tmb$env$random], c(
+             'dnorm_lin',
+             'dnorm_log',
+             'walk_step__1990__1',
+             'walk_step__1991__1',
+             'walk_step__1992__1',
+             'walk_step__1993__1',
+             'walk_step__1994__1',
+             'walk_step__1990__2',
+             'walk_step__1991__2',
+             'walk_step__1992__2',
+             'walk_step__1993__2',
+             'walk_step__1994__2',
+             'walk_step__1990__3',
+             'walk_step__1991__3',
+             'walk_step__1992__3',
+             'walk_step__1993__3',
+             'walk_step__1994__3',
+             'walk_step__1990__4',
+             'walk_step__1991__4',
+             'walk_step__1992__4',
+             'walk_step__1993__4',
+             'walk_step__1994__4',
+             'walk_year__1990',
+             'walk_year__1991',
+             'walk_year__1992',
+             'walk_year__1993',
+             'walk_year__1994',
+             NULL)), "env$random: TMB got expected random variables")
+         gadget3:::ut_tmb_r_compare(model_fn, model_tmb, param_template)
+     } else {
+         writeLines("# skip: not running TMB tests")
+     }
+ })
# g3l_random_dnorm
ok - dnorm_log matches dnorm
ok - dnorm_lin matches dnorm
ok - nll matches both (and has been included only once)
# skip: not running TMB tests
> 
> ok_group('g3l_random_walk', {
+     params <- attr(model_fn, 'parameter_template')
+     params['walk_year_enabled'] <- 1
+     params[grepl('walk_year\\.199', names(params))] <- runif(5, 1, 10)
+     params['walk_step_enabled'] <- 1
+     params[grepl('walk_step\\.199', names(params))] <- runif(5 * 4, 1, 10)
+     result <- model_fn(params)
+     
+     # Calculate the sum of a random walk along values
+     sum_walk_dnorm <- function (vals, sigma, is_log) {
+         vals <- vals[order(names(vals))]  # Sort by name, so 1991.1 is before 1991.2
+         lead <- head(vals, -1)
+         lag <- tail(vals, -1)
+         sum(vapply(
+             seq_along(lead),
+             function (i) -dnorm(lead[[i]], lag[[i]], sigma, is_log),
+             numeric(1)))
+     }
+ 
+     ok(ut_cmp_equal(
+         as.vector(attr(result, "nll_random_walk_walk_year__dnorm")),
+         sum_walk_dnorm(params[grepl('walk_year\\.199', names(params))],  params$walk_year_sigma, TRUE),
+         tolerance = 1e-7), "nll_random_walk_walk_year__dnorm")
+ 
+     ok(ut_cmp_equal(
+         as.vector(attr(result, "nll_random_walk_walk_step__dnorm")),
+         sum_walk_dnorm(params[grepl('walk_step\\.199', names(params))],  params$walk_step_sigma, TRUE),
+         tolerance = 1e-7), "nll_random_walk_walk_step__dnorm")
+ 
+     ok(ut_cmp_equal(
+         as.vector(result),
+         as.vector(sum(
+             attr(result, "nll_random_walk_walk_year__dnorm"),
+             attr(result, "nll_random_walk_walk_step__dnorm"),
+             0)),
+         tolerance = 1e-7), "nll matches both")
+ 
+     if (nzchar(Sys.getenv('G3_TEST_TMB'))) {
+         param_template <- attr(model_cpp, "parameter_template")
+         param_template$value <- params[param_template$switch]
+         # Reproduce model to include any unoptimised parameters
+         model_tmb <- g3_tmb_adfun(model_cpp, param_template, compile_flags = c("-O0", "-g"))
+         gadget3:::ut_tmb_r_compare(model_fn, model_tmb, param_template)
+     } else {
+         writeLines("# skip: not running TMB tests")
+     }
+ })
# g3l_random_walk
ok - nll_random_walk_walk_year__dnorm
ok - nll_random_walk_walk_step__dnorm
ok - nll matches both
# skip: not running TMB tests
> 
> if (nzchar(Sys.getenv('G3_TEST_TMB'))) {
+     # An end-to-end test, too complex to be a vignette example
+     in_param <- g3_parameterized('par', by_year = TRUE, random = TRUE, value = 50)
+     out_stock <- g3_stock('output', 1) |> g3s_time(year = 1990:2000)
+ 
+     simple_code <- g3_to_tmb(list(
+         g3a_time(1990, 2000),
+         gadget3:::g3_step(g3_formula(
+             quote( stock_iterate(out_stock, stock_ss(out_stock__val) <- force_type * in_param) ),
+             out_stock = out_stock,
+             # NB: We need to set an array<Type>
+             force_type = as.array(1),
+             out_stock__val = g3_stock_instance(out_stock, 0),
+             in_param = in_param )),
+         g3l_random_dnorm(
+             'rdnorm_par',
+             param_f = in_param,
+             # These need to be Types, not (double), thus g3_formula()
+             mean_f = g3_formula(cur_year * m, m = 0.001),
+             sigma_f = g3_formula(s, s = 1) ),
+         gadget3:::g3a_report_var(
+             'out_stock__val',
+             g3_stock_instance(out_stock, 0),
+             stock = out_stock,
+             out_prefix = NULL),
+         NULL))
+     obj.fn <- g3_tmb_adfun(simple_code)
+     out <- suppressWarnings(optim(obj.fn$par, obj.fn$fn, obj.fn$gr, method = "BFGS", control = list(maxit = 10)))
+     ok(ut_cmp_equal(
+         as.vector(obj.fn$report()$output__val),
+         c(1.99, 1.991, 1.992, 1.993, 1.994, 1.995, 1.996, 1.997, 1.998, 1.999, 2),
+         filter = NULL), "output__val: Found mean for each year")
+ }
> 
> proc.time()
   user  system elapsed 
   0.59    0.04    0.64 
# Looks like you passed all 6 tests.