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Type 'q()' to quit R. > library(unittest) > > library(gadget3) > > read.matrix <- function (x, ...) unname(as.matrix(read.table(text=x, ...))) > > teststock <- g3_stock('teststock', seq(10, 35, 5)) > > ok_group("g3a_grow_lengthvbsimple", { + # Run g3a_grow_lengthvbsimple for given linf and midlen + lvs <- function (linf, kappa = 100) { + as.numeric(g3_eval( + g3a_grow_lengthvbsimple(linf, kappa), + stock = g3_stock("s", seq(10, 100, 10) - 5), + cur_step_size = 1)) + } + ok(ut_cmp_equal( + lvs(linf = 150), + c(140, 130, 120, 110, 100, 90, 80, 70, 60, 50)), "linf = 150") + ok(ut_cmp_equal( + lvs(linf = 55), + c(45, 35, 25, 15, 5, 0, 0, 0, 0, 0), tolerance = 1e-7), "linf = 55 (linf doesn't fall negative)") + }) # g3a_grow_lengthvbsimple ok - linf = 150 ok - linf = 55 (linf doesn't fall negative) > > ok_group("g3a_grow_impl_bbinom:zero-growth", { + # Run g3a_grow_impl_bbinom for given linf and midlen + gim <- function (linf, kappa = 20, beta = 0.5, maxlengthgroupgrowth = 10) { + g3_eval( + g3a_grow_impl_bbinom(g3a_grow_lengthvbsimple(linf, kappa), ~0, beta, maxlengthgroupgrowth)$len, + stock = g3_stock("s", seq(10, 100, 10) - 5), + cur_step_size = 1) + } + + ok(ut_cmp_equal(round(gim(linf = 120, maxlengthgroupgrowth = 5), 2), read.matrix(' + 8.29 8.44 0.40 0.17 0.12 0.15 + 9.00 10.00 0.00 0.00 0.00 0.00 + 11.43 14.29 1.02 0.36 0.22 0.26 + 26.56 39.35 7.50 2.00 1.11 1.18 + 26.18 50.91 21.82 2.18 0.91 0.82 + 21.00 70.00 80.00 32.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 1.00 + 0.02 0.05 0.08 0.13 0.21 0.51 + 0.14 0.12 0.12 0.13 0.17 0.32 + 0.37 0.14 0.10 0.10 0.11 0.19 + ')),"linf=120, maxlengthgroupgrowth=5") + # TODO: rowSums(gim(linf = 120, maxlengthgroupgrowth = 5)) should be 1? + + ok(ut_cmp_equal(round(gim(linf = 40, maxlengthgroupgrowth = 5), 2), read.matrix(' + 0.14 0.12 0.12 0.13 0.17 0.32 + 0.37 0.14 0.10 0.10 0.11 0.19 + 0.66 0.09 0.06 0.05 0.05 0.09 + 1.00 0.00 0.00 0.00 0.00 0.00 + 1.00 0.00 0.00 0.00 0.00 0.00 + 1.00 0.00 0.00 0.00 0.00 0.00 + 1.00 0.00 0.00 0.00 0.00 0.00 + 1.00 0.00 0.00 0.00 0.00 0.00 + 1.00 0.00 0.00 0.00 0.00 0.00 + 1.00 0.00 0.00 0.00 0.00 0.00 + ')),"linf=40, maxlengthgroupgrowth=5 - Linf lower than Lmax produces valid output") + ok(ut_cmp_equal( + rowSums(gim(linf = 40, maxlengthgroupgrowth = 5)), + rep(1, 10), tolerance = 1e-2), "linf=40, maxlengthgroupgrowth=5 - Rows sum to 1") + }) # g3a_grow_impl_bbinom:zero-growth ok - linf=120, maxlengthgroupgrowth=5 ok - linf=40, maxlengthgroupgrowth=5 - Linf lower than Lmax produces valid output ok - linf=40, maxlengthgroupgrowth=5 - Rows sum to 1 > > ok_group("g3a_grow_impl_bbinom", { + actions <- list( # dmu, lengthgrouplen, binn, beta + g3a_time(2000, 2001, project_years = 0), + g3a_initialconditions(teststock, ~g3_param_vector("initial", value = c(10, 100, 1000, 1000, 10000, 100000)), ~0 * teststock__minlen), + g3a_growmature(teststock, + impl_f = g3a_grow_impl_bbinom( + delta_len_f = g3a_grow_lengthvbsimple(~g3_param('linf', value = 160), ~g3_param('kappa', value = 90)), + delta_wgt_f = g3a_grow_weightsimple(~g3_param('walpha', value = 3), ~g3_param('wbeta', value = 2)), + beta = ~g3_param('beta', value = 30), + maxlengthgroupgrowth = 4)), + list( + "999" = ~{ + REPORT(teststock__growth_l) + REPORT(teststock__growth_w) + nll <- nll + g3_param('x', value = 1.0) + return(nll) + })) + + # Compile model + # NB: Growth not valid, but not testing growth at this point + model_fn <- g3_to_r(actions, trace = FALSE, strict = FALSE) + # model_fn <- edit(model_fn) + if (nzchar(Sys.getenv('G3_TEST_TMB'))) { + model_cpp <- g3_to_tmb(actions, trace = FALSE, strict = FALSE) + # model_cpp <- edit(model_cpp) + model_tmb <- g3_tmb_adfun(model_cpp, attr(model_fn, 'parameter_template'), compile_flags = c("-O0", "-g")) + } else { + writeLines("# skip: not compiling TMB model") + } + + params <- attr(model_fn, 'parameter_template') + result <- model_fn(params) + r <- attributes(result) + # str(result) + # str(as.list(r), vec.len = 10000) + + #writeLines(deparse(r$teststock__growth_l)) + ok(ut_cmp_equal(r$teststock__growth_l, structure(c(12199.8976226175, 9352.23228375502, 7157.83523789257, + 5463.49450549465, 4154.31593595054, 3143.22179218075, 51322.2074676947, + 39560.4630926918, 30458.8733527337, 23399.2087912083, 17917.1342692155, + 13660.121314133, 81087.2009530949, 62860.2639001552, 48695.7187344743, + 37658.1016483506, 29043.7267350904, 22317.4314305221, 57032.8699935755, + 44472.5676572519, 34669.6583623158, 26995.0549450546, 20974.8144063369, + 16247.8860873661, 15068.9788855573, 11821.5345660349, 9275.97774268346, + 7273.66758241751, 5694.90600451131, 4448.35417879727), + .Dimnames = list(length = c("10:15", "15:20", "20:25", "25:30", "30:35", "35:Inf"), delta = c("0", "1", "2", "3", "4")), + .Dim = c(length = 6, delta = 5)), tolerance = 1e-5), "Matches baseline") + + if (nzchar(Sys.getenv('G3_TEST_TMB'))) { + param_template <- attr(model_cpp, "parameter_template") + param_template$value <- params[param_template$switch] + gadget3:::ut_tmb_r_compare(model_fn, model_tmb, param_template) + } + + # Try comparing with a few different inputs + for (x in 1:10) ok_group("g3a_grow_impl_bbinom random params", { + params <- attr(model_fn, 'parameter_template') + params$linf <- runif(1, 100, 200) + params$kappa <- runif(1, 50, 100) + params$walpha <- runif(1, 0.1, 3) + params$wbeta <- runif(1, 0.1, 2) + params$beta <- runif(1, 10, 30) + params$initial <- runif(6, 1000, 9000) + if (nzchar(Sys.getenv('G3_TEST_TMB'))) { + param_template <- attr(model_cpp, "parameter_template") + param_template$value <- params[param_template$switch] + gadget3:::ut_tmb_r_compare(model_fn, model_tmb, param_template) + } + }) + }) # g3a_grow_impl_bbinom # skip: not compiling TMB model ok - Matches baseline # g3a_grow_impl_bbinom random params # g3a_grow_impl_bbinom random params # g3a_grow_impl_bbinom random params # g3a_grow_impl_bbinom random params # g3a_grow_impl_bbinom random params # g3a_grow_impl_bbinom random params # g3a_grow_impl_bbinom random params # g3a_grow_impl_bbinom random params # g3a_grow_impl_bbinom random params # g3a_grow_impl_bbinom random params > > ok_group("g3a_growmature", { + actions <- list( + g3a_time(2000, 2001, project_years = 0), + g3a_initialconditions(teststock, + ~g3_param_vector("initial_num"), + ~g3_param_vector("initial_wgt")), + g3a_growmature(teststock, + impl_f = list( + delta_dim = as.character(0:6), + len = ~g3_param_array('growth_matrix'), + wgt = ~g3_param_array('weight_matrix'))), + list( + "999" = ~{ + REPORT(teststock__num) + REPORT(teststock__wgt) + nll <- nll + g3_param('x') + return(nll) + })) + params <- attr(model_fn, 'parameter_template') + params$initial_num <- c(10, 100, 1000, 1000, 10000, 100000) + params$initial_wgt <- c(100, 200, 300, 400, 500, 600) + params$growth_matrix <- array(dim = c(6, 7)) + params$weight_matrix <- array(0, dim = c(6, 7)) + + # Compile model + # NB: Our tests don't preserve counts, so we can't enable strict here + model_fn <- g3_to_r(actions, trace = FALSE, strict = FALSE) + # model_fn <- edit(model_fn) + if (nzchar(Sys.getenv('G3_TEST_TMB'))) { + model_cpp <- g3_to_tmb(actions, trace = FALSE, strict = FALSE) + # model_cpp <- edit(model_cpp) + model_tmb <- g3_tmb_adfun(model_cpp, params, compile_flags = c("-O0", "-g")) + } else { + writeLines("# skip: not compiling TMB model") + } + + gm <- array(c( + # 10 15 20 25 30 35 + 0, 0.25, 1, 0.5, 0.5, 1, # 0 + 0, 0, 0, 0, 0, 0, # +1 + 1, 0.75, 0, 0, 0, 0, # +2 + 0, 0, 0, 0, 0, 0, # +3 + 0, 0, 0, 0, 0.5, 0, # +4 + 0, 0, 0, 0, 0, 0, # +5 + 0, 0, 0, 0.5, 0, 0), dim = c(6,7)) + params <- attr(model_fn, 'parameter_template') + params$initial_num <- c(10, 100, 1000, 1000, 10000, 100000) + params$initial_wgt <- c(100, 200, 300, 400, 500, 600) + params$growth_matrix <- gm + params$weight_matrix <- array(0, dim = c(6, 7)) + result <- model_fn(params) + r <- attributes(result) + # str(result) + # str(as.list(r), vec.len = 10000) + + # model_fn <- edit(model_fn) + result <- model_fn(params) + ok(ut_cmp_identical( + as.vector(r$teststock__num), + c(0, 25, 1010, 575, 5000, 105500)), "Stock individuals have been scaled by matrix, can't escape plus-group") + ok(ut_cmp_equal(as.vector(r$teststock__wgt), c( + 0 / g3_env$logspace_add(0, 0), + (200 * 100*0.25) / 25, + (300 * 1000 + 100 * 10) / 1010, + (400 * 1000*0.5 + 200 * 100*0.75) / 575, + (500 * 10000*0.5) / 5000, + (600 * 100000 + 500 * 10000*0.5 + 400 * 1000*0.5) / 105500, + NULL), tolerance = 1e-5), "Weight scaled, didn't let weight go to infinity when dividing by zero") + + 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) + } + }) # g3a_growmature # skip: not compiling TMB model ok - Stock individuals have been scaled by matrix, can't escape plus-group ok - Weight scaled, didn't let weight go to infinity when dividing by zero > > proc.time() user system elapsed 0.89 0.10 0.98 # Looks like you passed all 8 tests.