R Under development (unstable) (2024-07-01 r86857 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64

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> library(magrittr)
> library(unittest)
> 
> library(gadget3)
> 
> capture_warnings <- function(x, full_object = FALSE) {
+     all_warnings <- list()
+     rv <- withCallingHandlers(x, warning = function (w) {
+         all_warnings <<- c(all_warnings, list(w))
+         invokeRestart("muffleWarning")
+     })
+     if (!full_object) all_warnings <- vapply(all_warnings, function (w) w$message, character(1))
+     return(list(rv = rv, warnings = all_warnings))
+ }
> 
> ok(ut_cmp_error({
+     invalid_subset <- array(dim = c(2,2,2))
+     g3_to_tmb(list(~{invalid_subset[,g3_idx(1),]}))
+ }, "invalid_subset"), "Complained when trying to subset in middle")
ok - Complained when trying to subset in middle
> ok(ut_cmp_error({
+     invalid_subset <- array(dim = c(2,2,2))
+     g3_to_tmb(list(~{invalid_subset[g3_idx(1),,] <- 0}))
+ }, "invalid_subset"), "Complained when trying to subset by row in an lvalue")
ok - Complained when trying to subset by row in an lvalue
> 
> ok(ut_cmp_error({
+     g3_to_tmb(list(~{ 2 + NA }))
+ }, "NA"), "No such thing as NA in C++")
ok - No such thing as NA in C++
> 
> ok(grepl(
+     "unknown_func(.*2.*)",
+     paste(g3_to_tmb(list(~{
+         unknown_func(2)
+     })), collapse = "\n"),
+     perl = TRUE), "Unknown functions that are valid C++ get included")
ok - Unknown functions that are valid C++ get included
> 
> ok(ut_cmp_error({
+     g3_to_tmb(list(~`0unknown0`(2)))
+ }, "0unknown0"), "An unknown function has to at least be a valid C++ function")
ok - An unknown function has to at least be a valid C++ function
> 
> ok(ut_cmp_error({
+     g3_to_tmb(list(~not.a.function(2)))
+ }, "not\\.a\\.function"), "An unknown function has to at least be a valid C++ function")
ok - An unknown function has to at least be a valid C++ function
> 
> ok(ut_cmp_error({
+     g3_tmb_adfun(g3_to_tmb(list(~{
+         g3_param('randomandoptimise', random = TRUE, optimise = TRUE)
+         g3_param('ro2', random = TRUE, optimise = TRUE)
+     })))
+ }, "randomandoptimise,ro2"), "Specifying random and optimise isn't allowed")
ok - Specifying random and optimise isn't allowed
> 
> ok(ut_cmp_error({
+     g3_tmb_adfun(g3_to_tmb(list(~{ g3_param_table('randomandoptimise', expand.grid(cur_step = 2:3), random = TRUE, optimise = TRUE) })))
+ }, "randomandoptimise"), "Specifying random and optimise isn't allowed")
ok - Specifying random and optimise isn't allowed
> 
> ok(ut_cmp_error({
+     g3_to_tmb(list(~g3_param("camel", optimize = FALSE)))
+ }, "optimise"), "Optimise is spelt with an s in g3_param()")
ok - Optimise is spelt with an s in g3_param()
> 
> ok_group("Exponentiate params")
# Exponentiate params
> params.in <- attr(g3_to_tmb(list( g3a_time(1990, 2000), g3_formula(
+     quote(d),
+     d = g3_parameterized('par.years', value = 0, by_year = TRUE, exponentiate = TRUE),
+     x = NA) )), 'parameter_template')
> ok(ut_cmp_identical(params.in[grep('^par', params.in$switch), 'switch'], c(
+     paste0('par.years.', 1990:2000, '_exp'),
+     NULL)), "exponentiate prefix ends up at the end of parameters")
ok - exponentiate prefix ends up at the end of parameters
> 
> ok_group('g3_tmb_par', {
+     param <- attr(g3_to_tmb(list(~{
+         g3_param('param.b')
+         g3_param_vector('param_vec')
+         g3_param('aaparam')
+         g3_param('randomparam', random = TRUE)
+     })), 'parameter_template')
+     param$value <- I(list(
+         aaparam = 55,
+         param.b = 66,
+         randomparam = 2,
+         param_vec = 6:10)[rownames(param)])
+ 
+     ok(ut_cmp_identical(g3_tmb_par(param, include_random = FALSE), c(
+         param__b = 66,
+         param_vec1 = 6, param_vec2 = 7, param_vec3 = 8, param_vec4 = 9, param_vec5 = 10,
+         aaparam = 55)), "g3_tmb_par: Flattened parameters in right order")
+ 
+     param['param_vec', 'optimise'] <- FALSE
+     ok(ut_cmp_identical(g3_tmb_par(param, include_random = FALSE), c(
+         param__b = 66,
+         aaparam = 55)), "g3_tmb_par: Turning off optimise removed values")
+ 
+     ok(ut_cmp_identical(g3_tmb_par(param, include_random = TRUE), c(
+         param__b = 66,
+         aaparam = 55,
+         randomparam = 2)), "g3_tmb_par: randomparam visible if include_random on")
+ })
# g3_tmb_par
ok - g3_tmb_par: Flattened parameters in right order
ok - g3_tmb_par: Turning off optimise removed values
ok - g3_tmb_par: randomparam visible if include_random on
> 
> ok_group('g3_tmb_lower', {
+     param <- attr(g3_to_tmb(list(~{
+         g3_param('param.b')
+         g3_param_vector('param_vec')
+         g3_param('aaparam')
+         # NB: Never visible
+         g3_param('randomparam', random = TRUE)
+     })), 'parameter_template')
+     param$value <- I(list(
+         aaparam = 55,
+         param.b = 66,
+         randomparam = 2,
+         param_vec = 6:10)[rownames(param)])
+     param$lower <- c(
+         aaparam = 500,
+         param.b = 600,
+         param_vec = 100)[rownames(param)]
+ 
+     ok(ut_cmp_identical(g3_tmb_lower(param), c(
+         param__b = 600,
+         param_vec1 = 100, param_vec2 = 100, param_vec3 = 100, param_vec4 = 100, param_vec5 = 100,
+         aaparam = 500)), "g3_tmb_lower: All lower bounds in right order")
+ 
+     param['param_vec', 'lower'] <- 3
+     ok(ut_cmp_identical(g3_tmb_lower(param), c(
+         param__b = 600,
+         param_vec1 = 3, param_vec2 = 3, param_vec3 = 3, param_vec4 = 3, param_vec5 = 3,
+         aaparam = 500)), "g3_tmb_lower: Set all lower values of param_vec in one go")
+     ok(ut_cmp_identical(
+         names(g3_tmb_par(param, include_random = FALSE)),
+         names(g3_tmb_lower(param))), "g3_tmb_lower: Structure matches par after setting param_vec")
+ 
+     param['param.b', 'optimise'] <- FALSE
+     ok(ut_cmp_identical(g3_tmb_lower(param), c(
+         param_vec1 = 3, param_vec2 = 3, param_vec3 = 3, param_vec4 = 3, param_vec5 = 3,
+         aaparam = 500)), "g3_tmb_lower: Cleared param.b by setting optimise = F")
+     ok(ut_cmp_identical(
+         names(g3_tmb_par(param, include_random = FALSE)),
+         names(g3_tmb_lower(param))), "g3_tmb_lower: Structure matches par after setting param.b")
+ })
# g3_tmb_lower
ok - g3_tmb_lower: All lower bounds in right order
ok - g3_tmb_lower: Set all lower values of param_vec in one go
ok - g3_tmb_lower: Structure matches par after setting param_vec
ok - g3_tmb_lower: Cleared param.b by setting optimise = F
ok - g3_tmb_lower: Structure matches par after setting param.b
> 
> ok_group('g3_tmb_upper', {
+     param <- attr(g3_to_tmb(list(~{
+         g3_param('param.b')
+         g3_param_vector('param_vec')
+         g3_param('aaparam')
+         # NB: Never visible
+         g3_param('randomparam', random = TRUE)
+     })), 'parameter_template')
+     param$value <- I(list(
+         aaparam = 55,
+         param.b = 66,
+         randomparam = 2,
+         param_vec = 6:10)[rownames(param)])
+     param$upper <- c(
+         aaparam = 500,
+         param.b = 600,
+         param_vec = 100)[rownames(param)]
+ 
+     ok(ut_cmp_identical(g3_tmb_upper(param), c(
+         param__b = 600,
+         param_vec1 = 100, param_vec2 = 100, param_vec3 = 100, param_vec4 = 100, param_vec5 = 100,
+         aaparam = 500)), "g3_tmb_upper: All upper bounds in right order")
+ 
+     param['param_vec', 'upper'] <- 3
+     ok(ut_cmp_identical(g3_tmb_upper(param), c(
+         param__b = 600,
+         param_vec1 = 3, param_vec2 = 3, param_vec3 = 3, param_vec4 = 3, param_vec5 = 3,
+         aaparam = 500)), "g3_tmb_upper: Set all lower values of param_vec in one go")
+     ok(ut_cmp_identical(
+         names(g3_tmb_par(param, include_random = FALSE)),
+         names(g3_tmb_lower(param))), "g3_tmb_upper: Structure matches par after setting param_vec")
+ 
+     param['param.b', 'optimise'] <- FALSE
+     ok(ut_cmp_identical(g3_tmb_upper(param), c(
+         param_vec1 = 3, param_vec2 = 3, param_vec3 = 3, param_vec4 = 3, param_vec5 = 3,
+         aaparam = 500)), "g3_tmb_upper: Cleared param.b by setting optimise = F")
+     ok(ut_cmp_identical(
+         names(g3_tmb_par(param, include_random = FALSE)),
+         names(g3_tmb_lower(param))), "g3_tmb_lower: Structure matches par after setting param.b")
+ })
# g3_tmb_upper
ok - g3_tmb_upper: All upper bounds in right order
ok - g3_tmb_upper: Set all lower values of param_vec in one go
ok - g3_tmb_upper: Structure matches par after setting param_vec
ok - g3_tmb_upper: Cleared param.b by setting optimise = F
ok - g3_tmb_lower: Structure matches par after setting param.b
> 
> ok_group('g3_tmb_parscale', {
+     param <- attr(g3_to_tmb(list(~{
+         g3_param('param.lu', lower = 4, upper = 8)
+         g3_param('param.ps', parscale = 22)
+         g3_param('param.lups', lower = 4, upper = 8, parscale = 44)
+     })), 'parameter_template')
+     ok(ut_cmp_identical(g3_tmb_parscale(param), c(
+         param__lu = NA,
+         param__ps = 22,
+         param__lups = 44)), "We populate parscale")
+ })
# g3_tmb_parscale
ok - We populate parscale
> 
> ok_group('g3_tmb_relist', {
+     param <- attr(g3_to_tmb(list(~{
+         g3_param('param.b')
+         g3_param_vector('param_vec')
+         g3_param('unopt_param', optimise = FALSE)
+         g3_param('randomparam', random = TRUE)
+         g3_param('aaparam')
+     })), 'parameter_template')
+     param$value <- I(list(
+         aaparam = 55,
+         param.b = 66,
+         unopt_param = 95,
+         randomparam = 2,
+         param_vec = 6:10)[rownames(param)])
+ 
+     ok(ut_cmp_identical(
+         g3_tmb_relist(param, c(
+             param__b = 660,
+             param_vec1 = 60, param_vec2 = 70, param_vec3 = 80, param_vec4 = 90, param_vec5 = 100,
+             aaparam = 550)),
+         list(
+             "param.b" = 660,
+             "param_vec" = c(60, 70, 80, 90, 100),
+             "unopt_param" = 95,
+             "randomparam" = 2,
+             "aaparam" = 550)), "g3_tmb_relist: Put parameters back in right slots, used old unopt_param value")
+     ok(ut_cmp_identical(
+         g3_tmb_relist(param, c(
+             param__b = 660,
+             param_vec1 = 60, param_vec2 = 70, param_vec3 = 80, param_vec4 = 90, param_vec5 = 100,
+             randomparam = 5,  # NB: randomparam included, so we update it
+             aaparam = 550)),
+         list(
+             "param.b" = 660,
+             "param_vec" = c(60, 70, 80, 90, 100),
+             "unopt_param" = 95,
+             "randomparam" = 5,
+             "aaparam" = 550)), "g3_tmb_relist: Put parameters back in right slots, including random")
+ 
+     param['param.b', 'optimise'] <- FALSE
+     ok(ut_cmp_error(
+         g3_tmb_relist(param, c(
+             param__b = 660,
+             param_vec1 = 60, param_vec2 = 70, param_vec3 = 80, param_vec4 = 90, param_vec5 = 100,
+             randomparam = 6,  # NB: randomparam included, so we update it
+             aaparam = 550)),
+         "par"), "g3_tmb_relist: Still included param__b in par, now an error")
+     ok(ut_cmp_identical(
+         g3_tmb_relist(param, c(
+             param_vec1 = 60, param_vec2 = 70, param_vec3 = 80, param_vec4 = 90, param_vec5 = 100,
+             aaparam = 550)),
+         list(
+             "param.b" = 66,
+             "param_vec" = c(60, 70, 80, 90, 100),
+             "unopt_param" = 95,
+             "randomparam" = 2,
+             "aaparam" = 550)), "g3_tmb_relist: Works without param.b set, use initial table value")
+ })
# g3_tmb_relist
ok - g3_tmb_relist: Put parameters back in right slots, used old unopt_param value
ok - g3_tmb_relist: Put parameters back in right slots, including random
ok - g3_tmb_relist: Still included param__b in par, now an error
ok - g3_tmb_relist: Works without param.b set, use initial table value
> 
> ok_group('g3_param', {
+     param <- attr(g3_to_tmb(list(g3a_time(2000, 2004), ~{
+         g3_param('a')
+         g3_param('b', value = 4, optimise = FALSE, random = TRUE, lower = 5, upper = 10)
+     })), 'parameter_template')
+     ok(ut_cmp_identical(
+         param[c('a', 'b'),],
+         data.frame(
+             row.names = c('a', 'b'),
+             switch = c('a', 'b'),
+             type = c("", ""),
+             value = I(list(a = 0, b = 4)),
+             optimise = c(TRUE, FALSE),
+             random = c(FALSE, TRUE),
+             lower = c(NA, 5),
+             upper = c(NA, 10),
+             parscale = as.numeric(c(NA, NA)),  # NB: Not derived yet, only when calling g3_tmb_parscale()
+             stringsAsFactors = FALSE)), "Param table included custom values")
+ })
# g3_param
ok - Param table included custom values
> 
> ok_group('g3_param_table', {
+     param <- attr(g3_to_tmb(list(g3a_time(2000, 2004, step_lengths = c(3,3,3,3)), ~{
+         g3_param_table('pt', expand.grid(  # NB: We can use base R
+             cur_year = seq(start_year, end_year),  # NB: We can use g3a_time's vars
+             cur_step = 2:3))
+         g3_param_table('pg', expand.grid(
+             cur_year = start_year,
+             cur_step = 1:2), value = 4, optimise = FALSE, random = TRUE, lower = 5, upper = 10)
+     })), 'parameter_template')
+     ok(ut_cmp_identical(
+         param[c(paste('pt', 2000:2004, 2, sep = '.'), paste('pt', 2000:2004, 3, sep = '.'), 'pg.2000.1', 'pg.2000.2'),],
+         data.frame(
+             row.names = c(paste('pt', 2000:2004, 2, sep = '.'), paste('pt', 2000:2004, 3, sep = '.'), 'pg.2000.1', 'pg.2000.2'),
+             switch = c(paste('pt', 2000:2004, 2, sep = '.'), paste('pt', 2000:2004, 3, sep = '.'), 'pg.2000.1', 'pg.2000.2'),
+             type = c("", "", "", "", "", "", "", "", "", "", "", ""),
+             value = I(list(
+                 "pt.2000.2" = 0,
+                 "pt.2001.2" = 0,
+                 "pt.2002.2" = 0,
+                 "pt.2003.2" = 0,
+                 "pt.2004.2" = 0,
+                 "pt.2000.3" = 0,
+                 "pt.2001.3" = 0,
+                 "pt.2002.3" = 0,
+                 "pt.2003.3" = 0,
+                 "pt.2004.3" = 0,
+                 "pg.2000.1" = 4,
+                 "pg.2000.2" = 4)),
+             optimise = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE),
+             random = c(FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE),
+             lower = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 5, 5),
+             upper = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 10, 10),
+             # NB: Not derived yet, only when calling g3_tmb_parscale()
+             parscale = as.numeric(c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA)),
+             stringsAsFactors = FALSE)), "Param table included custom values")
+     ok(ut_cmp_identical(
+         attr(g3_to_tmb(list(~{
+             g3_param_table('moo', expand.grid(cur_year=1990:1994))
+             g3_param('moo.1990')
+             g3_param('oink.2')
+         })), 'parameter_template')$switch,
+         c("moo.1990", "moo.1991", "moo.1992", "moo.1993", "moo.1994", "oink.2")), "Refering to individual parameters doesn't generate duplicate table entries")
+ })
# g3_param_table
ok - Param table included custom values
ok - Refering to individual parameters doesn't generate duplicate table entries
> 
> ok_group("g3_to_tmb: attr.actions", {
+     actions <- list(
+         list("001" = ~{ 1 + 1 }, "002" = ~{2 + 2}),
+         "003" = ~{3 + 3})
+     model_fn <- g3_to_tmb(actions)
+     ok(ut_cmp_identical(attr(model_fn, 'actions'), actions), "actions returned as attribute uncollated")
+ })
# g3_to_tmb: attr.actions
ok - actions returned as attribute uncollated
> 
> ok_group("g3_to_tmb: Can use random parameters without resorting to include_random", local({
+     # ./TMB/inst/examples/randomregression.R converted into gadget3
+     actions <- local({
+         set.seed(123)
+         n <- 1
+         ng <- 1
+         f <- gl(ng, n/ng)
+         t <- rnorm(n, mean=2, sd=5)
+         a <- rnorm(ng, mean=3, sd=4)
+         b <- rnorm(ng, mean=8, sd=7)
+         x <- a[f] * t + b[f] + rnorm(n, mean=0, sd=1)
+         set.seed(NULL)
+ 
+         list(
+             g3a_time(1990, 1991),
+             g3l_random_dnorm("a",
+                 ~g3_param('a', value=1, random=TRUE),
+                 ~g3_param('mu.a', value=1),
+                 ~g3_param('sigma.a', value=1), period="single"),
+             g3l_random_dnorm("b",
+                 ~g3_param('b', value=1, random=TRUE),
+                 ~g3_param('mu.b', value=1),
+                 ~g3_param('sigma.b', value=1), period="single"),
+             g3l_random_dnorm("x",
+                 ~x,
+                 ~g3_param('a', value=1, random=TRUE) * t + g3_param('b', value=1, random=TRUE),
+                 ~g3_param('sigma0', value=1), period="single" ))
+     })
+     model_fn <- g3_to_r(actions)
+ 
+     if (nzchar(Sys.getenv('G3_TEST_TMB'))) {
+         model_cpp <- g3_to_tmb(actions)
+         model_tmb <- g3_tmb_adfun(model_cpp, compile_flags = c("-O0", "-g"), inner.control = list(fnscale = -1))
+         param_tbl <- attr(model_cpp, 'parameter_template')
+         param_tbl[,'lower'] <- -2
+         param_tbl[,'upper'] <- 3
+         param_tbl[,'parscale'] <- 1
+ 
+         ok(ut_cmp_identical(names(model_tmb$env$last.par)[model_tmb$env$random], c(
+             "a",
+             "b",
+             NULL)), "env$random: TMB got the random parameters we expected")
+ 
+         ok(ut_cmp_error({
+             nlminb(g3_tmb_par(param_tbl), model_tmb$fn, model_tmb$gr)
+         }, "\\$par"), "g3_tmb_par: Not allowed in nlminb() call")
+         ok(ut_cmp_error({
+             optim(g3_tmb_par(param_tbl), model_tmb$fn, model_tmb$gr)
+         }, "\\$par"), "g3_tmb_par: Not allowed in optim() call")
+ 
+         res <- suppressWarnings({
+             nlminb(model_tmb$par, model_tmb$fn, model_tmb$gr,
+                 upper = g3_tmb_upper(param_tbl),
+                 lower = g3_tmb_lower(param_tbl),
+                 control = list(
+                     fnscale = -1,
+                     parscale = g3_tmb_parscale(param_tbl)))
+         })
+         ok(res$convergence == 0, "Model ran successfully and converged")
+ 
+         # The first won't have random parameters, the latter will. Both should work
+         value_no_random <- g3_tmb_relist(param_tbl, res$par)
+         value_inc_random <- g3_tmb_relist(param_tbl, model_tmb$env$last.par)
+         ok(ut_cmp_equal(
+             value_no_random[param_tbl[!param_tbl$random, 'switch']],
+             value_inc_random[param_tbl[!param_tbl$random, 'switch']]), "Non-random parameters match")
+         ok(ut_cmp_equal(
+             I(value_no_random[param_tbl[param_tbl$random, 'switch']]),
+             param_tbl$value[param_tbl[param_tbl$random, 'switch']]), "value_no_random: Random parameters as default")
+         ok(!isTRUE(all.equal(
+             I(value_inc_random[param_tbl[param_tbl$random, 'switch']]),
+             param_tbl$value[param_tbl[param_tbl$random, 'switch']])), "value_random: Random parameters have been updated")
+         param_tbl$value <- value_inc_random
+ 
+         # NB: ut_tmb_r_compare will be using g3_tmb_par()
+         gadget3:::ut_tmb_r_compare(model_fn, model_tmb, param_tbl)
+     } else {
+         writeLines("# skip: not compiling TMB model")
+     }
+ }))
# g3_to_tmb: Can use random parameters without resorting to include_random
# skip: not compiling TMB model
> 
> ok_group("cpp_code", {
+     ns <- function (s) gsub("\\s+", "", s)
+     ok(ut_cmp_identical(
+         ns(gadget3:::cpp_code(quote( 4 + 4 ))),
+         ns("(double)(4) + (double)(4)")),
+         "4 + 4: Defaulted to double")
+     ok(ut_cmp_identical(
+         ns(gadget3:::cpp_code(quote( (4 + 4) ))),
+         ns("((double)(4) + (double)(4))")),
+         "(4 + 4): Defaulted to double")
+     ok(ut_cmp_identical(
+         ns(gadget3:::cpp_code(quote( x[[4]] + 4 ))),
+         ns("x(3) + (double)(4)")),
+         "x[[4]] + 4: Subtracted one, assumed int")
+     # NB: We rely on this in g3_param_table(ifmissing_param_table) below
+     ok(ut_cmp_identical(
+         ns(gadget3:::cpp_code(quote( x[[(-4 + 1 - 1) / (2*8)]] + 4 ))),
+         ns("x( (-4 + 1 - 1) / (2*8) - 1 ) + (double)(4)")),
+         "x[[(-4 + 1 - 1) / (2*8)]] + 4: Assumed int passses through +, -, *, /, ( ")
+ })
# cpp_code
ok - 4 + 4: Defaulted to double
ok - (4 + 4): Defaulted to double
ok - x[[4]] + 4: Subtracted one, assumed int
ok - x[[(-4 + 1 - 1) / (2*8)]] + 4: Assumed int passses through +, -, *, /, ( 
> 
> 
> ###############################################################################
> actions <- list()
> expecteds <- new.env(parent = emptyenv())
> expected_warnings_r <- c()
> expected_warnings_tmb <- c()
> params <- list(rv=0)
> 
> # Check constants can pass through cleanly
> constants_integer <- 999
> constants_nan <- 999
> actions <- c(actions, ~{
+     comment('constants')
+     constants_integer <- 5L ; REPORT(constants_integer)
+     constants_nan <- NaN ; REPORT(constants_nan)
+ })
> expecteds$constants_integer <- 5L
> expecteds$constants_nan <- NaN
> 
> # Can assign a single value to 1x1 array
> assign_to_1_1 <- array(dim = c(1,1))
> actions <- c(actions, ~{
+     comment('assign_to_1_1')
+     assign_to_1_1[g3_idx(1)] <- 100.1
+     REPORT(assign_to_1_1)
+ })
> expecteds$assign_to_1_1 <- array(c(100.1), dim = c(1,1))
> 
> assign_to_2_1 <- array(dim = c(2,1))
> data_to_2_1 <- c(100.1, 200.2)
> actions <- c(actions, ~{
+     comment('assign_to_2_1')
+     assign_to_2_1[,g3_idx(1)] <- data_to_2_1
+     REPORT(assign_to_2_1)
+ })
> expecteds$assign_to_2_1 <- array(c(100.1, 200.2), dim = c(2,1))
>     
> assign_to_2_2 <- array(dim = c(2,2))
> data_to_2_2 <- c(110.1, 220.2)
> actions <- c(actions, ~{
+     comment('assign_to_2_2')
+     assign_to_2_2[,g3_idx(1)] <- data_to_2_1
+     assign_to_2_2[,g3_idx(2)] <- data_to_2_2
+     REPORT(assign_to_2_2)
+ })
> expecteds$assign_to_2_2 <- array(c(100.1, 200.2, 110.1, 220.2), dim = c(2,2))
> 
> # Assign single value, horizontally
> assign_to_2_2a <- array(dim = c(2,2))
> actions <- c(actions, ~{
+     comment('assign_to_2_2a')
+     assign_to_2_2a[[g3_idx(1),g3_idx(2)]] <- 99
+     assign_to_2_2a[[g3_idx(2),g3_idx(1)]] <- 88
+     assign_to_2_2a[[g3_idx(2),g3_idx(2)]] <- 0
+     assign_to_2_2a[[g3_idx(1),g3_idx(1)]] <- 0
+     REPORT(assign_to_2_2a)
+ })
> expecteds$assign_to_2_2a <- array(c(0, 88, 99, 0), dim = c(2,2))
> 
> # Assign zero and other scalars to column, arrays
> assign_scalar <- array(dim = c(2,4))
> params$assign_scalar_const <- runif(1, 100, 200)
> actions <- c(actions, ~{
+     comment('assign_scalar')
+     assign_scalar[] <- 0  # TODO: TMB auto-setZeros, R doesn't
+     assign_scalar[g3_idx(1),g3_idx(1)] <- 99  # NB: Overwritten
+     assign_scalar[,g3_idx(1)] <- 0
+     assign_scalar[,g3_idx(2)] <- 88
+     assign_scalar[g3_idx(2),g3_idx(3)] <- 27
+     assign_scalar[,g3_idx(4)] <- g3_param("assign_scalar_const")
+     REPORT(assign_scalar)
+ })
> expecteds$assign_scalar <- array(c(
+     0, 0,
+     88, 88,
+     0, 27,
+     params$assign_scalar_const, params$assign_scalar_const,
+     NULL), dim = c(2,4))
> 
> # Can subset from left and right, using transpose
> assign_subset <- array(
+     rep(seq(100, 200, 100), each = 3 * 5) +
+     rep(seq(10, 30, 10), each = 5, times = 2) +
+     rep(seq(1, 5, 1), each = 1, times = 2),
+     dim = c(5, 3, 2))
> assign_right <- assign_subset[,2,2] ; assign_right[] <- 0
> assign_leftright <- assign_subset[4,,2] ; assign_leftright[] <- 0
> actions <- c(actions, ~{
+     comment('assign_subset')
+     assign_right <- assign_subset[,g3_idx(2),g3_idx(2)]
+     REPORT(assign_right)
+     assign_leftright <- assign_subset[g3_idx(4),,g3_idx(2)]
+     REPORT(assign_leftright)
+ })
> expecteds$assign_right <- assign_subset[,2,2]
> expecteds$assign_leftright <- assign_subset[4,,2]
> 
> # Arrays with dynamic dimensions
> dynamic_dim_array <- array(0, dim = c(2,1))
> dynamic_dim_array_na <- array(NA, dim = c(2,1))
> attr(dynamic_dim_array, 'dynamic_dim') <- list(2, quote(dynamic_dim_array_dim_2))
> attr(dynamic_dim_array_na, 'dynamic_dim') <- list(2, quote(dynamic_dim_array_dim_2))
> dynamic_dim_array_dim_2 <- 4L
> dynamic_dim_array_dim_na_2 <- 4L
> actions <- c(actions, ~{
+     comment('assign_scalar')
+     # NB: Under TMB this won't be NA, so set it to hide differences.
+     dynamic_dim_array_na[] <- 5
+     REPORT(dynamic_dim_array)
+     REPORT(dynamic_dim_array_na)
+ })
> expecteds$dynamic_dim_array <- array(0, dim = c(2, 4))
> expecteds$dynamic_dim_array_na <- array(5, dim = c(2, 4))
> 
> # Data variable names are escaped
> escaped.data.scalar <- 44
> escaped.data.array <- c(1,2,3,4,5)
> escaped_data_output <- 0.0
> actions <- c(actions, ~{
+     comment('escaped.data.array')
+     escaped_data_output <- escaped.data.scalar + sum(escaped.data.array)
+     REPORT(escaped_data_output)
+ })
> # NB: In theory we could also report the escaped name, but we can't rename
> # items in the produced report, so reports will differ TMB/R
> expecteds$escaped_data_output <- escaped.data.scalar + sum(escaped.data.array)
> 
> # is.nan / is.finite
> is_nan_nan_scalar_input <- NaN
> is_nan_finite_scalar_input <- 4
> is_nan_finite_array_input <- as.array(1:4)
> is_nan_nan_array_input <- as.array(rep(NaN, 5))
> is_nan_finite_vector_input <- 1:4
> is_nan_nan_vector_input <- rep(NaN, 5)
> is_nan_finite_single_array_input <- as.array(1)
> is_nan_output <- 0L
> is_finite_output <- 0L
> actions <- c(actions, ~{
+     comment('is.nan / is.finite')
+     is_nan_output <- is_nan_output + (if (is.nan(is_nan_nan_scalar_input)) 1 else 0)
+     is_nan_output <- is_nan_output + (if (is.nan(is_nan_finite_scalar_input)) 2 else 0)
+     is_nan_output <- is_nan_output + (if (any(is.nan(is_nan_finite_array_input))) 4 else 0)
+     is_nan_output <- is_nan_output + (if (any(is.nan(is_nan_nan_array_input))) 8 else 0)
+     is_nan_output <- is_nan_output + (if (any(is.nan(is_nan_nan_vector_input))) 16 else 0)
+     is_nan_output <- is_nan_output + (if (any(is.nan(is_nan_finite_single_array_input))) 32 else 0)
+     REPORT(is_nan_output)
+     is_finite_output <- is_finite_output + (if (is.finite(is_nan_nan_scalar_input)) 1 else 0)
+     is_finite_output <- is_finite_output + (if (is.finite(is_nan_finite_scalar_input)) 2 else 0)
+     is_finite_output <- is_finite_output + (if (any(is.finite(is_nan_finite_array_input))) 4 else 0)
+     is_finite_output <- is_finite_output + (if (any(is.finite(is_nan_nan_array_input))) 8 else 0)
+     is_finite_output <- is_finite_output + (if (any(is.finite(is_nan_nan_vector_input))) 16 else 0)
+     is_finite_output <- is_finite_output + (if (any(is.finite(is_nan_finite_single_array_input))) 32 else 0)
+     REPORT(is_finite_output)
+ })
> expecteds$is_nan_output <- 1 + 8 + 16
> expecteds$is_finite_output <- 2 + 4 + 32
> 
> # as.vector() --> .vec()
> as_vector_array <- array(runif(20), dim=c(10, 2))
> as_vector_result1 <- rep(NaN, 10)
> as_vector_result2 <- rep(NaN, 10)
> as_vector_mean <- 0.5
> as_vector_sigma <- 1
> actions <- c(actions, ~{
+     comment('as_vector')
+     as_vector_result1 <- pnorm(as.vector(as_vector_array[,g3_idx(1)]), as_vector_mean, as_vector_sigma)
+     as_vector_result2 <- pnorm(as.vector(as_vector_array[,g3_idx(2)]), as_vector_mean, as_vector_sigma)
+     REPORT(as_vector_result1)
+     REPORT(as_vector_result2)
+ })
> expecteds$as_vector_result1 <- pnorm(as_vector_array[,1], as_vector_mean, as_vector_sigma)
> expecteds$as_vector_result2 <- pnorm(as_vector_array[,2], as_vector_mean, as_vector_sigma)
> 
> # mean() --> .mean()
> mean_vector <- array(c(1, 2, 88, 99))
> mean_vector_result <- 0
> actions <- c(actions, ~{
+     comment('mean_vector')
+     mean_vector_result <- mean(mean_vector)
+     REPORT(mean_vector_result)
+ })
> expecteds$mean_vector_result <- mean(mean_vector)
> 
> # colsums
> colsums_in <- array(1:6, dim = c(3,2))
> colsums_result <- c(0L, 0L)
> actions <- c(actions, ~{
+     comment('colsums')
+     colsums_result <- colSums(colsums_in)
+     REPORT(colsums_result)
+ })
> expecteds$colsums_result <- colSums(colsums_in)
> 
> # rowsums
> rowsums_in <- array(c(1,2,3,4,5,6), dim = c(3,2))
> rowsums_result <- c(0, 0, 0)
> actions <- c(actions, ~{
+     comment('rowsums')
+     rowsums_result <- rowSums(rowsums_in)
+     REPORT(rowsums_result)
+ })
> expecteds$rowsums_result <- rowSums(rowsums_in)
> 
> # if statement without braces
> if_no_brace_result <- 0.0
> actions <- c(actions, ~{
+     comment('if_without_braces')
+     if (FALSE) if_no_brace_result <- 1 else if_no_brace_result <- 0.2
+     REPORT(if_no_brace_result)
+ })
> expecteds$if_no_brace_result <- 0.2
> 
> # if expression (not statement) turns into tertiary
> tertiary_result_0 <- 3
> tertiary_result_1 <- 6
> tertiary_result_2 <- 6
> ok(ut_cmp_error({
+     g3_to_tmb(list(~{ tertiary_result_0 <- if (tertiary_result_0 == 3) 9  }))
+ }, "tertiary_result_0"), "Complained about missing else for tertiary")
ok - Complained about missing else for tertiary
> actions <- c(actions, ~{
+     comment('tertiary')
+     tertiary_result_0 <- if (tertiary_result_0 == 3) 9 else 4
+     tertiary_result_1 <- if (tertiary_result_1 == 3) 9 else 4
+     tertiary_result_2 <- 100 - if (tertiary_result_0 == -30) 20 else 40
+     REPORT(tertiary_result_0)
+     REPORT(tertiary_result_1)
+     REPORT(tertiary_result_2)
+ })
> expecteds$tertiary_result_0 <- 9
> expecteds$tertiary_result_1 <- 4
> expecteds$tertiary_result_2 <- 100 - 40  # NB: Operator precedence preserved
> 
> # g3_with()
> g3_with_result <- 0L
> # NB: We don't define g3_with_iterator, it's defined within the block
> actions <- c(actions, ~{
+     comment('g3_with')
+     g3_with(
+         g3_with_iterator := g3_idx(2L),  # NB: Tests we can use g3 functions in definition
+         g3_with_other_exp := 1L + 2L + 3L,
+         {
+             g3_with_result <- g3_with_iterator - g3_idx(1)  # NB: Reverse g3_idx from definition
+             REPORT(g3_with_result)
+             REPORT(g3_with_other_exp)
+         })
+ })
> expecteds$g3_with_result <- 1L  # i.e. 2 - 1 in R or 1 - 0 in TMB
> expecteds$g3_with_other_exp <- 1L + 2L + 3L
> 
> # min() & max()
> min_result <- 0.0
> max_result <- 0.0
> actions <- c(actions, ~{
+     comment('min/max')
+     min_result <- min(4, 9)
+     max_result <- max(sum(mean_vector), 2)  # NB: sum gets cast to Type
+     REPORT(min_result)
+     REPORT(max_result)
+ })
> expecteds$min_result <- 4
> expecteds$max_result <- sum(mean_vector)
> 
> # negate single value
> negate_x <- 10
> actions <- c(actions, ~{
+     comment('negate')
+     negate_x <- -negate_x
+     REPORT(negate_x)
+ })
> expecteds$negate_x <- -10
> 
> # Modulo assumes integer
> modulo_x <- 10
> modulo_y <- 11
> actions <- c(actions, ~{
+     comment('modulo')
+     modulo_x <- as_integer(modulo_x) %% 2
+     modulo_y <- as_integer(modulo_y) %% 2
+     REPORT(modulo_x)
+     REPORT(modulo_y)
+ })
> expecteds$modulo_x <- 0
> expecteds$modulo_y <- 1
> 
> # sum() & prod()
> sumprod_input <- runif(10)
> sumprod_sum <- 0
> sumprod_prod <- 0
> actions <- c(actions, ~{
+     comment('sum/prod')
+     sumprod_sum <- sum(sumprod_input)
+     sumprod_prod <- prod(sumprod_input)
+     REPORT(sumprod_sum)
+     REPORT(sumprod_prod)
+ })
> expecteds$sumprod_sum <- sum(sumprod_input)
> expecteds$sumprod_prod <- prod(sumprod_input)
> 
> # g3_param_table()
> param_table_out <- array(rep(0, 6))
> actions <- c(actions, ~{
+     for (pt_a in seq(1, 3, by = 1)) for (pt_b in seq(7, 8, by = 1)) {
+         param_table_out[[((pt_a - 1L) * 2L) + (pt_b - 7L) + 1L]] <- g3_param_table('param_table', expand.grid(pt_a = 1:2, pt_b = c(8, 7)))
+     }
+     REPORT(param_table_out)
+ })
> params[['param_table.1.8']] <- 18
> params[['param_table.1.7']] <- 17
> params[['param_table.2.8']] <- 28
> params[['param_table.2.7']] <- 27
> expecteds$param_table_out <- array(c(
+     17,
+     18,
+     27,
+     28,
+     NaN,
+     NaN,
+     NULL))
> expected_warnings_r <- c(expected_warnings_r,
+     "No value found in g3_param_table param_table, ifmissing not specified",
+     "No value found in g3_param_table param_table, ifmissing not specified",
+     NULL)
> expected_warnings_tmb <- c(expected_warnings_tmb,
+     "No value found in g3_param_table param_table, ifmissing not specified",
+     "No value found in g3_param_table param_table, ifmissing not specified",
+     NULL)
> 
> # g3_param_table(ifmissing)
> param_table_ifmissing_out <- array(c(1,2,3,4,5,6))
> actions <- c(actions, ~{
+     for (ifmissing in seq(1, 6, by = 1)) {
+         param_table_ifmissing_out[[ifmissing]] <- g3_param_table(
+             'param_table_ifmissing',
+             expand.grid(ifmissing = 2:4), ifmissing = -1)
+     }
+     REPORT(param_table_ifmissing_out)
+ })
> params[['param_table_ifmissing.2']] <- 27
> params[['param_table_ifmissing.3']] <- 47
> params[['param_table_ifmissing.4']] <- 22
> expecteds$param_table_ifmissing_out <- array(c(-1, 27, 47, 22, -1, -1))
> 
> # g3_param_table(ifmissing_param)
> param_table_ifmparam_out <- array(c(1,2,3,4,5,6))
> actions <- c(actions, ~{
+     for (ifmparam in seq(1, 6, by = 1)) {
+         param_table_ifmparam_out[[ifmparam]] <- g3_param_table(
+             'param_table_ifmparam',
+             expand.grid(ifmparam = 2:4), ifmissing = g3_param("param_table_ifmparam.missing"))
+     }
+     REPORT(param_table_ifmparam_out)
+ })
> params[['param_table_ifmparam.2']] <- floor(runif(1, 100, 200))
> params[['param_table_ifmparam.3']] <- floor(runif(1, 100, 200))
> params[['param_table_ifmparam.4']] <- floor(runif(1, 100, 200))
> params[['param_table_ifmparam.missing']] <- floor(runif(1, 100, 200))
> expecteds$param_table_ifmparam_out <- array(c(
+     params[['param_table_ifmparam.missing']],
+     params[['param_table_ifmparam.2']],
+     params[['param_table_ifmparam.3']],
+     params[['param_table_ifmparam.4']],
+     params[['param_table_ifmparam.missing']],
+     params[['param_table_ifmparam.missing']]))
> 
> # g3_param_table(ifmissing_param_table)
> param_table_ifmpartab_out <- array(c(1,2,3,4,5,6,7,8,9))
> actions <- c(actions, ~{
+     for (ifmpartab in seq(1, 3, by = 1)) for (ifmpartab_m in seq(1, 3, by = 1)) {
+         param_table_ifmpartab_out[[((ifmpartab - 1) * 3) + (ifmpartab_m - 1) + 1]] <- g3_param_table(
+             'param_table_ifmpartab',
+             expand.grid(ifmpartab = 2:3), ifmissing = g3_param_table(
+                 "param_table_ifmpartab_m",
+                 expand.grid(ifmpartab_m = 1:3)))
+     }
+     REPORT(param_table_ifmpartab_out)
+ })
> params[['param_table_ifmpartab.2']] <- floor(runif(1, 100, 200))
> params[['param_table_ifmpartab.3']] <- floor(runif(1, 100, 200))
> params[['param_table_ifmpartab_m.1']] <- floor(runif(1, 100, 200))
> params[['param_table_ifmpartab_m.2']] <- floor(runif(1, 100, 200))
> params[['param_table_ifmpartab_m.3']] <- floor(runif(1, 100, 200))
> expecteds$param_table_ifmpartab_out <- array(c(
+     params[['param_table_ifmpartab_m.1']],
+     params[['param_table_ifmpartab_m.2']],
+     params[['param_table_ifmpartab_m.3']],
+ 
+     params[['param_table_ifmpartab.2']],
+     params[['param_table_ifmpartab.2']],
+     params[['param_table_ifmpartab.2']],
+ 
+     params[['param_table_ifmpartab.3']],
+     params[['param_table_ifmpartab.3']],
+     params[['param_table_ifmpartab.3']],
+     NULL))
> 
> ###############################################################################
> 
> nll <- 0.0
> actions <- c(actions, ~{
+     comment('done')
+     nll <- nll + g3_param('rv')
+     return(nll)
+ })
> 
> # Compile model
> model_fn <- g3_to_r(actions, trace = FALSE)
> # model_fn <- edit(model_fn)
> if (nzchar(Sys.getenv('G3_TEST_TMB'))) {
+     model_cpp <- g3_to_tmb(actions, trace = FALSE)
+     # model_cpp <- edit(model_cpp)
+     model_tmb <- g3_tmb_adfun(model_cpp, params, compile_flags = c("-O0", "-g"))
+ } else {
+     writeLines("# skip: not compiling TMB model")
+ }
# skip: not compiling TMB model
> 
> # Compare everything we've been told to compare
> result <- capture_warnings(model_fn(params))
> # str(attributes(result), vec.len = 10000)
> for (n in ls(expecteds)) {
+     ok(ut_cmp_equal(
+         attr(result$rv, n),
+         expecteds[[n]], tolerance = 1e-6), n)
+ }
ok - as_vector_result1
ok - as_vector_result2
ok - assign_leftright
ok - assign_right
ok - assign_scalar
ok - assign_to_1_1
ok - assign_to_2_1
ok - assign_to_2_2
ok - assign_to_2_2a
ok - colsums_result
ok - constants_integer
ok - constants_nan
ok - dynamic_dim_array
ok - dynamic_dim_array_na
ok - escaped_data_output
ok - g3_with_other_exp
ok - g3_with_result
ok - if_no_brace_result
ok - is_finite_output
ok - is_nan_output
ok - max_result
ok - mean_vector_result
ok - min_result
ok - modulo_x
ok - modulo_y
ok - negate_x
ok - param_table_ifmissing_out
ok - param_table_ifmparam_out
ok - param_table_ifmpartab_out
ok - param_table_out
ok - rowsums_result
ok - sumprod_prod
ok - sumprod_sum
ok - tertiary_result_0
ok - tertiary_result_1
ok - tertiary_result_2
> ok(ut_cmp_identical(result$warnings, expected_warnings_r), "Warnings from R as expected")
ok - Warnings from R as expected
> if (nzchar(Sys.getenv('G3_TEST_TMB'))) {
+     param_template <- attr(model_cpp, "parameter_template")
+     param_template$value <- params[param_template$switch]
+     generated_warnings <- capture_warnings(gadget3:::ut_tmb_r_compare(model_fn, model_tmb, param_template))$warnings
+     ok(ut_cmp_identical(generated_warnings, c(expected_warnings_r, expected_warnings_tmb)), "Warnings from R+TMB as expected")
+ }
> 
> proc.time()
   user  system elapsed 
   1.21    0.04    1.25 
# Looks like you passed all 74 tests.