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Type 'q()' to quit R. > library(magrittr) > library(unittest) > if (!interactive()) options(warn=2, error = function() { sink(stderr()) ; traceback(3) ; q(status = 1) }) > > library(gadget3) > > cmp_code <- function (a, b) ut_cmp_identical(deparse(a), deparse(b)) > > # Generate parameter template for all given parameters (beginning with "ut.") > param_tmpl <- function (...) { + actions <- c( + list(g3a_time(1990, 1994)), + lapply(list(...), function (p) { + if (is.null(p)) return(~{}) + x <- 4 + stock <- g3_stock(c(species = 'had', sex = 'm', maturity = 'imm'), 1) + predstock <- g3_fleet(c(country = 'is', 'comm')) + gadget3:::g3_step(gadget3:::f_substitute( + ~{x <- p}, + list(p = p))) + })) + m <- g3_to_tmb(actions) + pt <- attr(m, 'parameter_template') + pt[grepl('paramut', rownames(pt), fixed = TRUE),] + } > > stock_mimm <- g3_stock(c(species = 'st', sex = 'm', maturity = 'imm'), seq(10, 35, 5)) %>% g3s_age(1, 5) > stock_mmat <- g3_stock(c(species = 'st', sex = 'm', maturity = 'mat'), seq(10, 35, 5)) %>% g3s_age(3, 7) > stock_fimm <- g3_stock(c(species = 'st', sex = 'f', maturity = 'imm'), seq(10, 35, 5)) %>% g3s_age(1, 5) > stock_fmat <- g3_stock(c(species = 'st', sex = 'f', maturity = 'mat'), seq(10, 35, 5)) %>% g3s_age(3, 7) > # Put x through g3_step() as a g3 action would, the "stock" being stock_mimm > pretend_stock_action <- function (x) { + rlang::f_rhs(gadget3:::g3_step(gadget3:::call_to_formula( + x, + env = list2env(list(stock = stock_mimm), parent = baseenv())))) + } > > ##### g3_parameterized_breakdown > ok(ut_cmp_identical( + gadget3:::g3_parameterized_breakdown(g3_parameterized('par', by_year = TRUE)), + c("cur_year"), + filter = NULL), "g3_parameterized_breakdown: by_year") ok - g3_parameterized_breakdown: by_year > ok(ut_cmp_identical( + gadget3:::g3_parameterized_breakdown(g3_parameterized('par', by_year = TRUE, by_step = TRUE)), + c("cur_year", "cur_step"), + filter = NULL), "g3_parameterized_breakdown: by_year, by_step") ok - g3_parameterized_breakdown: by_year, by_step > ok(ut_cmp_identical( + gadget3:::g3_parameterized_breakdown(g3_parameterized('par', by_stock = TRUE)), + c("stock"), + filter = NULL), "g3_parameterized_breakdown: by_stock") ok - g3_parameterized_breakdown: by_stock > ok(ut_cmp_identical( + gadget3:::g3_parameterized_breakdown(g3_parameterized('par', by_stock = TRUE, by_year = TRUE)), + c("stock", "cur_year"), + filter = NULL), "g3_parameterized_breakdown: by_stock, by_year") ok - g3_parameterized_breakdown: by_stock, by_year > ok(ut_cmp_identical( + gadget3:::g3_parameterized_breakdown(g3_parameterized('par', by_stock = TRUE, by_year = TRUE, exponentiate = TRUE)), + c("stock", "cur_year"), + filter = NULL), "g3_parameterized_breakdown: by_stock, by_year, exponentiate") ok - g3_parameterized_breakdown: by_stock, by_year, exponentiate > ok(ut_cmp_identical( + gadget3:::g3_parameterized_breakdown(g3_parameterized('par', by_stock = TRUE, scale = 4, avoid_zero = TRUE)), + c("stock"), + filter = NULL), "g3_parameterized_breakdown: by_stock, scale, avoid_zero") ok - g3_parameterized_breakdown: by_stock, scale, avoid_zero > ok(ut_cmp_identical( + gadget3:::g3_parameterized_breakdown(g3_parameterized('par', by_stock = TRUE, offset = 4)), + c("stock"), + filter = NULL), "g3_parameterized_breakdown: by_stock, offset") ok - g3_parameterized_breakdown: by_stock, offset > > #### g3_parameterized > > ok(cmp_code( + call("{", # } + g3_parameterized('parp', by_stock = FALSE), + NULL), quote({ + g3_param("parp") + NULL})), "Not 'by' anything, so just a regular parameter") ok - Not 'by' anything, so just a regular parameter > > ok(cmp_code( + call("{", # } + g3_parameterized('parp', by_stock = FALSE, exponentiate = TRUE, offset = 5), + g3_parameterized('parp', by_stock = FALSE, scale = 0.001, offset = 2), + g3_parameterized('parp_avz', by_stock = FALSE, scale = 0.2, offset = 4, avoid_zero = TRUE), + NULL), quote({ + exp(g3_param("parp_exp")) + 5 + g3_param("parp") * 0.001 + 2 + avoid_zero(g3_param("parp_avz") * 0.2) + 4 + NULL})), "Can wrap with exp(), scale, offset, avoid_zero") ok - Can wrap with exp(), scale, offset, avoid_zero > > ok(cmp_code( + call("{", # } + g3_parameterized('parp', by_stock = FALSE, value = 4, lower = 2, upper = 9), + g3_parameterized('parp', by_stock = FALSE, optimise = FALSE), + g3_parameterized('parp', by_stock = FALSE, random = TRUE), + g3_parameterized('parp', by_year = TRUE, ifmissing = g3_parameterized('peep')), + NULL), quote({ + g3_param("parp", value = 4, lower = 2, upper = 9) + g3_param("parp", optimise = FALSE) + g3_param("parp", random = TRUE) + g3_param_table("parp", expand.grid(cur_year = seq(start_year, end_year)), ifmissing = g3_param("peep")) + NULL})), "Extra parameters passed through") ok - Extra parameters passed through > > ok(cmp_code( + pretend_stock_action(g3_parameterized('parp', by_stock = TRUE)), + quote(g3_param("st_m_imm.parp"))), "by_stock, so will use stock_prepend() to rename variables") ok - by_stock, so will use stock_prepend() to rename variables > > ok(ut_cmp_error( + g3_parameterized('parp', by_stock = FALSE, by_age = TRUE), + 'by_age'), "!by_stock and by_age is nonsensical, throws error") ok - !by_stock and by_age is nonsensical, throws error > > ok(cmp_code( + pretend_stock_action(call("{", # } + g3_parameterized('parp', by_stock = TRUE, by_year = TRUE), + g3_parameterized('parp', by_stock = TRUE, by_year = TRUE, by_age = TRUE), + NULL)), quote({ + g3_param_table("st_m_imm.parp", expand.grid( + cur_year = seq(start_year, end_year))) + g3_param_table("st_m_imm.parp", expand.grid( + cur_year = seq(start_year, end_year), + age = seq(st_m_imm__minage, st_m_imm__maxage))) + NULL})), "Adding by_year or by_age turns it into a table") ok - Adding by_year or by_age turns it into a table > > ok(cmp_code( + pretend_stock_action(call("{", # } + g3_parameterized('yr', by_year = TRUE), + g3_parameterized('st', by_step = TRUE), + g3_parameterized('yrst', by_year = TRUE, by_step = TRUE), + NULL)), quote({ + g3_param_table("yr", expand.grid( + cur_year = seq(start_year, end_year))) + g3_param_table("st", expand.grid( + cur_step = seq_along(step_lengths))) + g3_param_table("yrst", expand.grid( + cur_year = seq(start_year, end_year), + cur_step = seq_along(step_lengths))) + NULL})), "by_year & by_step can be combined") ok - by_year & by_step can be combined > > ok(cmp_code( + pretend_stock_action(call("{", # } + g3_parameterized('parp', by_stock = 'species', lower = 3), + g3_parameterized('parp', by_stock = c('species', 'sex'), lower = 3), + g3_parameterized('parp', by_stock = 'sex', by_year = TRUE), + NULL)), quote({ + g3_param("st.parp", lower = 3) + g3_param("st_m.parp", lower = 3) + g3_param_table("m.parp", expand.grid(cur_year = seq(start_year, end_year))) + NULL})), "Can specify which name_part should be used in the name") ok - Can specify which name_part should be used in the name > > ok(cmp_code( + call("{", # } + g3_parameterized('parp', by_stock = list(stock_mimm, stock_mmat)), + g3_parameterized('parp', by_stock = list(stock_mimm, stock_fmat)), # M vs F, so only species matches + g3_parameterized('parp', by_stock = list(stock_fimm, stock_fmat), by_age = TRUE), + NULL), quote({ + stock_prepend("st.m", g3_param("parp")) + stock_prepend("st", g3_param("parp")) + stock_prepend("st.f", g3_param_table("parp", expand.grid( + age = seq(min(st_f_imm__minage, st_f_mat__minage), max(st_f_imm__maxage, st_f_mat__maxage))))) + NULL})), "Can give a list of stocks, in which case it works out name parts for you") ok - Can give a list of stocks, in which case it works out name parts for you > > ok(cmp_code( + call("{", # } + g3_parameterized('rec', by_stock = 'species', scale = 'rec.scalar'), + g3_parameterized('rec', by_stock = 'species', scale = 'rec.scalar', offset = 'rec.offset'), + g3_parameterized('rec', by_stock = 'species', by_age = TRUE, scale = 'rec.scalar'), + NULL), quote({ + stock_prepend(stock, g3_param("rec"), name_part = "species") * stock_prepend(stock, g3_param("rec.scalar"), name_part = "species") + stock_prepend(stock, g3_param("rec"), name_part = "species") * stock_prepend(stock, g3_param("rec.scalar"), name_part = "species") + stock_prepend(stock, g3_param("rec.offset"), name_part = "species") + stock_prepend(stock, g3_param_table("rec", expand.grid(age = seq(stock__minage, stock__maxage))), name_part = "species") * stock_prepend(stock, g3_param("rec.scalar"), name_part = "species") + NULL})), "scale / offset can be character, in which case they are also a param. Only by_stock is honoured though") ok - scale / offset can be character, in which case they are also a param. Only by_stock is honoured though > > year_range <- 1982:1986 > ok(ut_cmp_identical(param_tmpl( + g3_parameterized('paramut.def', by_year = TRUE), + g3_parameterized('paramut.var', by_year = year_range), + g3_parameterized('paramut.custom', by_year = 1999:2004), + NULL)$switch, c( + "paramut.def.1990", "paramut.def.1991", "paramut.def.1992", "paramut.def.1993", "paramut.def.1994", + "paramut.var.1982", "paramut.var.1983", "paramut.var.1984", "paramut.var.1985", "paramut.var.1986", + "paramut.custom.1999", "paramut.custom.2000", "paramut.custom.2001", + "paramut.custom.2002", "paramut.custom.2003", "paramut.custom.2004")), "by_year: Can customise ranges") ok - by_year: Can customise ranges > > ok(ut_cmp_identical(param_tmpl( + g3_parameterized('paramut.fleet', by_predator = TRUE), + g3_parameterized('paramut.stockfleet', by_predator = TRUE, by_stock = TRUE), + g3_parameterized('paramut.stockfleetcty', by_predator = "country", by_stock = TRUE), + NULL)$switch, c( + "is_comm.paramut.fleet", + "had_m_imm.is_comm.paramut.stockfleet", + "had_m_imm.is.paramut.stockfleetcty", + NULL)), "by_predator: Can combine with by_stock") ok - by_predator: Can combine with by_stock > > proc.time() user system elapsed 0.56 0.04 0.61 # Looks like you passed all 19 tests.