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(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(ut_cmp_identical( gadget3:::g3_parameterized_breakdown(g3_parameterized('par', by_stock = TRUE)), c("stock"), filter = NULL), "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(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(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(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") #### 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(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(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(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(ut_cmp_error( g3_parameterized('parp', by_stock = FALSE, by_age = TRUE), 'by_age'), "!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(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(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(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(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") 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)$switch, c( "paramut.def.1990", "paramut.def.1991", "paramut.def.1992", "paramut.def.1993", "paramut.def.1994", "paramut.var.1982", "paramut.var.1983", "paramut.var.1984", "paramut.var.1985", "paramut.var.1986", "paramut.custom.1999", "paramut.custom.2000", "paramut.custom.2001", "paramut.custom.2002", "paramut.custom.2003", "paramut.custom.2004")), "by_year: Can customise ranges") ok(ut_cmp_identical(param_tmpl( g3_parameterized('paramut.fleet', by_predator = TRUE), g3_parameterized('paramut.stockfleet', by_predator = TRUE, by_stock = TRUE), g3_parameterized('paramut.stockfleetcty', by_predator = "country", by_stock = TRUE), NULL)$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")