Last updated on 2025-07-09 11:50:59 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| gadget3 | 1 | 12 | |
| mfdb | 4 | 9 | |
| unittest | 13 |
Current CRAN status: ERROR: 1, OK: 12
Version: 0.13-0
Check: tests
Result: ERROR
Running 'test-aab_env.R' [1s]
Running 'test-action_age.R' [2s]
Running 'test-action_grow-methods.R' [4s]
Running 'test-action_grow.R' [2s]
Running 'test-action_mature.R' [2s]
Running 'test-action_migrate.R' [2s]
Running 'test-action_naturalmortality.R' [1s]
Running 'test-action_predate-catchability.R' [5s]
Running 'test-action_predate-numberfleet.R' [2s]
Running 'test-action_predate-predator.R' [11s]
Running 'test-action_predate-timebasedsuitability.R' [2s]
Running 'test-action_predate.R' [5s]
Running 'test-action_renewal-otherfood.R' [7s]
Running 'test-action_renewal.R' [4s]
Running 'test-action_report.R' [1s]
Running 'test-action_spawn-multipleoutputs.R' [4s]
Running 'test-action_spawn.R' [4s]
Running 'test-action_spmodel.R' [2s]
Running 'test-action_tagging.R' [2s]
Running 'test-action_time.R' [1s]
Running 'test-action_weightloss.R' [2s]
Running 'test-array_utils.R' [4s]
Running 'test-env_dif.R' [1s]
Running 'test-eval.R' [1s]
Running 'test-formula_utils.R' [1s]
Running 'test-init_val.R' [1s]
Running 'test-likelihood_bounds.R' [3s]
Running 'test-likelihood_data.R' [3s]
Running 'test-likelihood_distribution-surveyindices.R' [2s]
Running 'test-likelihood_distribution.R' [13s]
Running 'test-likelihood_random.R' [1s]
Running 'test-likelihood_sparsesample.R' [3s]
Running 'test-likelihood_tagging_ckmr.R' [3s]
Running 'test-likelihood_understocking.R' [0s]
Running 'test-param_project-ar1.R' [3s]
Running 'test-param_project-logar1.R' [3s]
Running 'test-param_project.R' [2s]
Running 'test-params.R' [2s]
Running 'test-quota-assess.R' [5s]
Running 'test-quota-hockeyfleet.R' [3s]
Running 'test-quota.R' [1s]
Running 'test-regression.R' [1s]
Running 'test-run.R' [1s]
Running 'test-run_r.R' [2s]
Running 'test-run_tmb-reporting_enabled.R' [1s]
Running 'test-run_tmb.R' [3s]
Running 'test-step.R' [2s]
Running 'test-stock.R' [1s]
Running 'test-stock_age.R' [2s]
Running 'test-stock_areas.R' [2s]
Running 'test-stock_product.R' [0s]
Running 'test-stock_tag.R' [1s]
Running 'test-stock_time-fishingyear.R' [2s]
Running 'test-stock_time.R' [1s]
Running 'test-suitability-report.R' [6s]
Running 'test-suitability.R' [2s]
Running 'test-timedata.R' [1s]
Running 'test-timevariable.R' [1s]
Running the tests in 'tests/test-likelihood_distribution.R' failed.
Complete output:
> library(magrittr)
> library(unittest)
>
> library(gadget3)
>
> # Zip name/value arguments together into a list
> named_list <- function(...) {
+ x <- list(...)
+ structure(
+ x[seq_along(x) %% 2 == 0],
+ names = as.character(x[seq_along(x) %% 2 == 1]))
+ }
>
> cmp_grep <- function (a, ...) {
+ re <- paste0('\\Q', c(...), '\\E', collapse = ".*")
+ if (grepl(re, a, perl = TRUE)) return(TRUE)
+ c(re, "Not found in:", a)
+ }
>
> # NB: Name has to be different, or it gets sucked into the model
> g3_avoid_zero <- g3_env$avoid_zero
> g3_logspace_add <- g3_env$logspace_add
> g3_lgamma_vec <- lgamma
>
> ok_group("g3_distribution_preview", {
+ dat <- expand.grid(year = 1990:1994, step = 2, area = 'IXa')
+ dat$number <- seq_len(nrow(dat))
+ out <- g3_distribution_preview(dat, area_group = c(IXa = 1))
+ ok(ut_cmp_equal(out, structure(
+ 1:5,
+ dim = c(length = 1L, time = 5L, area = 1L),
+ dimnames = list(
+ length = "0:Inf",
+ time = c("1990-02", "1991-02", "1992-02", "1993-02", "1994-02"),
+ area = "IXa") )), "Returned number array")
+
+ dat <- expand.grid(year = 1990:1994, step = 2, area = 'IXa')
+ dat$weight <- seq_len(nrow(dat)) * 40
+ out <- g3_distribution_preview(dat, area_group = c(IXa = 1))
+ ok(ut_cmp_equal(out, structure(
+ 1:5 * 40,
+ dim = c(length = 1L, time = 5L, area = 1L),
+ dimnames = list(
+ length = "0:Inf",
+ time = c("1990-02", "1991-02", "1992-02", "1993-02", "1994-02"),
+ area = "IXa") )), "Returned weight array")
+
+ dat <- expand.grid(year = 1990:1994, step = 2, area = 'IXa')
+ dat$number <- seq_len(nrow(dat)) * 9
+ dat$weight <- seq_len(nrow(dat)) * 40
+ out <- g3_distribution_preview(dat, area_group = c(IXa = 1))
+ ok(ut_cmp_equal(out, structure(
+ 1:5 * 9,
+ dim = c(length = 1L, time = 5L, area = 1L),
+ dimnames = list(
+ length = "0:Inf",
+ time = c("1990-02", "1991-02", "1992-02", "1993-02", "1994-02"),
+ area = "IXa") )), "Number array wins if both present")
+
+ stocks <- list(
+ g3_stock(c(species = 'fish', 'imm', 'f'), 1:10),
+ g3_stock(c(species = 'fish', 'imm', 'm'), 1:10),
+ g3_stock(c(species = 'fish', 'mat', 'f'), 1:10),
+ g3_stock(c(species = 'fish', 'mat', 'm'), 1:10) )
+ dat <- expand.grid(year = 1990:1994, stock = c("imm", "mat"), number = 0)
+ out <- drop(g3_distribution_preview(dat, stocks = stocks, area_group = c(IXa = 1)))
+ ok(ut_cmp_identical(out, structure(
+ array(0, dim = c(stock = 2L, time = 5L), dimnames = list(stock = c("imm", "mat"), time = c("1990", "1991", "1992", "1993", "1994"))),
+ stock_map = c(fish_imm_f = "imm", fish_imm_m = "imm", fish_mat_f = "mat", fish_mat_m = "mat") )), "Included stock map for stock column")
+
+ fleets <- list(
+ g3_fleet(c('comm', 'se')),
+ g3_fleet(c('comm', 'no')),
+ g3_fleet(c('surv')) )
+ dat <- expand.grid(year = 1990:1994, fleet = c("comm", "surv"), number = 0)
+ out <- drop(g3_distribution_preview(dat, fleets = fleets, area_group = c(IXa = 1)))
+ ok(ut_cmp_identical(out, structure(
+ array(0, dim = c(fleet = 2L, time = 5L), dimnames = list(fleet = c("comm", "surv"), time = c("1990", "1991", "1992", "1993", "1994"))),
+ fleet_map = c(comm_se = "comm", comm_no = "comm", surv = "surv") )), "Included fleet map for fleet column")
+ })
# g3_distribution_preview
ok - Returned number array
ok - Returned weight array
ok - Number array wins if both present
ok - Included stock map for stock column
ok - Included fleet map for fleet column
>
> ok_group("g3l_distribution_sumofsquares", {
+ ok(cmp_grep(
+ deparse1(environment(g3l_distribution_sumofsquares(c('area', 'age')))$modelstock__sstotal),
+ 'sum(stock_ssinv(modelstock__x, "time", "area", "age"))',
+ NULL), "Added custom totals to sumofsquares modelstock__x")
+ ok(cmp_grep(
+ deparse1(environment(g3l_distribution_sumofsquares(c('area', 'age')))$obsstock__sstotal),
+ 'sum(stock_ssinv(obsstock__x, "time", "area", "age"))',
+ NULL), "Added custom totals to sumofsquares modelstock__x")
+ ok(cmp_grep(
+ deparse1(g3l_distribution_sumofsquares(c('area', 'length'))),
+ 'stock_ss(modelstock__x, length = default)',
+ 'modelstock__sstotal[[modelstock__length_idx]]',
+ 'stock_ss(obsstock__x, length = default)',
+ 'obsstock__sstotal[[obsstock__length_idx]]',
+ NULL), "Adding length also adds to the stock_ss()")
+
+ # Stratified sumofsquares
+ prey_a <- g3_stock('prey_a', seq(1, 5, by = 1)) %>% g3s_age(1,5)
+ prey_a__init <- g3_stock_instance(prey_a)
+ prey_a__init[] <- runif(length(prey_a__init))
+ obsdata <- expand.grid(
+ year = 2000,
+ length = seq(1, 5, by = 1),
+ age = 3:4) # NB: Only report age 3,4
+ obsdata$number <- runif(nrow(obsdata))
+ model_fn <- g3_to_r(list(
+ # Keep TMB happy
+ g3_formula({
+ nll <- nll + g3_param("dummy", value = 0)
+ REPORT(prey_a__num)
+ }),
+ g3a_time(2000, 2001),
+ g3a_initialconditions(prey_a,
+ num_f = g3_formula(stock_ss(prey_a__init), prey_a__init = prey_a__init),
+ wgt_f = 10),
+ g3l_abundancedistribution("adist",
+ obsdata,
+ function_f = g3l_distribution_sumofsquares(over = c("area", "length")),
+ stocks = list(prey_a),
+ report = TRUE)))
+ model_cpp <- g3_to_tmb(attr(model_fn, 'actions'), trace = FALSE)
+ if (Sys.getenv('G3_TEST_TMB') == "2") {
+ #model_cpp <- edit(model_cpp)
+ #writeLines(TMB::gdbsource(g3_tmb_adfun(model_cpp, compile_flags = "-g", output_script = TRUE)))
+ model_tmb <- g3_tmb_adfun(model_cpp, trace = TRUE, compile_flags = c("-O0", "-g"))
+ }
+
+ params <- attr(model_fn, 'parameter_template')
+ r <- model_fn(params)
+ modeldata <- attr(r, 'prey_a__num')
+ expected_nll <- 0
+ for (age in 3:4) for (length in 1:5) {
+ # Proportion compared to others in age group, for that length
+ expected_nll <- expected_nll + (
+ # Proportion compared to others in this length group
+ modeldata[length, age] / sum(modeldata[length, c(3,4)]) -
+ obsdata[obsdata$age == age & obsdata$length == length, 'number'] / sum(obsdata[obsdata$length == length, 'number'])
+ ) ** 2
+ }
+ ok(ut_cmp_equal(as.numeric(r), expected_nll), "g3l_distribution_sumofsquares statified over length")
+ if (Sys.getenv('G3_TEST_TMB') == "2") gadget3:::ut_tmb_r_compare(model_fn, model_tmb, params, model_cpp = model_cpp)
+ })
# g3l_distribution_sumofsquares
ok - Added custom totals to sumofsquares modelstock__x
ok - Added custom totals to sumofsquares modelstock__x
ok - Adding length also adds to the stock_ss()
not ok - g3l_distribution_sumofsquares statified over length
# Test returned non-TRUE value:
# Mean relative difference: 0.001187689
# --- as.numeric(r)
# +++ expected_nll
# [1] [-1.369097-]{+1.370723+}
>
> ok_group("g3l_distribution:transform_fs", {
+ prey_a <- g3_stock('prey_a', seq(1, 5, by = 1)) %>% g3s_age(1,5) %>% g3s_livesonareas(1:2)
+ prey_a__init <- g3_stock_instance(prey_a)
+ prey_a__init[] <- runif(length(prey_a__init))
+ obsdata <- expand.grid(
+ year = 2000,
+ length = seq(1, 5, by = 1),
+ age = 1:5)
+ obsdata$number <- runif(nrow(obsdata))
+ model_fn <- g3_to_r(list(
+ g3a_time(2000, 2001),
+ g3a_initialconditions(prey_a,
+ num_f = g3_formula(stock_ss(prey_a__init), prey_a__init = prey_a__init),
+ wgt_f = 10),
+ g3l_abundancedistribution("wt",
+ obsdata,
+ function_f = g3l_distribution_sumofsquares(),
+ stocks = list(prey_a),
+ transform_fs = list(
+ age = g3_formula( g3_param_array('reader1matrix', value = diag(5))[g3_idx(preage), g3_idx(age)] )),
+ report = TRUE),
+ g3l_abundancedistribution("len",
+ obsdata,
+ function_f = g3l_distribution_sumofsquares(),
+ stocks = list(prey_a),
+ transform_fs = list(
+ length = quote(diag(10 * prey_a__midlen)) ),
+ report = TRUE),
+ g3l_abundancedistribution("wtperstock",
+ obsdata,
+ function_f = g3l_distribution_sumofsquares(),
+ stocks = list(prey_a),
+ transform_fs = list(age = list(
+ prey_a = g3_formula(g3_param_array('reader1matrix', value = diag(prey_a__maxage - prey_a__minage + 1))[prey_a__preage_idx, prey_a__age_idx] ))),
+ report = TRUE),
+ g3l_abundancedistribution("nt",
+ obsdata,
+ function_f = g3l_distribution_sumofsquares(),
+ stocks = list(prey_a),
+ report = TRUE),
+ # Keep TMB happy
+ g3_formula( nll <- nll + g3_param("dummy", value = 0) )))
+ model_cpp <- g3_to_tmb(attr(model_fn, 'actions'), trace = FALSE)
+ if (Sys.getenv('G3_TEST_TMB') == "2") {
+ #model_cpp <- edit(model_cpp)
+ #writeLines(TMB::gdbsource(g3_tmb_adfun(model_cpp, compile_flags = "-g", output_script = TRUE)))
+ model_tmb <- g3_tmb_adfun(model_cpp, trace = TRUE, compile_flags = c("-O0", "-g"))
+ }
+
+ # Given results / params, apply matrix manually and make sure the results match
+ do_test <- function (r, params, msg) {
+ nt <- attr(r, 'adist_sumofsquares_nt_model__num')
+ wt <- attr(r, 'adist_sumofsquares_wt_model__num')
+ wtperstock <- attr(r, 'adist_sumofsquares_wtperstock_model__num')
+ m <- params$reader1matrix
+ apply_matrix <- function (destage) {
+ nt[,1,] * m[1,destage] +
+ nt[,2,] * m[2,destage] +
+ nt[,3,] * m[3,destage] +
+ nt[,4,] * m[4,destage] +
+ nt[,5,] * m[5,destage] +
+ 0
+ }
+ ok(ut_cmp_equal(wt, wtperstock), paste0("wt / wtperstock: ", msg))
+ ok(ut_cmp_equal(apply_matrix(1), wt[,1,]), paste0("age1: ", msg))
+ ok(ut_cmp_equal(apply_matrix(2), wt[,2,]), paste0("age2: ", msg))
+ ok(ut_cmp_equal(apply_matrix(3), wt[,3,]), paste0("age3: ", msg))
+ ok(ut_cmp_equal(apply_matrix(4), wt[,4,]), paste0("age4: ", msg))
+ ok(ut_cmp_equal(apply_matrix(5), wt[,5,]), paste0("age5: ", msg))
+ }
+
+ params <- attr(model_fn, 'parameter_template')
+ r <- model_fn(params)
+ do_test(r, params, "Identity matrix")
+ if (Sys.getenv('G3_TEST_TMB') == "2") gadget3:::ut_tmb_r_compare(model_fn, model_tmb, params, model_cpp = model_cpp)
+
+ # Length vector applied for len
+ ok(ut_cmp_equal(
+ attr(r, "adist_sumofsquares_len_model__num"),
+ attr(r, "adist_sumofsquares_nt_model__num") * (10 * g3_stock_def(prey_a, 'midlen')),
+ unused = NULL), "r$adist_sumofsquares_len_model__num: Length vector applied")
+
+ params <- attr(model_fn, 'parameter_template')
+ # Age 1 smeared over bottom 3 groups
+ params$reader1matrix[1,] <- c(0.5, 0.25, 0.25, 0, 0)
+ # Age 2 smeared over 2 groups
+ params$reader1matrix[2,] <- c(0, 0.75, 0.25, 0, 0)
+ r <- model_fn(params)
+ do_test(r, params, "age1, age2 smeared")
+ if (Sys.getenv('G3_TEST_TMB') == "2") gadget3:::ut_tmb_r_compare(model_fn, model_tmb, params, model_cpp = model_cpp)
+ })
# g3l_distribution:transform_fs
ok - wt / wtperstock: Identity matrix
ok - age1: Identity matrix
ok - age2: Identity matrix
ok - age3: Identity matrix
ok - age4: Identity matrix
ok - age5: Identity matrix
ok - r$adist_sumofsquares_len_model__num: Length vector applied
ok - wt / wtperstock: age1, age2 smeared
ok - age1: age1, age2 smeared
ok - age2: age1, age2 smeared
ok - age3: age1, age2 smeared
ok - age4: age1, age2 smeared
ok - age5: age1, age2 smeared
>
> # g3l_distribution_sumofsquaredlogratios
> ok(ut_cmp_identical(
+ deparse1(g3l_distribution_sumofsquaredlogratios()),
+ "~sum((log(stock_ss(obsstock__x) + 10) - log(stock_ss(modelstock__x) + 10))^2)"), "g3l_distribution_sumofsquaredlogratios: Formula code as expected")
ok - g3l_distribution_sumofsquaredlogratios: Formula code as expected
> ok(ut_cmp_identical(
+ length(environment(g3l_distribution_sumofsquaredlogratios())), 0L), "g3l_distribution_sumofsquaredlogratios: Environment empty")
ok - g3l_distribution_sumofsquaredlogratios: Environment empty
>
> # NB: Also added some aggregate areas for fleet data
> areas <- list(a = 1, b = 2, c = 3, x = 1:2, y = 3)
> prey_a <- g3_stock('prey_a', seq(1, 10)) %>% g3s_livesonareas(areas[c('a')])
> prey_b <- g3_stock('prey_b', seq(1, 10)) %>% g3s_livesonareas(areas[c('b')])
> prey_c <- g3_stock('prey_c', seq(1, 10)) %>% g3s_livesonareas(areas[c('c')])
> fleet_abc <- g3_fleet('fleet_abc') %>% g3s_livesonareas(areas[c('a', 'b', 'c')])
>
> # Generate observation data for stock distribution
> # NB: No prey_b, only compare prey_a and prey_c
> sd_data <- expand.grid(year = 1999:2000, step = c(1, 2), area = c('x', 'y'), stock = c("prey_a", "prey_c"), length = c(1,6))
> sd_data$number <- floor(runif(length(sd_data$year), min=100, max=999))
>
> # Generate observation data for catch distribution
> cd_data <- expand.grid(year = 1999:2000, step = c(1, 2), area = c('x', 'y'), length = c(1,6))
> cd_data$number <- floor(runif(length(cd_data$year), min=100, max=999))
>
> # Generate observation data for catch distribution by biomass
> cd_weight_data <- expand.grid(year = 1999:2000, step = c(1, 2), area = c('x', 'y'), length = c(1,6))
> cd_weight_data$weight <- floor(runif(length(cd_data$year), min=1000, max=9999))
>
> # Generate observation data for catch distribution (multinomial)
> multinomial_data <- expand.grid(year = 1999:2000, step = c(1, 2), length = c(1,6))
> multinomial_data$number <- floor(runif(length(multinomial_data$year), min=100, max=999))
>
> surveyindices_data <- expand.grid(year = 1999:2000, step = c(1, 2))
> surveyindices_data$number <- floor(runif(length(surveyindices_data$year), min=100, max=999))
>
> # Can't make catchdistribution without fleets
> ok(ut_cmp_error(g3l_catchdistribution(
+ 'utcd',
+ cd_data,
+ fleets = list(),
+ stocks = list(prey_a, prey_b, prey_c),
+ area_group = areas,
+ g3l_distribution_sumofsquares()), "fleets/predators must be supplied"), "g3l_catchdistribution: Invalid without fleets")
ok - g3l_catchdistribution: Invalid without fleets
> ok(ut_cmp_error(g3l_abundancedistribution(
+ 'utcd',
+ cd_data,
+ fleets = list(fleet_abc),
+ stocks = list(prey_a, prey_b, prey_c),
+ area_group = areas,
+ g3l_distribution_sumofsquares()), "fleets/predators must not be supplied"), "g3l_abundancedistribution: Invalid with fleets")
ok - g3l_abundancedistribution: Invalid with fleets
>
> # Generate a step that reports the value of (var_name) into separate variable (steps) times
> # (initial_val) provides a definition to use to set variable type
> report_step <- function (var_name, steps, initial_val) {
+ out <- ~{}
+ for (i in seq(steps - 1, 0, by = -1)) {
+ step_var_name <- paste0("step", i, "_", var_name)
+ assign(step_var_name, initial_val)
+ out <- gadget3:::f_optimize(gadget3:::f_substitute(~if (cur_time == i) {
+ comment(report_comment)
+ if (is_nll) {
+ # nll is a scalar, and should have attributes stripped
+ step_var <- as.numeric(nll)
+ } else {
+ step_var[] <- var
+ }
+ REPORT(step_var)
+ } else rest, list(
+ report_comment = paste0("Reporting on ", var_name, " at step ", i),
+ is_nll = var_name == 'nll',
+ step_var = as.symbol(step_var_name),
+ var = as.symbol(var_name),
+ i = i,
+ rest = out )))
+ }
+ return(out)
+ }
>
> base_actions <- list(
+ g3a_time(1999,2000, step_lengths = c(6, 6), project_years = 0),
+ g3a_initialconditions(prey_a, ~10 * prey_a__midlen, ~100 * prey_a__midlen),
+ g3a_initialconditions(prey_b, ~10 * prey_b__midlen, ~100 * prey_b__midlen),
+ g3a_initialconditions(prey_c, ~10 * prey_c__midlen, ~100 * prey_c__midlen),
+ g3a_predate_totalfleet(
+ fleet_abc,
+ list(prey_a, prey_b, prey_c),
+ suitabilities = list(
+ prey_a = ~g3_param_vector("fleet_abc_a") + 0 * stock__midlen,
+ prey_b = ~g3_param_vector("fleet_abc_b") + 0 * stock__midlen,
+ prey_c = ~g3_param_vector("fleet_abc_c") + 0 * stock__midlen),
+ amount_f = ~g3_param('amount_ab', value = 100) * area),
+ named_list(
+ # Capture data just before final step erases it
+ gadget3:::step_id(10, 'g3l_distribution', 'cdist_sumofsquares_utcd', 1, 'zzzz'), report_step('cdist_sumofsquares_utcd_model__num', 4, array(
+ # NB: Lift definition from deparse(r$cdist_sumofsquares_utcd_model__num)
+ dim = c(2L, 2L),
+ dimnames = list(
+ c("1:6", "6:10"),
+ c("x", "y")))),
+ gadget3:::step_id(10, 'g3l_distribution', 'cdist_sumofsquares_utsd', 1, 'zzzz'), report_step('cdist_sumofsquares_utsd_model__num', 4, array(
+ # NB: Lift definition from deparse(r$cdist_sumofsquares_utsd_model__num)
+ dim = c(2L, 2L, 2L),
+ dimnames = list(
+ c("1:6", "6:10"),
+ c("prey_a", "prey_c"),
+ c("x", "y")))),
+ gadget3:::step_id(10, 'g3l_distribution', 'cdist_sumofsquares_utcd_weight', 1, 'zzzz'), report_step('cdist_sumofsquares_utcd_weight_model__wgt', 4, array(
+ # NB: Lift definition from deparse(r$cdist_sumofsquares_utcd_weight_model__wgt)
+ dim = c(2L, 2L),
+ dimnames = list(
+ c("1:6", "6:10"),
+ c("x", "y")))),
+ gadget3:::step_id(10, 'g3l_distribution', 'cdist_multinomial_multinom', 1, 'zzzz'), report_step('cdist_multinomial_multinom_model__num', 4, array(
+ # NB: Lift definition from deparse(r$cdist_multinomial_multinom_model__num)
+ dim = c(2L),
+ dimnames = list(
+ c("1:6", "6:10")))),
+ gadget3:::step_id(990, 'prey_a__num'), report_step('prey_a__num', 4, g3_stock_instance(prey_a)),
+ gadget3:::step_id(990, 'prey_b__num'), report_step('prey_b__num', 4, g3_stock_instance(prey_b)),
+ gadget3:::step_id(990, 'prey_c__num'), report_step('prey_c__num', 4, g3_stock_instance(prey_c)),
+ gadget3:::step_id(990, 'nll'), report_step('nll', 4, 0.0),
+ gadget3:::step_id(999), ~{
+ REPORT(cdist_sumofsquares_utcd_model__num)
+ REPORT(cdist_sumofsquares_utcd_obs__num)
+ REPORT(cdist_sumofsquares_utcd_weight_model__wgt)
+ REPORT(cdist_sumofsquares_utcd_weight_obs__wgt)
+ REPORT(cdist_sumofsquares_utsd_model__num)
+ REPORT(cdist_sumofsquares_utsd_obs__num)
+ REPORT(cdist_multinomial_multinom_model__num)
+ REPORT(cdist_multinomial_multinom_obs__num)
+ REPORT(prey_a__wgt)
+ REPORT(prey_b__wgt)
+ REPORT(prey_c__wgt)
+ REPORT(prey_a__num)
+ REPORT(prey_b__num)
+ REPORT(prey_c__num)
+
+ # NB: In theory we could inspect the return value, but TMB doesn't give an easy public method for that
+ REPORT(nll)
+ }))
> actions <- c(base_actions, list(
+ g3l_catchdistribution(
+ 'utcd',
+ cd_data,
+ list(fleet_abc),
+ list(prey_a, prey_b, prey_c),
+ area_group = areas,
+ g3l_distribution_sumofsquares()),
+ g3l_catchdistribution(
+ 'utcd_weight',
+ cd_weight_data,
+ list(fleet_abc),
+ list(prey_a, prey_b, prey_c),
+ area_group = areas,
+ g3l_distribution_sumofsquares()),
+ g3l_catchdistribution(
+ 'utsd',
+ sd_data,
+ list(fleet_abc),
+ list(prey_a, prey_b, prey_c),
+ area_group = areas,
+ g3l_distribution_sumofsquares()),
+ g3l_catchdistribution(
+ 'multinom',
+ multinomial_data,
+ list(fleet_abc),
+ list(prey_a),
+ area_group = areas,
+ g3l_distribution_multinomial()),
+ g3l_abundancedistribution(
+ 'surveyindices',
+ surveyindices_data,
+ fleets = list(),
+ stocks = list(prey_b),
+ area_group = areas,
+ report = TRUE, # NB: Using built-in reporting vs. version hacked in tests
+ g3l_distribution_surveyindices_log(alpha = ~g3_param("si_alpha", value = 0), beta = ~g3_param("si_beta", value = 0))),
+ NULL))
> actions <- c(actions, list(
+ # NB: Don't use _detail, since it doesn't play well with report_step()
+ # Ideally we'd remove report_step, but we have to time it exactly between data-collect and reset
+ g3a_report_history(actions, '__cons$', out_prefix = "detail_") ))
>
> # Compile model
> model_fn <- g3_to_r(actions, trace = FALSE)
> # model_fn <- edit(model_fn)
> if (nzchar(Sys.getenv('G3_TEST_TMB'))) {
+ params <- attr(model_fn, 'parameter_template')
+ params$fleet_abc_a <- c(0, 0, 0, 0.1, 0.2, 0.1, 0, 0, 0, 0)
+ params$fleet_abc_b <- c(0, 0, 0, 0, 0, 0.1, 0.2, 0.1, 0, 0)
+ params$fleet_abc_c <- c(0, 0, 0, 0, 0, 0, 0.1, 0.2, 0.1, 0)
+
+ model_cpp <- g3_to_tmb(actions, trace = FALSE)
+ # model_cpp <- edit(model_cpp)
+ model_tmb <- g3_tmb_adfun(model_cpp, params, compile_flags = c("-O0", "-g"))
+ } else {
+ writeLines("# skip: not compiling TMB model")
+ model_cpp <- c()
+ }
# skip: not compiling TMB model
>
> ok_group("Likelihood per step", {
+ params <- attr(model_fn, 'parameter_template')
+ # Randomly catch, but get something everywhere
+ params$fleet_abc_a <- runif(10, min=0.1, max=0.9)
+ params$fleet_abc_b <- runif(10, min=0.1, max=0.9)
+ params$fleet_abc_c <- runif(10, min=0.1, max=0.9)
+ params$amount_ab <- 1000000
+ params$si_alpha <- 4
+ params$si_beta <- 2
+ params$cdist_sumofsquares_utcd_weight <- 1
+ params$cdist_sumofsquares_utcd_weight_weight <- 1
+ params$cdist_sumofsquares_utsd_weight <- 1
+ params$cdist_multinomial_multinom_weight <- 1
+ params$adist_surveyindices_log_surveyindices_weight <- 1
+
+ result <- model_fn(params)
+ r <- attributes(result)
+ # str(result)
+ # str(as.list(r), vec.len = 10000)
+
+ ok(ut_cmp_equal(
+ sort(as.vector(r$cdist_sumofsquares_utsd_obs__num)),
+ sort(sd_data$number)), "cdist_sumofsquares_utsd_obs__num: Imported from data.frame, order not necessarily the same")
+
+ ok(ut_cmp_equal(
+ r$adist_surveyindices_log_surveyindices_model__params,
+ c(params$si_alpha, params$si_beta)), "adist_surveyindices_log_surveyindices_model__params: Reported our hard-coded linear regression parameters")
+
+ ######## cdist_sumofsquares_utsd_model__num
+ ok(ut_cmp_equal(as.vector(r$step0_cdist_sumofsquares_utsd_model__num[,'prey_a', 1]), c(
+ sum(r$detail_prey_a_fleet_abc__cons[1:5,,1] / r$prey_a__wgt[1:5,]),
+ sum(r$detail_prey_a_fleet_abc__cons[6:10,,1] / r$prey_a__wgt[6:10,]))), "step0_cdist_sumofsquares_utsd_model__num[,'prey_a',1]: prey_a in area 1")
+ ok(ut_cmp_equal(as.vector(r$step0_cdist_sumofsquares_utsd_model__num[,'prey_c', 1]), c(
+ 0,
+ 0)), "step0_cdist_sumofsquares_utsd_model__num[,'prey_c',1]: No prey_c in area 1")
+ ok(ut_cmp_equal(as.vector(r$step0_cdist_sumofsquares_utsd_model__num[,'prey_a', 2]), c(
+ 0,
+ 0)), "step0_cdist_sumofsquares_utsd_model__num[,'prey_a',2]: No prey_a in area 2")
+ ok(ut_cmp_equal(as.vector(r$step0_cdist_sumofsquares_utsd_model__num[,'prey_c', 2]), c(
+ sum(r$detail_prey_c_fleet_abc__cons[1:5,,1] / r$prey_c__wgt[1:5,]),
+ sum(r$detail_prey_c_fleet_abc__cons[6:10,,1] / r$prey_c__wgt[6:10,]))), "step0_cdist_sumofsquares_utsd_model__num[,'prey_c',2]: prey_c in area 2")
+
+ ok(ut_cmp_equal(as.vector(r$step1_cdist_sumofsquares_utsd_model__num[,'prey_a', 1]), c(
+ sum(r$detail_prey_a_fleet_abc__cons[1:5,,2] / r$prey_a__wgt[1:5,]),
+ sum(r$detail_prey_a_fleet_abc__cons[6:10,,2] / r$prey_a__wgt[6:10,]))), "step1_cdist_sumofsquares_utsd_model__num[,'prey_a',1]: prey_a in area 1")
+ ok(ut_cmp_equal(as.vector(r$step1_cdist_sumofsquares_utsd_model__num[,'prey_c', 1]), c(
+ 0,
+ 0)), "step1_cdist_sumofsquares_utsd_model__num[,'prey_c',1]: No prey_c in area 1")
+ ok(ut_cmp_equal(as.vector(r$step1_cdist_sumofsquares_utsd_model__num[,'prey_a', 2]), c(
+ 0,
+ 0)), "step1_cdist_sumofsquares_utsd_model__num[,'prey_a',2]: No prey_a in area 2")
+ ok(ut_cmp_equal(as.vector(r$step1_cdist_sumofsquares_utsd_model__num[,'prey_c', 2]), c(
+ sum(r$detail_prey_c_fleet_abc__cons[1:5,,2] / r$prey_c__wgt[1:5,]),
+ sum(r$detail_prey_c_fleet_abc__cons[6:10,,2] / r$prey_c__wgt[6:10,]))), "step1_cdist_sumofsquares_utsd_model__num[,'prey_c',2]: prey_c in area 2")
+
+ ok(ut_cmp_equal(as.vector(r$step2_cdist_sumofsquares_utsd_model__num[,'prey_a', 1]), c(
+ sum(r$detail_prey_a_fleet_abc__cons[1:5,,3] / r$prey_a__wgt[1:5,]),
+ sum(r$detail_prey_a_fleet_abc__cons[6:10,,3] / r$prey_a__wgt[6:10,]))), "step2_cdist_sumofsquares_utsd_model__num[,'prey_a',1]: prey_a in area 1")
+ ok(ut_cmp_equal(as.vector(r$step2_cdist_sumofsquares_utsd_model__num[,'prey_c', 1]), c(
+ 0,
+ 0)), "step2_cdist_sumofsquares_utsd_model__num[,'prey_c',1]: No prey_c in area 1")
+ ok(ut_cmp_equal(as.vector(r$step2_cdist_sumofsquares_utsd_model__num[,'prey_a', 2]), c(
+ 0,
+ 0)), "step2_cdist_sumofsquares_utsd_model__num[,'prey_a',2]: No prey_a in area 2")
+ ok(ut_cmp_equal(as.vector(r$step2_cdist_sumofsquares_utsd_model__num[,'prey_c', 2]), c(
+ sum(r$detail_prey_c_fleet_abc__cons[1:5,,3] / r$prey_c__wgt[1:5,]),
+ sum(r$detail_prey_c_fleet_abc__cons[6:10,,3] / r$prey_c__wgt[6:10,]))), "step2_cdist_sumofsquares_utsd_model__num[,'prey_c',2]: prey_c in area 2")
+
+ ok(ut_cmp_equal(as.vector(r$step3_cdist_sumofsquares_utsd_model__num[,'prey_a', 1]), c(
+ sum(r$detail_prey_a_fleet_abc__cons[1:5,,4] / r$prey_a__wgt[1:5,]),
+ sum(r$detail_prey_a_fleet_abc__cons[6:10,,4] / r$prey_a__wgt[6:10,]))), "step3_cdist_sumofsquares_utsd_model__num[,'prey_a',1]: prey_a in area 1")
+ ok(ut_cmp_equal(as.vector(r$step3_cdist_sumofsquares_utsd_model__num[,'prey_c', 1]), c(
+ 0,
+ 0)), "step3_cdist_sumofsquares_utsd_model__num[,'prey_c',1]: No prey_c in area 1")
+ ok(ut_cmp_equal(as.vector(r$step3_cdist_sumofsquares_utsd_model__num[,'prey_a', 2]), c(
+ 0,
+ 0)), "step3_cdist_sumofsquares_utsd_model__num[,'prey_a',2]: No prey_a in area 2")
+ ok(ut_cmp_equal(as.vector(r$step3_cdist_sumofsquares_utsd_model__num[,'prey_c', 2]), c(
+ sum(r$detail_prey_c_fleet_abc__cons[1:5,,4] / r$prey_c__wgt[1:5,]),
+ sum(r$detail_prey_c_fleet_abc__cons[6:10,,4] / r$prey_c__wgt[6:10,]))), "step3_cdist_sumofsquares_utsd_model__num[,'prey_c',2]: prey_c in area 2")
+ ########
+
+ ######## cdist_sumofsquares_utcd_model__num
+ ok(ut_cmp_equal(as.vector(r$step0_cdist_sumofsquares_utcd_model__num[,1]), c(
+ sum(
+ sum(r$detail_prey_a_fleet_abc__cons[1:5,1,1] / r$prey_a__wgt[1:5,1]),
+ sum(r$detail_prey_b_fleet_abc__cons[1:5,1,1] / r$prey_b__wgt[1:5,1])),
+ sum(
+ sum(r$detail_prey_a_fleet_abc__cons[6:10,1,1] / r$prey_a__wgt[6:10,1]),
+ sum(r$detail_prey_b_fleet_abc__cons[6:10,1,1] / r$prey_b__wgt[6:10,1])),
+ NULL)), "step0_cdist_sumofsquares_utsd_model__num[,1]: all prey in area a/b")
+ ok(ut_cmp_equal(as.vector(r$step0_cdist_sumofsquares_utcd_model__num[,2]), c(
+ sum(
+ sum(r$detail_prey_c_fleet_abc__cons[1:5,1,1] / r$prey_c__wgt[1:5,1])),
+ sum(
+ sum(r$detail_prey_c_fleet_abc__cons[6:10,1,1] / r$prey_c__wgt[6:10,1])),
+ NULL)), "step0_cdist_sumofsquares_utsd_model__num[,2]: all prey in area c")
+
+ ok(ut_cmp_equal(as.vector(r$step1_cdist_sumofsquares_utcd_model__num[,1]), c(
+ sum(
+ sum(r$detail_prey_a_fleet_abc__cons[1:5,1,2] / r$prey_a__wgt[1:5,1]),
+ sum(r$detail_prey_b_fleet_abc__cons[1:5,1,2] / r$prey_b__wgt[1:5,1])),
+ sum(
+ sum(r$detail_prey_a_fleet_abc__cons[6:10,1,2] / r$prey_a__wgt[6:10,1]),
+ sum(r$detail_prey_b_fleet_abc__cons[6:10,1,2] / r$prey_b__wgt[6:10,1])),
+ NULL)), "step1_cdist_sumofsquares_utsd_model__num[,1]: all prey in area a/b")
+ ok(ut_cmp_equal(as.vector(r$step1_cdist_sumofsquares_utcd_model__num[,2]), c(
+ sum(
+ sum(r$detail_prey_c_fleet_abc__cons[1:5,1,2] / r$prey_c__wgt[1:5,1])),
+ sum(
+ sum(r$detail_prey_c_fleet_abc__cons[6:10,1,2] / r$prey_c__wgt[6:10,1])),
+ NULL)), "step1_cdist_sumofsquares_utsd_model__num[,2]: all prey in area c")
+
+ ok(ut_cmp_equal(as.vector(r$step2_cdist_sumofsquares_utcd_model__num[,1]), c(
+ sum(
+ sum(r$detail_prey_a_fleet_abc__cons[1:5,1,3] / r$prey_a__wgt[1:5,1]),
+ sum(r$detail_prey_b_fleet_abc__cons[1:5,1,3] / r$prey_b__wgt[1:5,1])),
+ sum(
+ sum(r$detail_prey_a_fleet_abc__cons[6:10,1,3] / r$prey_a__wgt[6:10,1]),
+ sum(r$detail_prey_b_fleet_abc__cons[6:10,1,3] / r$prey_b__wgt[6:10,1])),
+ NULL)), "step2_cdist_sumofsquares_utsd_model__num[,1]: all prey in area a/b")
+ ok(ut_cmp_equal(as.vector(r$step2_cdist_sumofsquares_utcd_model__num[,2]), c(
+ sum(
+ sum(r$detail_prey_c_fleet_abc__cons[1:5,1,3] / r$prey_c__wgt[1:5,1])),
+ sum(
+ sum(r$detail_prey_c_fleet_abc__cons[6:10,1,3] / r$prey_c__wgt[6:10,1])),
+ NULL)), "step2_cdist_sumofsquares_utsd_model__num[,2]: all prey in area c")
+
+ ok(ut_cmp_equal(as.vector(r$step3_cdist_sumofsquares_utcd_model__num[,1]), c(
+ sum(
+ sum(r$detail_prey_a_fleet_abc__cons[1:5,1,4] / r$prey_a__wgt[1:5,1]),
+ sum(r$detail_prey_b_fleet_abc__cons[1:5,1,4] / r$prey_b__wgt[1:5,1])),
+ sum(
+ sum(r$detail_prey_a_fleet_abc__cons[6:10,1,4] / r$prey_a__wgt[6:10,1]),
+ sum(r$detail_prey_b_fleet_abc__cons[6:10,1,4] / r$prey_b__wgt[6:10,1])),
+ NULL)), "step3_cdist_sumofsquares_utsd_model__num[,1]: all prey in area a/b")
+ ok(ut_cmp_equal(as.vector(r$step3_cdist_sumofsquares_utcd_model__num[,2]), c(
+ sum(
+ sum(r$detail_prey_c_fleet_abc__cons[1:5,1,4] / r$prey_c__wgt[1:5,1])),
+ sum(
+ sum(r$detail_prey_c_fleet_abc__cons[6:10,1,4] / r$prey_c__wgt[6:10,1])),
+ NULL)), "step3_cdist_sumofsquares_utsd_model__num[,2]: all prey in area c")
+ ########
+
+ ######## adist_surveyindices_log_surveyindices_model__num
+ ok(ut_cmp_equal(
+ as.vector(r$adist_surveyindices_log_surveyindices_model__num),
+ c(
+ sum(r$step0_prey_b__num),
+ sum(r$step1_prey_b__num),
+ sum(r$step2_prey_b__num),
+ sum(r$step3_prey_b__num),
+ NULL)), "adist_surveyindices_log_surveyindices_model__num: Built-in reporting gave us step 0..3 abundance")
+ ########
+
+ ok(ut_cmp_equal(r$step0_nll, sum(
+ # utsd: stock 1 / area 1
+ (r$step0_cdist_sumofsquares_utsd_model__num[,1,1] / sum(r$step0_cdist_sumofsquares_utsd_model__num[,,1]) -
+ r$cdist_sumofsquares_utsd_obs__num[,1,1,1] / sum(r$cdist_sumofsquares_utsd_obs__num[,,1,1])) ** 2,
+ # utsd: stock 2 / area 1
+ (r$step0_cdist_sumofsquares_utsd_model__num[,2,1] / sum(r$step0_cdist_sumofsquares_utsd_model__num[,,1]) -
+ r$cdist_sumofsquares_utsd_obs__num[,2,1,1] / sum(r$cdist_sumofsquares_utsd_obs__num[,,1,1])) ** 2,
+ # utsd: stock 1 / area 2
+ (r$step0_cdist_sumofsquares_utsd_model__num[,1,2] / sum(r$step0_cdist_sumofsquares_utsd_model__num[,,2]) -
+ r$cdist_sumofsquares_utsd_obs__num[,1,1,2] / sum(r$cdist_sumofsquares_utsd_obs__num[,,1,2])) ** 2,
+ # utsd: stock 2 / area 2
+ (r$step0_cdist_sumofsquares_utsd_model__num[,2,2] / sum(r$step0_cdist_sumofsquares_utsd_model__num[,,2]) -
+ r$cdist_sumofsquares_utsd_obs__num[,2,1,2] / sum(r$cdist_sumofsquares_utsd_obs__num[,,1,2])) ** 2,
+ # utcd: area 1
+ (r$step0_cdist_sumofsquares_utcd_model__num[,1] / sum(r$step0_cdist_sumofsquares_utcd_model__num[,1]) -
+ r$cdist_sumofsquares_utcd_obs__num[,1,1] / sum(r$cdist_sumofsquares_utcd_obs__num[,1,1])) ** 2,
+ # utcd: area 2
+ (r$step0_cdist_sumofsquares_utcd_model__num[,2] / sum(r$step0_cdist_sumofsquares_utcd_model__num[,2]) -
+ r$cdist_sumofsquares_utcd_obs__num[,1,2] / sum(r$cdist_sumofsquares_utcd_obs__num[,1,2])) ** 2,
+ # utcd_weight: area 1
+ (r$step0_cdist_sumofsquares_utcd_weight_model__wgt[,1] / g3_avoid_zero(sum(r$step0_cdist_sumofsquares_utcd_weight_model__wgt[,1])) -
+ r$cdist_sumofsquares_utcd_weight_obs__wgt[,1,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_weight_obs__wgt[,1,1]))) ** 2,
+ # utcd_weight: area 2
+ (r$step0_cdist_sumofsquares_utcd_weight_model__wgt[,2] / g3_avoid_zero(sum(r$step0_cdist_sumofsquares_utcd_weight_model__wgt[,2])) -
+ r$cdist_sumofsquares_utcd_weight_obs__wgt[,1,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_weight_obs__wgt[,1,2]))) ** 2,
+ # multinom:
+ (2 * (-sum(r$cdist_multinomial_multinom_obs__num[,1] * log(g3_logspace_add(r$step0_cdist_multinomial_multinom_model__num/g3_avoid_zero(sum(r$step0_cdist_multinomial_multinom_model__num)) *
+ 10000, (1/(length(r$cdist_multinomial_multinom_obs__num[,1]) * 10)) * 10000)/10000)) +
+ (sum(g3_lgamma_vec(1 + r$cdist_multinomial_multinom_obs__num[,1])) - lgamma(1 +
+ sum(r$cdist_multinomial_multinom_obs__num[,1]))))),
+ # surveyindices:
+ 0, # NB: We don't calculate until end
+ 0)), "step0_nll: Sum of squares")
+
+ ok(ut_cmp_equal(r$step1_nll, sum(
+ # utsd: stock 1 / area 1
+ (r$step1_cdist_sumofsquares_utsd_model__num[,1,1] / g3_avoid_zero(sum(r$step1_cdist_sumofsquares_utsd_model__num[,,1])) -
+ r$cdist_sumofsquares_utsd_obs__num[,1,2,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,2,1]))) ** 2,
+ # utsd: stock 2 / area 1
+ (r$step1_cdist_sumofsquares_utsd_model__num[,2,1] / g3_avoid_zero(sum(r$step1_cdist_sumofsquares_utsd_model__num[,,1])) -
+ r$cdist_sumofsquares_utsd_obs__num[,2,2,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,2,1]))) ** 2,
+ # utsd: stock 1 / area 2
+ (r$step1_cdist_sumofsquares_utsd_model__num[,1,2] / g3_avoid_zero(sum(r$step1_cdist_sumofsquares_utsd_model__num[,,2])) -
+ r$cdist_sumofsquares_utsd_obs__num[,1,2,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,2,2]))) ** 2,
+ # utsd: stock 2 / area 2
+ (r$step1_cdist_sumofsquares_utsd_model__num[,2,2] / g3_avoid_zero(sum(r$step1_cdist_sumofsquares_utsd_model__num[,,2])) -
+ r$cdist_sumofsquares_utsd_obs__num[,2,2,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,2,2]))) ** 2,
+ # utcd: area 1
+ (r$step1_cdist_sumofsquares_utcd_model__num[,1] / g3_avoid_zero(sum(r$step1_cdist_sumofsquares_utcd_model__num[,1])) -
+ r$cdist_sumofsquares_utcd_obs__num[,2,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_obs__num[,2,1]))) ** 2,
+ # utcd: area 2
+ (r$step1_cdist_sumofsquares_utcd_model__num[,2] / g3_avoid_zero(sum(r$step1_cdist_sumofsquares_utcd_model__num[,2])) -
+ r$cdist_sumofsquares_utcd_obs__num[,2,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_obs__num[,2,2]))) ** 2,
+ # utcd_weight: area 1
+ (r$step1_cdist_sumofsquares_utcd_weight_model__wgt[,1] / g3_avoid_zero(sum(r$step1_cdist_sumofsquares_utcd_weight_model__wgt[,1])) -
+ r$cdist_sumofsquares_utcd_weight_obs__wgt[,2,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_weight_obs__wgt[,2,1]))) ** 2,
+ # utcd_weight: area 2
+ (r$step1_cdist_sumofsquares_utcd_weight_model__wgt[,2] / g3_avoid_zero(sum(r$step1_cdist_sumofsquares_utcd_weight_model__wgt[,2])) -
+ r$cdist_sumofsquares_utcd_weight_obs__wgt[,2,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_weight_obs__wgt[,2,2]))) ** 2,
+ # multinom:
+ (2 * (-sum(r$cdist_multinomial_multinom_obs__num[,2] * log(g3_logspace_add(r$step1_cdist_multinomial_multinom_model__num/g3_avoid_zero(sum(r$step1_cdist_multinomial_multinom_model__num)) *
+ 10000, (1/(length(r$cdist_multinomial_multinom_obs__num[,2]) * 10)) * 10000)/10000)) +
+ (sum(g3_lgamma_vec(1 + r$cdist_multinomial_multinom_obs__num[,2])) - lgamma(1 +
+ sum(r$cdist_multinomial_multinom_obs__num[,2]))))),
+ # surveyindices:
+ 0, # NB: We don't calculate until end
+ r$step0_nll)), "step1_nll: Sum of squares, including step0_nll")
+
+ ok(ut_cmp_equal(r$step2_nll, sum(
+ # utsd: stock 1 / area 1
+ (r$step2_cdist_sumofsquares_utsd_model__num[,1,1] / g3_avoid_zero(sum(r$step2_cdist_sumofsquares_utsd_model__num[,,1])) -
+ r$cdist_sumofsquares_utsd_obs__num[,1,3,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,3,1]))) ** 2,
+ # utsd: stock 2 / area 1
+ (r$step2_cdist_sumofsquares_utsd_model__num[,2,1] / g3_avoid_zero(sum(r$step2_cdist_sumofsquares_utsd_model__num[,,1])) -
+ r$cdist_sumofsquares_utsd_obs__num[,2,3,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,3,1]))) ** 2,
+ # utsd: stock 1 / area 2
+ (r$step2_cdist_sumofsquares_utsd_model__num[,1,2] / g3_avoid_zero(sum(r$step2_cdist_sumofsquares_utsd_model__num[,,2])) -
+ r$cdist_sumofsquares_utsd_obs__num[,1,3,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,3,2]))) ** 2,
+ # utsd: stock 2 / area 2
+ (r$step2_cdist_sumofsquares_utsd_model__num[,2,2] / g3_avoid_zero(sum(r$step2_cdist_sumofsquares_utsd_model__num[,,2])) -
+ r$cdist_sumofsquares_utsd_obs__num[,2,3,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,3,2]))) ** 2,
+ # utcd: area 1
+ (r$step2_cdist_sumofsquares_utcd_model__num[,1] / g3_avoid_zero(sum(r$step2_cdist_sumofsquares_utcd_model__num[,1])) -
+ r$cdist_sumofsquares_utcd_obs__num[,3,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_obs__num[,3,1]))) ** 2,
+ # utcd: area 2
+ (r$step2_cdist_sumofsquares_utcd_model__num[,2] / g3_avoid_zero(sum(r$step2_cdist_sumofsquares_utcd_model__num[,2])) -
+ r$cdist_sumofsquares_utcd_obs__num[,3,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_obs__num[,3,2]))) ** 2,
+ # utcd_weight: area 1
+ (r$step2_cdist_sumofsquares_utcd_weight_model__wgt[,1] / g3_avoid_zero(sum(r$step2_cdist_sumofsquares_utcd_weight_model__wgt[,1])) -
+ r$cdist_sumofsquares_utcd_weight_obs__wgt[,3,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_weight_obs__wgt[,3,1]))) ** 2,
+ # utcd_weight: area 2
+ (r$step2_cdist_sumofsquares_utcd_weight_model__wgt[,2] / g3_avoid_zero(sum(r$step2_cdist_sumofsquares_utcd_weight_model__wgt[,2])) -
+ r$cdist_sumofsquares_utcd_weight_obs__wgt[,3,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_weight_obs__wgt[,3,2]))) ** 2,
+ # multinom:
+ (2 * (-sum(r$cdist_multinomial_multinom_obs__num[,3] * log(g3_logspace_add(r$step2_cdist_multinomial_multinom_model__num/g3_avoid_zero(sum(r$step2_cdist_multinomial_multinom_model__num)) *
+ 10000, (1/(length(r$cdist_multinomial_multinom_obs__num[,3]) * 10)) * 10000)/10000)) +
+ (sum(g3_lgamma_vec(1 + r$cdist_multinomial_multinom_obs__num[,3])) - lgamma(1 +
+ sum(r$cdist_multinomial_multinom_obs__num[,3]))))),
+ # surveyindices:
+ 0, # NB: We don't calculate until end
+ r$step1_nll)), "step2_nll: Sum of squares, including step1_nll")
+
+ ok(ut_cmp_equal(r$step3_nll, sum(
+ # utsd: stock 1 / area 1
+ (r$step3_cdist_sumofsquares_utsd_model__num[,1,1] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utsd_model__num[,,1])) -
+ r$cdist_sumofsquares_utsd_obs__num[,1,4,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,4,1]))) ** 2,
+ # utsd: stock 2 / area 1
+ (r$step3_cdist_sumofsquares_utsd_model__num[,2,1] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utsd_model__num[,,1])) -
+ r$cdist_sumofsquares_utsd_obs__num[,2,4,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,4,1]))) ** 2,
+ # utsd: stock 1 / area 2
+ (r$step3_cdist_sumofsquares_utsd_model__num[,1,2] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utsd_model__num[,,2])) -
+ r$cdist_sumofsquares_utsd_obs__num[,1,4,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,4,2]))) ** 2,
+ # utsd: stock 2 / area 2
+ (r$step3_cdist_sumofsquares_utsd_model__num[,2,2] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utsd_model__num[,,2])) -
+ r$cdist_sumofsquares_utsd_obs__num[,2,4,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,4,2]))) ** 2,
+ # utcd: area 1
+ (r$step3_cdist_sumofsquares_utcd_model__num[,1] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utcd_model__num[,1])) -
+ r$cdist_sumofsquares_utcd_obs__num[,4,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_obs__num[,4,1]))) ** 2,
+ # utcd: area 2
+ (r$step3_cdist_sumofsquares_utcd_model__num[,2] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utcd_model__num[,2])) -
+ r$cdist_sumofsquares_utcd_obs__num[,4,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_obs__num[,4,2]))) ** 2,
+ # utcd_weight: area 1
+ (r$step3_cdist_sumofsquares_utcd_weight_model__wgt[,1] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utcd_weight_model__wgt[,1])) -
+ r$cdist_sumofsquares_utcd_weight_obs__wgt[,4,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_weight_obs__wgt[,4,1]))) ** 2,
+ # utcd_weight: area 2
+ (r$step3_cdist_sumofsquares_utcd_weight_model__wgt[,2] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utcd_weight_model__wgt[,2])) -
+ r$cdist_sumofsquares_utcd_weight_obs__wgt[,4,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_weight_obs__wgt[,4,2]))) ** 2,
+ # multinom:
+ (2 * (-sum(r$cdist_multinomial_multinom_obs__num[,4] * log(g3_logspace_add(r$step3_cdist_multinomial_multinom_model__num/g3_avoid_zero(sum(r$step3_cdist_multinomial_multinom_model__num)) *
+ 10000, (1/(length(r$cdist_multinomial_multinom_obs__num[,4]) * 10)) * 10000)/10000)) +
+ (sum(g3_lgamma_vec(1 + r$cdist_multinomial_multinom_obs__num[,4])) - lgamma(1 +
+ sum(r$cdist_multinomial_multinom_obs__num[,4]))))),
+ # surveyindices:
+ sum((params$si_alpha +
+ params$si_beta * log(g3_avoid_zero(r$adist_surveyindices_log_surveyindices_model__num[,])) -
+ log(g3_avoid_zero(r$adist_surveyindices_log_surveyindices_obs__num[,])))**2),
+ r$step2_nll)), "step3_nll: Sum of squares, including step2_nll")
+
+ 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)
+ }
+ })
# Likelihood per step
ok - cdist_sumofsquares_utsd_obs__num: Imported from data.frame, order not necessarily the same
ok - adist_surveyindices_log_surveyindices_model__params: Reported our hard-coded linear regression parameters
ok - step0_cdist_sumofsquares_utsd_model__num[,'prey_a',1]: prey_a in area 1
ok - step0_cdist_sumofsquares_utsd_model__num[,'prey_c',1]: No prey_c in area 1
ok - step0_cdist_sumofsquares_utsd_model__num[,'prey_a',2]: No prey_a in area 2
ok - step0_cdist_sumofsquares_utsd_model__num[,'prey_c',2]: prey_c in area 2
ok - step1_cdist_sumofsquares_utsd_model__num[,'prey_a',1]: prey_a in area 1
ok - step1_cdist_sumofsquares_utsd_model__num[,'prey_c',1]: No prey_c in area 1
ok - step1_cdist_sumofsquares_utsd_model__num[,'prey_a',2]: No prey_a in area 2
ok - step1_cdist_sumofsquares_utsd_model__num[,'prey_c',2]: prey_c in area 2
ok - step2_cdist_sumofsquares_utsd_model__num[,'prey_a',1]: prey_a in area 1
ok - step2_cdist_sumofsquares_utsd_model__num[,'prey_c',1]: No prey_c in area 1
ok - step2_cdist_sumofsquares_utsd_model__num[,'prey_a',2]: No prey_a in area 2
ok - step2_cdist_sumofsquares_utsd_model__num[,'prey_c',2]: prey_c in area 2
ok - step3_cdist_sumofsquares_utsd_model__num[,'prey_a',1]: prey_a in area 1
ok - step3_cdist_sumofsquares_utsd_model__num[,'prey_c',1]: No prey_c in area 1
ok - step3_cdist_sumofsquares_utsd_model__num[,'prey_a',2]: No prey_a in area 2
ok - step3_cdist_sumofsquares_utsd_model__num[,'prey_c',2]: prey_c in area 2
ok - step0_cdist_sumofsquares_utsd_model__num[,1]: all prey in area a/b
ok - step0_cdist_sumofsquares_utsd_model__num[,2]: all prey in area c
ok - step1_cdist_sumofsquares_utsd_model__num[,1]: all prey in area a/b
ok - step1_cdist_sumofsquares_utsd_model__num[,2]: all prey in area c
ok - step2_cdist_sumofsquares_utsd_model__num[,1]: all prey in area a/b
ok - step2_cdist_sumofsquares_utsd_model__num[,2]: all prey in area c
ok - step3_cdist_sumofsquares_utsd_model__num[,1]: all prey in area a/b
ok - step3_cdist_sumofsquares_utsd_model__num[,2]: all prey in area c
ok - adist_surveyindices_log_surveyindices_model__num: Built-in reporting gave us step 0..3 abundance
ok - step0_nll: Sum of squares
ok - step1_nll: Sum of squares, including step0_nll
ok - step2_nll: Sum of squares, including step1_nll
ok - step3_nll: Sum of squares, including step2_nll
>
> ok_group("Likelihood per year", {
+ # Change model to aggregate over a year
+ # NB: No prey_b, only compare prey_a and prey_c
+ # NB: No step column now
+ sd_data <- expand.grid(year = 1999:2000, area = c('x', 'y'), stock = c("prey_a", "prey_c"), length = c(1,6))
+ sd_data$number <- floor(runif(length(sd_data$year), min=100, max=999))
+ attr(sd_data, 'area') <- list(
+ x = areas[c('a', 'b')],
+ y = areas[c('c')])
+
+ # Change model to aggregate over a year
+ # NB: No step column now
+ cd_data <- expand.grid(year = 1999:2000, area = c('x', 'y'), length = c(1,6))
+ cd_data$number <- floor(runif(length(cd_data$year), min=100, max=999))
+ attr(cd_data, 'area') <- list(
+ x = areas[c('a', 'b')],
+ y = areas[c('c')])
+
+ # Change model to aggregate over a year
+ cd_weight_data <- expand.grid(year = 1999:2000, area = c('x', 'y'), length = c(1,6))
+ cd_weight_data$weight <- floor(runif(length(cd_data$year), min=1000, max=9999))
+
+ # Change model to aggregate over a year
+ # NB: No step column now
+ multinomial_data <- expand.grid(year = 1999:2000, length = c(1,6))
+ multinomial_data$number <- floor(runif(length(multinomial_data$year), min=100, max=999))
+
+ # NB: No step column now
+ surveyindices_data <- expand.grid(year = 1999:2000)
+ surveyindices_data$number <- floor(runif(length(surveyindices_data$year), min=100, max=999))
+
+ actions <- c(base_actions, list(
+ g3l_catchdistribution(
+ 'utcd',
+ cd_data,
+ list(fleet_abc),
+ list(prey_a, prey_b, prey_c),
+ area_group = areas,
+ g3l_distribution_sumofsquares()),
+ g3l_catchdistribution(
+ 'utcd_weight',
+ cd_weight_data,
+ list(fleet_abc),
+ list(prey_a, prey_b, prey_c),
+ area_group = areas,
+ g3l_distribution_sumofsquares()),
+ g3l_catchdistribution(
+ 'utsd',
+ sd_data,
+ list(fleet_abc),
+ list(prey_a, prey_b, prey_c),
+ area_group = areas,
+ g3l_distribution_sumofsquares()),
+ g3l_catchdistribution(
+ 'multinom',
+ multinomial_data,
+ list(fleet_abc),
+ list(prey_a),
+ area_group = areas,
+ g3l_distribution_multinomial()),
+ g3l_abundancedistribution(
+ 'surveyindices',
+ surveyindices_data,
+ fleets = list(),
+ stocks = list(prey_b),
+ area_group = areas,
+ report = TRUE,
+ g3l_distribution_surveyindices_log(alpha = ~g3_param("si_alpha", value = 0), beta = ~g3_param("si_beta", value = 0)))))
+ actions <- c(actions, list(
+ g3a_report_history(actions, '__cons$', out_prefix = "detail_") ))
+
+ # Compile model
+ model_fn <- g3_to_r(actions, trace = FALSE)
+ # model_fn <- edit(model_fn)
+ if (nzchar(Sys.getenv('G3_TEST_TMB'))) {
+ model_cpp <- g3_to_tmb(actions, trace = FALSE)
+ # model_cpp <- edit(model_cpp)
+ model_tmb <- g3_tmb_adfun(model_cpp, params, compile_flags = c("-O0", "-g"))
+ } else {
+ writeLines("# skip: not compiling TMB model")
+ }
+
+ params <- attr(model_fn, 'parameter_template')
+ params$fleet_abc_a <- runif(10, min=0.1, max=0.9)
+ params$fleet_abc_b <- runif(10, min=0.1, max=0.9)
+ params$fleet_abc_c <- runif(10, min=0.1, max=0.9)
+ params$amount_ab <- 1000000
+ params$si_alpha <- 1.82
+ params$si_beta <- 3.74
+ params$cdist_sumofsquares_utcd_weight <- 1
+ params$cdist_sumofsquares_utcd_weight_weight <- 1
+ params$cdist_sumofsquares_utsd_weight <- 1
+ params$cdist_multinomial_multinom_weight <- 1
+ params$adist_surveyindices_log_surveyindices_weight <- 1
+
+ result <- model_fn(params)
+ r <- attributes(result)
+ # str(result)
+ # str(as.list(r), vec.len = 10000)
+
+ ok(ut_cmp_equal(
+ sort(as.vector(r$cdist_sumofsquares_utsd_obs__num)),
+ sort(sd_data$number)), "cdist_sumofsquares_utsd_obs__num: Imported from data.frame, order not necessarily the same")
+
+ ok(ut_cmp_equal(
+ r$adist_surveyindices_log_surveyindices_model__params,
+ c(params$si_alpha, params$si_beta)), "adist_surveyindices_log_surveyindices_model__params: Reported our hard-coded linear regression parameters")
+
+
+ ######## cdist_sumofsquares_utsd_model__num
+ ok(ut_cmp_equal(as.vector(r$step1_cdist_sumofsquares_utsd_model__num[,'prey_a', 1]), c(
+ sum(
+ (r$detail_prey_a_fleet_abc__cons[1:5,,1] / r$prey_a__wgt[1:5,]),
+ (r$detail_prey_a_fleet_abc__cons[1:5,,2] / r$prey_a__wgt[1:5,])),
+ sum(
+ sum(r$detail_prey_a_fleet_abc__cons[6:10,,1] / r$prey_a__wgt[6:10,]),
+ sum(r$detail_prey_a_fleet_abc__cons[6:10,,2] / r$prey_a__wgt[6:10,])),
+ NULL)), "step1_cdist_sumofsquares_utsd_model__num[,'prey_a',1]: prey_a summed over year")
+ ok(ut_cmp_equal(as.vector(r$step1_cdist_sumofsquares_utsd_model__num[,'prey_c', 1]), c(
+ 0,
+ 0,
+ NULL)), "step1_cdist_sumofsquares_utsd_model__num[,'prey_c',1]: No prey_c in first area")
+ ok(ut_cmp_equal(as.vector(r$step1_cdist_sumofsquares_utsd_model__num[,'prey_a', 2]), c(
+ 0,
+ 0,
+ NULL)), "step1_cdist_sumofsquares_utsd_model__num[,'prey_a',2]: No prey_a in second area")
+ ok(ut_cmp_equal(as.vector(r$step1_cdist_sumofsquares_utsd_model__num[,'prey_c', 2]), c(
+ sum(
+ (r$detail_prey_c_fleet_abc__cons[1:5,,1] / r$prey_c__wgt[1:5,]),
+ (r$detail_prey_c_fleet_abc__cons[1:5,,2] / r$prey_c__wgt[1:5,])),
+ sum(
+ sum(r$detail_prey_c_fleet_abc__cons[6:10,,1] / r$prey_c__wgt[6:10,]),
+ sum(r$detail_prey_c_fleet_abc__cons[6:10,,2] / r$prey_c__wgt[6:10,])),
+ NULL)), "step1_cdist_sumofsquares_utsd_model__num[,'prey_c',2]: prey_c summed over year")
+ ########
+
+ ######## cdist_sumofsquares_utcd_model__num
+ ok(ut_cmp_equal(as.vector(r$step1_cdist_sumofsquares_utcd_model__num[,1]), c(
+ sum(
+ sum(r$detail_prey_a_fleet_abc__cons[1:5,1,1] / r$prey_a__wgt[1:5,1]),
+ sum(r$detail_prey_b_fleet_abc__cons[1:5,1,1] / r$prey_b__wgt[1:5,1]),
+ sum(r$detail_prey_a_fleet_abc__cons[1:5,1,2] / r$prey_a__wgt[1:5,1]),
+ sum(r$detail_prey_b_fleet_abc__cons[1:5,1,2] / r$prey_b__wgt[1:5,1])),
+ sum(
+ sum(r$detail_prey_a_fleet_abc__cons[6:10,1,1] / r$prey_a__wgt[6:10,1]),
+ sum(r$detail_prey_b_fleet_abc__cons[6:10,1,1] / r$prey_b__wgt[6:10,1]),
+ sum(r$detail_prey_a_fleet_abc__cons[6:10,1,2] / r$prey_a__wgt[6:10,1]),
+ sum(r$detail_prey_b_fleet_abc__cons[6:10,1,2] / r$prey_b__wgt[6:10,1])),
+ NULL)), "step1_cdist_sumofsquares_utcd_model__num[,1]: all prey from a/b and steps 0 & 1")
+
+ ok(ut_cmp_equal(as.vector(r$step1_cdist_sumofsquares_utcd_model__num[,2]), c(
+ sum(
+ sum(r$detail_prey_c_fleet_abc__cons[1:5,1,1] / r$prey_c__wgt[1:5,1]),
+ sum(r$detail_prey_c_fleet_abc__cons[1:5,1,2] / r$prey_c__wgt[1:5,1])),
+ sum(
+ sum(r$detail_prey_c_fleet_abc__cons[6:10,1,1] / r$prey_c__wgt[6:10,1]),
+ sum(r$detail_prey_c_fleet_abc__cons[6:10,1,2] / r$prey_c__wgt[6:10,1])),
+ NULL)), "step1_cdist_sumofsquares_utcd_model__num[,2]: all prey from c and steps 0/1")
+ ########
+
+ ######## cdist_sumofsquares_utcd_weight_model__wgt
+ ok(ut_cmp_equal(as.vector(r$step1_cdist_sumofsquares_utcd_weight_model__wgt[,1]), c(
+ sum(
+ sum(r$detail_prey_a_fleet_abc__cons[1:5,1,1]),
+ sum(r$detail_prey_b_fleet_abc__cons[1:5,1,1]),
+ sum(r$detail_prey_a_fleet_abc__cons[1:5,1,2]),
+ sum(r$detail_prey_b_fleet_abc__cons[1:5,1,2])),
+ sum(
+ sum(r$detail_prey_a_fleet_abc__cons[6:10,1,1]),
+ sum(r$detail_prey_b_fleet_abc__cons[6:10,1,1]),
+ sum(r$detail_prey_a_fleet_abc__cons[6:10,1,2]),
+ sum(r$detail_prey_b_fleet_abc__cons[6:10,1,2])),
+ NULL)), "step1_cdist_sumofsquares_utcd_weight_model__wgt[,1]: total biomass of prey from a/b and steps 0 & 1")
+
+ ok(ut_cmp_equal(as.vector(r$step1_cdist_sumofsquares_utcd_weight_model__wgt[,2]), c(
+ sum(
+ sum(r$detail_prey_c_fleet_abc__cons[1:5,1,1]),
+ sum(r$detail_prey_c_fleet_abc__cons[1:5,1,2])),
+ sum(
+ sum(r$detail_prey_c_fleet_abc__cons[6:10,1,1]),
+ sum(r$detail_prey_c_fleet_abc__cons[6:10,1,2])),
+ NULL)), "step1_cdist_sumofsquares_utcd_weight_model__wgt[,2]: total biomass of prey from c and steps 0/1")
+ ########
+
+ ######## adist_surveyindices_surveyindices_model__num
+ ok(ut_cmp_equal(
+ as.vector(r$adist_surveyindices_log_surveyindices_model__num),
+ c(
+ sum(r$step0_prey_b__num) + sum(r$step1_prey_b__num),
+ sum(r$step2_prey_b__num) + sum(r$step3_prey_b__num),
+ NULL)), "adist_surveyindices_log_surveyindices_model__num: Built-in reporting gave us step 0..3 abundance")
+ ########
+
+ ok(ut_cmp_equal(r$step0_nll, 0), "step0_nll: nll not calculated yet")
+
+ ok(ut_cmp_equal(r$step1_nll, sum(
+ # utsd: stock 1 / area 1
+ (r$step1_cdist_sumofsquares_utsd_model__num[,1,1] / sum(r$step1_cdist_sumofsquares_utsd_model__num[,,1]) -
+ # NB: Still using first time data, unlike per-step example
+ r$cdist_sumofsquares_utsd_obs__num[,1,1,1] / sum(r$cdist_sumofsquares_utsd_obs__num[,,1,1])) ** 2,
+ # utsd: stock 2 / area 1
+ (r$step1_cdist_sumofsquares_utsd_model__num[,2,1] / sum(r$step1_cdist_sumofsquares_utsd_model__num[,,1]) -
+ r$cdist_sumofsquares_utsd_obs__num[,2,1,1] / sum(r$cdist_sumofsquares_utsd_obs__num[,,1,1])) ** 2,
+ # utsd: stock 1 / area 2
+ (r$step1_cdist_sumofsquares_utsd_model__num[,1,2] / sum(r$step1_cdist_sumofsquares_utsd_model__num[,,2]) -
+ r$cdist_sumofsquares_utsd_obs__num[,1,1,2] / sum(r$cdist_sumofsquares_utsd_obs__num[,,1,2])) ** 2,
+ # utsd: stock 2 / area 2
+ (r$step1_cdist_sumofsquares_utsd_model__num[,2,2] / sum(r$step1_cdist_sumofsquares_utsd_model__num[,,2]) -
+ r$cdist_sumofsquares_utsd_obs__num[,2,1,2] / sum(r$cdist_sumofsquares_utsd_obs__num[,,1,2])) ** 2,
+ # utcd: area 1
+ (r$step1_cdist_sumofsquares_utcd_model__num[,1] / sum(r$step1_cdist_sumofsquares_utcd_model__num[,1]) -
+ r$cdist_sumofsquares_utcd_obs__num[,1,1] / sum(r$cdist_sumofsquares_utcd_obs__num[,1,1])) ** 2,
+ # utcd: area 2
+ (r$step1_cdist_sumofsquares_utcd_model__num[,2] / sum(r$step1_cdist_sumofsquares_utcd_model__num[,2]) -
+ r$cdist_sumofsquares_utcd_obs__num[,1,2] / sum(r$cdist_sumofsquares_utcd_obs__num[,1,2])) ** 2,
+ # utcd_weight: area 1
+ (r$step1_cdist_sumofsquares_utcd_weight_model__wgt[,1] / sum(r$step1_cdist_sumofsquares_utcd_weight_model__wgt[,1]) -
+ r$cdist_sumofsquares_utcd_weight_obs__wgt[,1,1] / sum(r$cdist_sumofsquares_utcd_weight_obs__wgt[,1,1])) ** 2,
+ # utcd_weight: area 2
+ (r$step1_cdist_sumofsquares_utcd_weight_model__wgt[,2] / sum(r$step1_cdist_sumofsquares_utcd_weight_model__wgt[,2]) -
+ r$cdist_sumofsquares_utcd_weight_obs__wgt[,1,2] / sum(r$cdist_sumofsquares_utcd_weight_obs__wgt[,1,2])) ** 2,
+ # multinom:
+ (2 * (-sum(r$cdist_multinomial_multinom_obs__num[,1] * log(g3_logspace_add(r$step1_cdist_multinomial_multinom_model__num/g3_avoid_zero(sum(r$step1_cdist_multinomial_multinom_model__num)) *
+ 10000, (1/(length(r$cdist_multinomial_multinom_obs__num[,1]) * 10)) * 10000)/10000)) +
+ (sum(g3_lgamma_vec(1 + r$cdist_multinomial_multinom_obs__num[,1])) - lgamma(1 +
+ sum(r$cdist_multinomial_multinom_obs__num[,1]))))),
+ # surveyindices:
+ 0, # NB: We don't calculate until end
+ 0)), "step1_nll: Sum of squares")
+
+ ok(ut_cmp_equal(r$step3_nll, sum(
+ # utsd: stock 1 / area 1
+ (r$step3_cdist_sumofsquares_utsd_model__num[,1,1] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utsd_model__num[,,1])) -
+ # NB: Second time data, not 4th as in per-step example
+ r$cdist_sumofsquares_utsd_obs__num[,1,2,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,2,1]))) ** 2,
+ # utsd: stock 2 / area 1
+ (r$step3_cdist_sumofsquares_utsd_model__num[,2,1] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utsd_model__num[,,1])) -
+ r$cdist_sumofsquares_utsd_obs__num[,2,2,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,2,1]))) ** 2,
+ # utsd: stock 1 / area 2
+ (r$step3_cdist_sumofsquares_utsd_model__num[,1,2] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utsd_model__num[,,2])) -
+ r$cdist_sumofsquares_utsd_obs__num[,1,2,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,2,2]))) ** 2,
+ # utsd: stock 2 / area 2
+ (r$step3_cdist_sumofsquares_utsd_model__num[,2,2] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utsd_model__num[,,2])) -
+ r$cdist_sumofsquares_utsd_obs__num[,2,2,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utsd_obs__num[,,2,2]))) ** 2,
+ # utcd: area 1
+ (r$step3_cdist_sumofsquares_utcd_model__num[,1] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utcd_model__num[,1])) -
+ r$cdist_sumofsquares_utcd_obs__num[,2,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_obs__num[,2,1]))) ** 2,
+ # utcd: area 2
+ (r$step3_cdist_sumofsquares_utcd_model__num[,2] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utcd_model__num[,2])) -
+ r$cdist_sumofsquares_utcd_obs__num[,2,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_obs__num[,2,2]))) ** 2,
+ # utcd_weight: area 1
+ (r$step3_cdist_sumofsquares_utcd_weight_model__wgt[,1] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utcd_weight_model__wgt[,1])) -
+ r$cdist_sumofsquares_utcd_weight_obs__wgt[,2,1] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_weight_obs__wgt[,2,1]))) ** 2,
+ # utcd_weight: area 2
+ (r$step3_cdist_sumofsquares_utcd_weight_model__wgt[,2] / g3_avoid_zero(sum(r$step3_cdist_sumofsquares_utcd_weight_model__wgt[,2])) -
+ r$cdist_sumofsquares_utcd_weight_obs__wgt[,2,2] / g3_avoid_zero(sum(r$cdist_sumofsquares_utcd_weight_obs__wgt[,2,2]))) ** 2,
+ # multinom:
+ (2 * (-sum(r$cdist_multinomial_multinom_obs__num[,2] * log(g3_logspace_add(r$step3_cdist_multinomial_multinom_model__num/g3_avoid_zero(sum(r$step3_cdist_multinomial_multinom_model__num)) *
+ 10000, (1/(length(r$cdist_multinomial_multinom_obs__num[,2]) * 10)) * 10000)/10000)) +
+ (sum(g3_lgamma_vec(1 + r$cdist_multinomial_multinom_obs__num[,2])) - lgamma(1 +
+ sum(r$cdist_multinomial_multinom_obs__num[,2]))))),
+ # surveyindices:
+ sum((params$si_alpha +
+ params$si_beta * log(g3_avoid_zero(r$adist_surveyindices_log_surveyindices_model__num[,])) -
+ log(g3_avoid_zero(r$adist_surveyindices_log_surveyindices_obs__num[,])))**2),
+ r$step1_nll)), "step3_nll: Sum of squares, including step1_nll")
+
+ 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)
+ }
+ })
# Likelihood per year
# skip: not compiling TMB model
ok - cdist_sumofsquares_utsd_obs__num: Imported from data.frame, order not necessarily the same
ok - adist_surveyindices_log_surveyindices_model__params: Reported our hard-coded linear regression parameters
ok - step1_cdist_sumofsquares_utsd_model__num[,'prey_a',1]: prey_a summed over year
ok - step1_cdist_sumofsquares_utsd_model__num[,'prey_c',1]: No prey_c in first area
ok - step1_cdist_sumofsquares_utsd_model__num[,'prey_a',2]: No prey_a in second area
ok - step1_cdist_sumofsquares_utsd_model__num[,'prey_c',2]: prey_c summed over year
ok - step1_cdist_sumofsquares_utcd_model__num[,1]: all prey from a/b and steps 0 & 1
ok - step1_cdist_sumofsquares_utcd_model__num[,2]: all prey from c and steps 0/1
ok - step1_cdist_sumofsquares_utcd_weight_model__wgt[,1]: total biomass of prey from a/b and steps 0 & 1
ok - step1_cdist_sumofsquares_utcd_weight_model__wgt[,2]: total biomass of prey from c and steps 0/1
ok - adist_surveyindices_log_surveyindices_model__num: Built-in reporting gave us step 0..3 abundance
ok - step0_nll: nll not calculated yet
ok - step1_nll: Sum of squares
ok - step3_nll: Sum of squares, including step1_nll
>
> proc.time()
user system elapsed
12.20 0.29 12.75
1..71
# Looks like you failed 1 of 71 tests.
# 9: g3l_distribution_sumofsquares statified over length
Flavor: r-devel-windows-x86_64
Current CRAN status: NOTE: 4, OK: 9
Version: 7.3-1
Check: for unstated dependencies in ‘demo’
Result: NOTE
'library' or 'require' call not declared from: ‘tibble’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Current CRAN status: OK: 13
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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