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Type 'q()' to quit R. > library(magrittr) > library(unittest) > > library(gadget3) > > prey_a <- g3_stock('prey_a', seq(1, 10)) > prey_b <- g3_stock('prey_b', seq(1, 10)) > report_a <- g3s_clone(prey_a, 'report_a') %>% gadget3:::g3s_modeltime() > report_b <- g3s_clone(prey_b, 'report_b') %>% gadget3:::g3s_modeltime() > fleet_numberfleet <- g3_fleet('fleet_numberfleet') > fleet_linearfleet <- g3_fleet('fleet_linearfleet') > fleet_effortfleet <- g3_fleet('fleet_effortfleet') > fleet_quotafleet <- g3_fleet('fleet_quotafleet') > report_numberfleet <- g3s_clone(fleet_numberfleet, 'report_numberfleet') %>% gadget3:::g3s_modeltime() > report_linearfleet <- g3s_clone(fleet_linearfleet, 'report_linearfleet') %>% gadget3:::g3s_modeltime() > report_effortfleet <- g3s_clone(fleet_effortfleet, 'report_effortfleet') %>% gadget3:::g3s_modeltime() > report_quotafleet <- g3s_clone(fleet_quotafleet, 'report_quotafleet') %>% gadget3:::g3s_modeltime() > > actions <- list( + g3a_time(2000, 2005, step_lengths = c(6,6), project_years = 0), + g3a_initialconditions(prey_a, ~1000000 * prey_a__midlen, ~100 * prey_a__midlen), + g3a_initialconditions(prey_b, ~1000000 * prey_b__midlen, ~100 * prey_b__midlen), + g3a_predate_fleet( + fleet_numberfleet, + list(prey_a, prey_b), + suitabilities = list(prey_a = 0.1, prey_b = 0.1), + catchability_f = g3a_predate_catchability_numberfleet(10)), + g3a_predate_fleet( + fleet_linearfleet, + list(prey_a, prey_b), + suitabilities = list(prey_a = 0.1, prey_b = 0.1), + catchability_f = g3a_predate_catchability_linearfleet(10)), + g3a_predate_fleet( + fleet_effortfleet, + list(prey_a, prey_b), + suitabilities = list(prey_a = 0.1, prey_b = 0.1), + catchability_f = g3a_predate_catchability_effortfleet(list(prey_a = 5, prey_b= 6), 10)), + g3a_predate_fleet( + fleet_quotafleet, + list(prey_a, prey_b), + suitabilities = list(prey_a = 0.1, prey_b = 0.1), + catchability_f = g3a_predate_catchability_quotafleet( + data.frame( + biomass = c(100, Inf), + quota = I(list(~g3_param('quota.low', value = 1000), ~g3_param('quota.high', value = 9000)))), + E = 10, + recalc_f = ~cur_step == 1)), + g3a_report_stock(report_a, prey_a, ~stock_ss(prey_a__num)), + g3a_report_stock(report_a, prey_a, ~stock_ss(prey_a__wgt)), + g3a_report_stock(report_a, prey_a, ~stock_ss(prey_a__totalpredate)), + g3a_report_stock(report_a, prey_a, ~stock_ss(prey_a__consratio)), + g3a_report_stock(report_a, prey_a, ~stock_ss(prey_a__predby_fleet_numberfleet)), + g3a_report_stock(report_a, prey_a, ~stock_ss(prey_a__predby_fleet_linearfleet)), + g3a_report_stock(report_a, prey_a, ~stock_ss(prey_a__predby_fleet_effortfleet)), + g3a_report_stock(report_a, prey_a, ~stock_ss(prey_a__predby_fleet_quotafleet)), + + g3a_report_stock(report_b, prey_b, ~stock_ss(prey_b__num)), + g3a_report_stock(report_b, prey_b, ~stock_ss(prey_b__wgt)), + g3a_report_stock(report_b, prey_b, ~stock_ss(prey_b__totalpredate)), + g3a_report_stock(report_b, prey_b, ~stock_ss(prey_b__consratio)), + g3a_report_stock(report_b, prey_b, ~stock_ss(prey_b__predby_fleet_numberfleet)), + g3a_report_stock(report_b, prey_b, ~stock_ss(prey_b__predby_fleet_linearfleet)), + g3a_report_stock(report_b, prey_b, ~stock_ss(prey_b__predby_fleet_effortfleet)), + g3a_report_stock(report_b, prey_b, ~stock_ss(prey_b__predby_fleet_quotafleet)), + + g3a_report_stock(report_numberfleet, fleet_numberfleet, ~stock_ss(fleet_numberfleet__catch)), + g3a_report_stock(report_numberfleet, fleet_numberfleet, ~stock_ss(fleet_numberfleet__catchnum)), + g3a_report_stock(report_linearfleet, fleet_linearfleet, ~stock_ss(fleet_linearfleet__catch)), + g3a_report_stock(report_effortfleet, fleet_effortfleet, ~stock_ss(fleet_effortfleet__catch)), + + g3a_report_stock(report_quotafleet, fleet_quotafleet, ~stock_ss(fleet_quotafleet__catch)), + list()) > > # 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, compile_flags = c("-O0", "-g")) + } else { + writeLines("# skip: not compiling TMB model") + } # skip: not compiling TMB model > > ok_group("Catchability", { + params <- attr(model_fn, 'parameter_template') + + result <- model_fn(params) + r <- attributes(result) + # str(as.list(r), vec.len = 10000) + + # Make sure everything is internally consistent + ok(all(r$report_a__consratio > 0.9499), "report_a__consratio: No overconsumption") + ok(all(r$report_b__consratio > 0.9499), "report_b__consratio: No overconsumption") + ok(ut_cmp_equal( + r$report_a__predby_fleet_numberfleet + r$report_a__predby_fleet_linearfleet + r$report_a__predby_fleet_effortfleet + r$report_a__predby_fleet_quotafleet, + r$report_a__totalpredate), "report_a__totalpredate: Equal to sum of fleet consumption") + ok(ut_cmp_equal( + r$report_b__predby_fleet_numberfleet + r$report_b__predby_fleet_linearfleet + r$report_b__predby_fleet_effortfleet + r$report_b__predby_fleet_quotafleet, + r$report_b__totalpredate), "report_b__totalpredate: Equal to sum of fleets") + ok(ut_cmp_equal( + as.numeric(colSums(r$report_a__predby_fleet_numberfleet + r$report_b__predby_fleet_numberfleet)), + as.numeric(r$report_numberfleet__catch)), "report_numberfleet__catch: Equal to sum of preys") + ok(ut_cmp_equal( + as.numeric(colSums((r$report_a__predby_fleet_numberfleet/r$report_a__wgt) + (r$report_b__predby_fleet_numberfleet/r$report_b__wgt))), + as.numeric(r$report_numberfleet__catchnum)), "report_numberfleet__catchnum: Consistent with __predby_fleet_numberfleet") + ok(ut_cmp_equal( + as.numeric(colSums(r$report_a__predby_fleet_linearfleet + r$report_b__predby_fleet_linearfleet)), + as.numeric(r$report_linearfleet__catch)), "report_linearfleet__catch: Equal to sum of preys") + ok(ut_cmp_equal( + as.numeric(colSums(r$report_a__predby_fleet_effortfleet + r$report_b__predby_fleet_effortfleet)), + as.numeric(r$report_effortfleet__catch)), "report_effortfleet__catch: Equal to sum of preys") + ok(ut_cmp_equal( + as.numeric(colSums(r$report_a__predby_fleet_quotafleet + r$report_b__predby_fleet_quotafleet)), + as.numeric(r$report_quotafleet__catch)), "report_quotafleet__catch: Equal to sum of preys") + + if (nzchar(Sys.getenv('G3_TEST_TMB'))) { + param_template <- attr(model_cpp, "parameter_template") + param_template$value <- params[param_template$switch] + gadget3:::ut_tmb_r_compare(model_fn, model_tmb, param_template) + } + }) # Catchability ok - report_a__consratio: No overconsumption ok - report_b__consratio: No overconsumption ok - report_a__totalpredate: Equal to sum of fleet consumption ok - report_b__totalpredate: Equal to sum of fleets ok - report_numberfleet__catch: Equal to sum of preys ok - report_numberfleet__catchnum: Consistent with __predby_fleet_numberfleet ok - report_linearfleet__catch: Equal to sum of preys ok - report_effortfleet__catch: Equal to sum of preys ok - report_quotafleet__catch: Equal to sum of preys > > proc.time() user system elapsed 1.84 0.03 1.87 # Looks like you passed all 9 tests.