R Under development (unstable) (2024-07-02 r86866 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(magrittr)
> library(unittest)
> 
> library(gadget3)
> 
> ok_group("g3_stock_def", {
+     stock_a <- g3_stock('stock_a', seq(10, 10, 5))
+     stock_a <- g3s_age(stock_a, 10, 20)
+ 
+     # Make sure both minage & stock__minage forms work (the latter should be deprecated though)
+     ok(ut_cmp_identical(g3_stock_def(stock_a, 'minage'), 10L), "Fetched minage")
+     ok(ut_cmp_identical(g3_stock_def(stock_a, 'maxage'), 20L), "Fetched maxage")
+     ok(ut_cmp_identical(g3_stock_def(stock_a, 'stock__minage'), 10L), "Fetched minage")
+     ok(ut_cmp_identical(g3_stock_def(stock_a, 'stock__maxage'), 20L), "Fetched maxage")
+ 
+     # Make sure old internal method call works
+     ok(ut_cmp_identical(suppressWarnings(gadget3:::stock_definition(stock_a, 'minage')), 10L), "Fetched minage with old gadget3:::stock_definition")
+     ok(ut_cmp_identical(suppressWarnings(gadget3:::stock_definition(stock_a, 'maxage')), 20L), "Fetched maxage with old gadget3:::stock_definition")
+ })
# g3_stock_def
ok - Fetched minage
ok - Fetched maxage
ok - Fetched minage
ok - Fetched maxage
ok - Fetched minage with old gadget3:::stock_definition
ok - Fetched maxage with old gadget3:::stock_definition
> 
> ok(ut_cmp_error(
+     g3_stock('stock_a', c()),
+     "lengthgroups"), "Can't create stock with 0 length groups")
ok - Can't create stock with 0 length groups
> 
> multipart <- g3_stock(c(species = "ling", "imm"), 1:5)
> ok(ut_cmp_identical(
+     multipart$name,
+     "ling_imm"), "multipart$name: Stock name got concatenated")
ok - multipart$name: Stock name got concatenated
> ok(ut_cmp_identical(
+     multipart$name_parts[['species']],
+     "ling"), "multipart$name_parts: Can dig out just species name from multipart name")
ok - multipart$name_parts: Can dig out just species name from multipart name
> 
> stock_a <- g3_stock('stock_a', seq(10, 10, 5))
> stock_b <- g3_stock('stock_b', seq(50, 54, 1))
> stock_wonky <- g3_stock('stock_wonky', c(0, 10, 100, 200, 1000))
> nll <- 0.0
> 
> actions <- list(
+     list(
+         '999' = gadget3:::g3_step(~{
+             # NB: stock_with also includes the stock environment, which is why we need it
+             stock_with(stock_a, {
+                 REPORT(stock_a__minlen)
+                 REPORT(stock_a__midlen)
+                 REPORT(stock_a__maxmidlen)
+                 REPORT(stock_a__minmidlen)
+                 REPORT(stock_a__dl)
+                 REPORT(stock_a__plusdl)
+             })
+ 
+             stock_with(stock_b, {
+                 REPORT(stock_b__minlen)
+                 REPORT(stock_b__midlen)
+                 REPORT(stock_b__maxmidlen)
+                 REPORT(stock_b__minmidlen)
+                 REPORT(stock_b__dl)
+                 REPORT(stock_b__plusdl)
+             })
+ 
+             stock_with(stock_wonky, {
+                 REPORT(stock_wonky__minlen)
+                 REPORT(stock_wonky__midlen)
+                 REPORT(stock_wonky__maxmidlen)
+                 REPORT(stock_wonky__minmidlen)
+                 REPORT(stock_wonky__dl)
+                 REPORT(stock_wonky__plusdl)
+             })
+ 
+             nll <- nll + g3_param('x', value = 1.0)
+             return(nll)
+         })))
> 
> model_fn <- g3_to_r(actions)
> # 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")
+     model_cpp <- c()
+ }
# skip: not compiling TMB model
> 
> params <- attr(model_fn, 'parameter_template')
> result <- model_fn(params)
> r <- attributes(result)
> 
> # We populated min/mean/dl
> ok(ut_cmp_identical(
+     r$stock_a__minlen,
+     c("10:Inf" = 10)), "stock_a__minlen")
ok - stock_a__minlen
> ok(ut_cmp_identical(
+     r$stock_a__midlen,
+     structure(
+         c(10.5),
+         names = c("10:Inf"))), "stock_a__midlen")
ok - stock_a__midlen
> ok(ut_cmp_identical(r$stock_a__minmidlen, 10.5), "stock_a__minmidlen")
ok - stock_a__minmidlen
> ok(ut_cmp_identical(r$stock_a__maxmidlen, 10.5), "stock_a__maxmidlen")
ok - stock_a__maxmidlen
> ok(ut_cmp_identical(
+     r$stock_a__dl,
+     c(1)), "stock_a__dl")
ok - stock_a__dl
> ok(ut_cmp_identical(
+     r$stock_a__plusdl,
+     1), "stock_a__plusdl")
ok - stock_a__plusdl
> ok(ut_cmp_identical(
+     r$stock_b__minlen,
+     structure(
+         c(50, 51, 52, 53, 54),
+         names = c("50:51", "51:52", "52:53", "53:54", "54:Inf"))), "stock_b__minlen")
ok - stock_b__minlen
> ok(ut_cmp_identical(
+     r$stock_b__midlen,
+     structure(
+         c(50.5, 51.5, 52.5, 53.5, 54.5),
+         names = c("50:51", "51:52", "52:53", "53:54", "54:Inf"))), "stock_b__midlen")
ok - stock_b__midlen
> ok(ut_cmp_identical(r$stock_b__minmidlen, 50.5), "stock_b__minmidlen")
ok - stock_b__minmidlen
> ok(ut_cmp_identical(r$stock_b__maxmidlen, 54.5), "stock_b__maxmidlen")
ok - stock_b__maxmidlen
> ok(ut_cmp_identical(
+     r$stock_b__dl,
+     c(1,1,1,1,1)), "stock_b__dl")
ok - stock_b__dl
> ok(ut_cmp_identical(
+     r$stock_b__plusdl,
+     1), "stock_b__plusdl")
ok - stock_b__plusdl
> ok(ut_cmp_identical(
+     r$stock_wonky__minlen,
+     structure(
+         c(0, 10, 100, 200, 1000),
+         names = c("0:10", "10:100", "100:200", "200:1000", "1000:Inf"))), "stock_wonky__minlen")
ok - stock_wonky__minlen
> ok(ut_cmp_equal(
+     r$stock_wonky__midlen,
+     structure(
+         c(5, 55, 150, 600, 1005),
+         names = c("0:10", "10:100", "100:200", "200:1000", "1000:Inf"))), "stock_wonky__midlen")
ok - stock_wonky__midlen
> ok(ut_cmp_identical(r$stock_wonky__minmidlen, 5), "stock_wonky__minmidlen")
ok - stock_wonky__minmidlen
> ok(ut_cmp_identical(r$stock_wonky__maxmidlen, 1005), "stock_wonky__maxmidlen")
ok - stock_wonky__maxmidlen
> ok(ut_cmp_equal(
+     r$stock_wonky__dl,
+     c(10, 90, 100, 800, 10)), "stock_wonky__dl")
ok - stock_wonky__dl
> ok(ut_cmp_equal(
+     r$stock_wonky__plusdl,
+     10), "stock_wonky__plusdl")
ok - stock_wonky__plusdl
> 
> 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)
+ } else {
+     writeLines("# skip: not running TMB tests")
+ }
# skip: not running TMB tests
> 
> proc.time()
   user  system elapsed 
   0.34    0.04    0.36 
# Looks like you passed all 27 tests.