From 140c9220343c841f54cf9c2c487c4cd6202dc0be Mon Sep 17 00:00:00 2001
From: Bai Li - NOAA <59936250+Bai-Li-NOAA@users.noreply.github.com>
Date: Thu, 19 Dec 2024 19:37:10 +0000
Subject: [PATCH] return a list of modules when calling intialize_fims()

---
 R/initialize_modules.R                        | 20 ++++++++++++++++++-
 .../testthat/helper-integration-tests-setup.R |  4 ++--
 tests/testthat/test-initialize_modules.R      |  2 +-
 ...ntegration-fims-estimation-with-wrappers.R |  4 ++--
 vignettes/fims-demo.Rmd                       |  8 ++++----
 vignettes/logging_system.Rmd                  |  2 +-
 6 files changed, 29 insertions(+), 11 deletions(-)

diff --git a/R/initialize_modules.R b/R/initialize_modules.R
index fc817c02..3ad5e3f2 100644
--- a/R/initialize_modules.R
+++ b/R/initialize_modules.R
@@ -762,8 +762,26 @@ initialize_fims <- function(parameters, data) {
   CreateTMBModel()
   # Create parameter list from Rcpp modules
   parameter_list <- list(p = get_fixed())
+  module_list <- list(
+    fleet = fleet,
+    fleet_selectivity = fleet_selectivity,
+    fleet_index = fleet_index,
+    fleet_index_distribution = fleet_index_distribution,
+    fleet_age_comp = fleet_age_comp,
+    fleet_agecomp_distribution = fleet_agecomp_distribution,
+    fleet_length_comp = fleet_length_comp,
+    fleet_lengthcomp_distribution = fleet_lengthcomp_distribution,
+    recruitment = recruitment,
+    recruitment_distribution = recruitment_distribution,
+    growth = growth,
+    maturity = maturity,
+    population = population
+  )
 
-  return(parameter_list)
+  output <- list(
+    parameter_list = parameter_list,
+    module_list = module_list
+  )
 }
 
 #' Set parameter vector values based on module input
diff --git a/tests/testthat/helper-integration-tests-setup.R b/tests/testthat/helper-integration-tests-setup.R
index f1133486..9be04078 100644
--- a/tests/testthat/helper-integration-tests-setup.R
+++ b/tests/testthat/helper-integration-tests-setup.R
@@ -558,13 +558,13 @@ setup_and_run_FIMS_with_wrappers <- function(iter_id,
       modified_parameters = modified_parameters
     )
 
-  parameter_list <- initialize_fims(
+  output <- initialize_fims(
     parameters = parameters,
     data = data
   )
 
   input <- list()
-  input$parameters <- parameter_list
+  input$parameters <- output$parameter_list
   input$version <- "Model Comparison Project example"
   fit <- fit_fims(input, optimize = estimation_mode)
 
diff --git a/tests/testthat/test-initialize_modules.R b/tests/testthat/test-initialize_modules.R
index 8aaf5dbe..6fe19fa5 100644
--- a/tests/testthat/test-initialize_modules.R
+++ b/tests/testthat/test-initialize_modules.R
@@ -44,7 +44,7 @@ test_that("initialize_fims works", {
   result <- initialize_fims(parameters = default_parameters, data = data)
 
   expect_type(result, "list")
-  expect_named(result, "p")
+  expect_named(result, c("parameter_list", "module_list"))
   clear()
 })
 
diff --git a/tests/testthat/test-integration-fims-estimation-with-wrappers.R b/tests/testthat/test-integration-fims-estimation-with-wrappers.R
index 4eebf043..58e00337 100644
--- a/tests/testthat/test-integration-fims-estimation-with-wrappers.R
+++ b/tests/testthat/test-integration-fims-estimation-with-wrappers.R
@@ -302,12 +302,12 @@ test_that("estimation test of fims using high-level wrappers", {
 
   # Clear any previous FIMS settings
   clear()
-  parameter_list <- initialize_fims(
+  output <- initialize_fims(
     parameters = parameters,
     data = data
   )
   input <- list()
-  input$parameters <- parameter_list
+  input$parameters <- output$parameter_list
   input$version <- "Model Comparison Project example"
   fit <- fit_fims(input, optimize = TRUE)
 
diff --git a/vignettes/fims-demo.Rmd b/vignettes/fims-demo.Rmd
index 30355958..c5a736bd 100644
--- a/vignettes/fims-demo.Rmd
+++ b/vignettes/fims-demo.Rmd
@@ -161,13 +161,13 @@ With data and parameters in place, we can now initialize modules using `initiali
 # Run the model without optimization to help ensure a viable model
 test_fit <- parameters |>
   initialize_fims(data = fims_frame) |>
-  (\(parameter_list) list(parameters = parameter_list, version = "FIMS run without optimization"))() |>
+  (\(output) list(parameters = output$parameter_list, version = "FIMS run without optimization"))() |>
   fit_fims(optimize = FALSE)
 
 # Run the  model with optimization
 fit <- parameters |>
   initialize_fims(data = fims_frame) |>
-  (\(parameter_list) list(parameters = parameter_list, version = "FIMS run with optimization"))() |>
+  (\(output) list(parameters = output$parameter_list, version = "FIMS run with optimization"))() |>
   fit_fims(optimize = TRUE)
 
 # Clear memory post-run
@@ -194,14 +194,14 @@ parameters_low_slope <- parameters |>
 
 high_slope_fit <- parameters_high_slope |>
   initialize_fims(data = fims_frame) |>
-  (\(parameter_list) list(parameters = parameter_list, version = "High slope run"))() |>
+  (\(output) list(parameters = output$parameter_list, version = "High slope run"))() |>
   fit_fims(optimize = TRUE)
 
 clear()
 
 low_slope_fit <- parameters_low_slope |>
   initialize_fims(data = fims_frame) |>
-  (\(parameter_list) list(parameters = parameter_list, version = "Low slope run"))() |>
+  (\(output) list(parameters = output$parameter_list, version = "low slope run"))() |>
   fit_fims(optimize = TRUE)
 
 clear()
diff --git a/vignettes/logging_system.Rmd b/vignettes/logging_system.Rmd
index 7e79c805..678109bd 100644
--- a/vignettes/logging_system.Rmd
+++ b/vignettes/logging_system.Rmd
@@ -123,7 +123,7 @@ Assuming a model has already been defined, below is an example of using the logg
 ```{r example_code, eval = TRUE}
 fit <- default_parameters |>
   initialize_fims(data = fims_frame) |>
-  (\(parameter_list) list(parameters = parameter_list, version = "FIMS run with optimization"))() |>
+  (\(output) list(parameters = output$parameter_list, version = "FIMS run with optimization"))() |>
   fit_fims(optimize = TRUE)
 
 # get the log as a string in JSON format and parse into a list