R Under development (unstable) (2024-03-18 r86148 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64

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> library(magrittr)
> library(unittest)
> 
> library(gadget3)
> 
> # Compare array by turning it back into a table first
> cmp_array <- function (ar, table_text) {
+     tbl <- read.table(
+         header = TRUE,
+         stringsAsFactors = FALSE,
+         colClasses = c(rep("character", length(dim(ar))), "numeric"),
+         text = table_text)
+     ut_cmp_identical(as.data.frame.table(ar, stringsAsFactors = FALSE), tbl)
+ }
> 
> 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_group("action_reports")
# action_reports
> ok(ut_cmp_equal(
+     gadget3:::action_reports(list(g3_formula(quote({
+         const_var <- 4
+         arr_var[2] <- 4
+         doublearr_var[2][[1]] <- 4
+     }))), REPORT = '.'), quote({
+         REPORT(arr_var)
+         REPORT(const_var)
+         REPORT(doublearr_var)
+     })), "action_reports: Removed subsets")
ok - action_reports: Removed subsets
> 
> #######################################
> 
> prey_a <- g3_stock('prey_a', c(1)) %>% g3s_age(1, 5)
> 
> # Report that aggregates ages together
> agg_report <- g3_stock('agg_report', c(1)) %>% 
+     g3s_agegroup(list(young = 1:3, old = 4:5)) %>%
+     g3s_time(year = 2000:2002)
> # Generate dissaggregated report by cloning the source stock, adding time
> raw_report <- g3s_clone(prey_a, 'raw_report') %>%
+     g3s_time(year = 2000:2002)
> 
> actions <- list(
+     g3a_time(2000, 2002, step_lengths = c(6, 6), project_years = 0),
+     g3a_initialconditions(prey_a, ~10 * age + prey_a__midlen * 0, ~100 * age + prey_a__midlen * 0),
+     g3a_age(prey_a),
+     g3a_report_stock(agg_report, prey_a, ~stock_ss(prey_a__num), include_adreport = TRUE),
+     g3a_report_stock(raw_report, prey_a, ~stock_ss(input_stock__num)),  # NB: We can let g3_step rename it for us
+     list('999' = ~{ nll <- nll + g3_param('x', value = 1.0) }))
> actions <- c(actions, list(g3a_report_history(actions, '^prey_a__(num|wgt)')))
>             
> # 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("report", {
+     params <- attr(model_fn, 'parameter_template')
+     result <- capture_warnings(model_fn(params))
+     ok(ut_cmp_identical(result$warnings, "No ADREPORT functionality available in R"), "Tried to ADREPORT, moved on")
+     result <- result$rv
+     r <- attributes(result)
+     # str(result)
+     # str(as.list(r), vec.len = 10000)
+ 
+     ok(cmp_array(r$raw_report__num, "
+         length  age time Freq
+          1:Inf age1 2000   20
+          1:Inf age2 2000   40
+          1:Inf age3 2000   60
+          1:Inf age4 2000   80
+          1:Inf age5 2000  100
+          1:Inf age1 2001    0
+          1:Inf age2 2001   20
+          1:Inf age3 2001   40
+          1:Inf age4 2001   60
+          1:Inf age5 2001  180
+          1:Inf age1 2002    0
+          1:Inf age2 2002    0
+          1:Inf age3 2002   20
+          1:Inf age4 2002   40
+          1:Inf age5 2002  240
+     "), "raw_report__num: Can see growth happening")
+ 
+     ok(cmp_array(r$agg_report__num, "
+         length   age time Freq
+          1:Inf young 2000  120
+          1:Inf   old 2000  180
+          1:Inf young 2001   60
+          1:Inf   old 2001  240
+          1:Inf young 2002   20
+          1:Inf   old 2002  280
+     "), "agg_report__num: Aggregated report only has young/old")
+ 
+     ok(ut_cmp_identical(
+         grep('^hist_', names(r), value = TRUE),
+         c("hist_prey_a__num", "hist_prey_a__wgt")), "Logged history of numbers / weight (ignored reports though)")
+     ok(cmp_array(r$hist_prey_a__num, "
+         length   age    time Freq
+          1:Inf  age1 2000-01   10
+          1:Inf  age2 2000-01   20
+          1:Inf  age3 2000-01   30
+          1:Inf  age4 2000-01   40
+          1:Inf  age5 2000-01   50
+          1:Inf  age1 2000-02   10
+          1:Inf  age2 2000-02   20
+          1:Inf  age3 2000-02   30
+          1:Inf  age4 2000-02   40
+          1:Inf  age5 2000-02   50
+          1:Inf  age1 2001-01    0
+          1:Inf  age2 2001-01   10
+          1:Inf  age3 2001-01   20
+          1:Inf  age4 2001-01   30
+          1:Inf  age5 2001-01   90
+          1:Inf  age1 2001-02    0
+          1:Inf  age2 2001-02   10
+          1:Inf  age3 2001-02   20
+          1:Inf  age4 2001-02   30
+          1:Inf  age5 2001-02   90
+          1:Inf  age1 2002-01    0
+          1:Inf  age2 2002-01    0
+          1:Inf  age3 2002-01   10
+          1:Inf  age4 2002-01   20
+          1:Inf  age5 2002-01  120
+          1:Inf  age1 2002-02    0
+          1:Inf  age2 2002-02    0
+          1:Inf  age3 2002-02   10
+          1:Inf  age4 2002-02   20
+          1:Inf  age5 2002-02  120
+   "), "hist_prey_a__num: Full history")
+ 
+     if (nzchar(Sys.getenv('G3_TEST_TMB'))) {
+         param_template <- attr(model_cpp, "parameter_template")
+         param_template$value <- params[param_template$switch]
+         capture_warnings(gadget3:::ut_tmb_r_compare(model_fn, model_tmb, param_template))
+     }
+ })
# report
ok - Tried to ADREPORT, moved on
ok - raw_report__num: Can see growth happening
ok - agg_report__num: Aggregated report only has young/old
ok - Logged history of numbers / weight (ignored reports though)
ok - hist_prey_a__num: Full history
> 
> ok_group("adreport", {
+     params <- attr(model_fn, 'parameter_template')
+     result <- capture_warnings(model_fn(params))
+     ok(ut_cmp_identical(result$warnings, "No ADREPORT functionality available in R"), "Tried to ADREPORT, moved on")
+     result <- result$rv
+     r <- attributes(result)
+     # str(result)
+     # str(as.list(r), vec.len = 10000)
+ 
+     if (nzchar(Sys.getenv('G3_TEST_TMB'))) {
+         sdrep <- TMB::sdreport(model_tmb)
+         ok(ut_cmp_equal(
+             summary(sdrep, 'report'),
+             array(
+               c(rep(0, 15), rep(NaN, 15)),
+               dim = c(15, 2),
+               dimnames = list(
+                   rep("report_stock__num", 15),
+                   c("Estimate", "Std. Error")))), "TMB included report_stock__num in adreport")
+     }
+ })
# adreport
ok - Tried to ADREPORT, moved on
> 
> proc.time()
   user  system elapsed 
   0.62    0.09    0.70 
# Looks like you passed all 7 tests.