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Merge pull request #146 from gadget-framework/spawning-multiple-stocks
Fix splitting g3a_spawn() offspring over multiple stocks
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,92 @@ | ||
| library(unittest) | ||
| if (!interactive()) options(warn=2, error = function() { sink(stderr()) ; traceback(3) ; q(status = 1) }) | ||
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| library(gadget3) | ||
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| actions <- list() | ||
| area_names <- g3_areas(c('AA', 'BB', 'CC')) | ||
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| st_imm_f <- g3_stock(c(species = "fish", maturity = 'imm', sex = 'f'), seq(5L, 25L, 5)) |> | ||
| g3s_livesonareas(area_names["AA"]) |> | ||
| g3s_age(1L, 5L) | ||
| st_imm_m <- g3_stock(c(species = "fish", maturity = 'imm', sex = 'm'), seq(5L, 25L, 5)) |> | ||
| g3s_livesonareas(area_names["AA"]) |> | ||
| g3s_age(1L, 5L) | ||
| st_mat <- g3_stock(c(species = "fish", maturity = 'mat'), seq(5L, 25L, 5)) |> | ||
| g3s_livesonareas(area_names["AA"]) |> | ||
| g3s_age(3L, 10L) | ||
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| actions <- list( | ||
| g3a_time( | ||
| 1980, 1995, | ||
| step_lengths = c(6L, 6L)), | ||
| g3a_initialconditions(st_imm_f, quote( 0 * stock__midlen ), quote( 0 * stock__midlen )), | ||
| g3a_initialconditions(st_imm_m, quote( 0 * stock__midlen ), quote( 0 * stock__midlen )), | ||
| g3a_initialconditions_normalcv(st_mat), | ||
| g3a_spawn( | ||
| st_mat, | ||
| recruitment_f = g3a_spawn_recruitment_bevertonholt( | ||
| mu = g3_parameterized('spawn_mu', value = 5, by_year = TRUE), | ||
| lambda = g3_parameterized("spawn_lambda", value = 1, by_stock = TRUE) ), | ||
| proportion_f = g3_suitability_exponentiall50(), | ||
| output_stocks = list(st_imm_f, st_imm_m), | ||
| output_ratios = list( | ||
| st_imm_f = quote( g3_param('spawn_ratio', value = 0.5) ), | ||
| st_imm_m = quote( 1 - g3_param('spawn_ratio', value = 0.5) )), | ||
| run_f = quote( cur_step == 1 ) ), | ||
| g3a_age(st_imm_f), | ||
| g3a_age(st_imm_m), | ||
| g3a_age(st_mat) ) | ||
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| # Compile model | ||
| model_fn <- g3_to_r(c(actions, list( | ||
| g3a_report_history(actions, c( | ||
| '__offspringnum$', | ||
| '__num$', | ||
| '__wgt$' ))))) | ||
| if (nzchar(Sys.getenv('G3_TEST_TMB'))) { | ||
| model_cpp <- g3_to_tmb(c(actions, list( | ||
| g3a_report_history(actions, c( | ||
| '__offspringnum$', | ||
| '__num$', | ||
| '__wgt$' ))))) | ||
| # model_cpp <- edit(model_cpp) | ||
| model_tmb <- g3_tmb_adfun(model_cpp, compile_flags = c("-O0", "-g")) | ||
| } else { | ||
| writeLines("# skip: not compiling TMB model") | ||
| } | ||
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| estimate_l50 <- g3_stock_def(st_mat, "midlen")[[length(g3_stock_def(st_mat, "midlen")) / 2]] | ||
| estimate_linf <- max(g3_stock_def(st_mat, "midlen")) | ||
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| for (spawn_ratio in runif(5)) ok_group(paste0("spawn_ratio: ", spawn_ratio), { | ||
| attr(model_fn, 'parameter_template') |> | ||
| g3_init_val("*.Linf", estimate_linf, spread = 0.2) |> | ||
| g3_init_val("*.walpha", 0.01, optimise = FALSE) |> | ||
| g3_init_val("*.wbeta", 3, optimise = FALSE) |> | ||
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| g3_init_val("*.*.l50", estimate_l50, spread = 0.25) |> | ||
| g3_init_val("spawn_ratio", spawn_ratio) |> | ||
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| identity() -> params | ||
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| r <- attributes(model_fn(params)) | ||
| num_spawn <- colSums(r$hist_fish_mat__offspringnum, dims = 3) | ||
| num_m <- colSums(r$hist_fish_imm_m__num, dims = 3) | ||
| num_f <- colSums(r$hist_fish_imm_f__num, dims = 3) | ||
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| ok(ut_cmp_equal( | ||
| cumsum(num_spawn * (1 - spawn_ratio)), | ||
| num_m, | ||
| tolerance = 1e-8), "hist_fish_imm_m__num: Cumulative proportion of __offspringnum") | ||
| ok(ut_cmp_equal( | ||
| cumsum(num_spawn * spawn_ratio), | ||
| num_f, | ||
| tolerance = 1e-8), "hist_fish_imm_f__num: Cumulatve proportion of __offspringnum") | ||
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| if (nzchar(Sys.getenv('G3_TEST_TMB'))) { | ||
| param_template <- attr(model_cpp, "parameter_template") | ||
| param_template$value <- params[param_template$switch] | ||
| gadget3:::ut_tmb_r_compare(model_fn, model_tmb, param_template) | ||
| } | ||
| }) |