From 2956bcd7810689a5bf3752f5c8ceca4001e7b0de Mon Sep 17 00:00:00 2001
From: Andrea-Havron-NOAA
 <85530309+Andrea-Havron-NOAA@users.noreply.github.com>
Date: Sat, 5 Oct 2024 22:18:51 +0000
Subject: [PATCH] replace process distribution with helper function in tests

---
 .../testthat/helper-integration-tests-setup.R | 21 ++++++-------------
 vignettes/fims-demo.Rmd                       | 17 +++++----------
 2 files changed, 11 insertions(+), 27 deletions(-)

diff --git a/tests/testthat/helper-integration-tests-setup.R b/tests/testthat/helper-integration-tests-setup.R
index 5c58fa77..7690a150 100644
--- a/tests/testthat/helper-integration-tests-setup.R
+++ b/tests/testthat/helper-integration-tests-setup.R
@@ -82,21 +82,12 @@ setup_and_run_FIMS <- function(iter_id,
   # alternative setting: recruitment$log_devs <- rep(0, length(om_input$logR.resid))
   recruitment$log_devs <- methods::new(ParameterVector, om_input$logR.resid[-1], om_input$nyr-1)
 
-  recruitment_distribution <- new(TMBDnormDistribution)
-  # set up logR_sd using the normal log_sd parameter
-  # logR_sd is NOT logged. It needs to enter the model logged b/c the exp() is
-  # taken before the likelihood calculation
-  recruitment_distribution$log_sd <- new(ParameterVector, 1)
-  recruitment_distribution$log_sd[1]$value <- log(om_input$logR_sd)
-  recruitment_distribution$log_sd[1]$estimated <- FALSE
-  recruitment_distribution$x <- new(ParameterVector, om_input$nyr)
-  recruitment_distribution$expected_values <- new(ParameterVector, om_input$nyr)
-  for (i in 1:om_input$nyr) {
-    recruitment_distribution$x[i]$value <- 0
-    recruitment_distribution$expected_values[i]$value <- 0
-  }
-  recruitment_distribution$set_distribution_links("random_effects", recruitment$log_devs$get_id())
-  recruitment$estimate_log_devs <- TRUE
+  recruitment_distribution <- 
+    new_process_distribution(par = "log_devs", module = recruitment, family = gaussian(),
+                            sd = list(value = om_input$logR_sd, estimated = FALSE),
+                            is_random_effect = FALSE)
+
+  recruitment$estimate_log_devs = TRUE
 
   # Data
   catch <- em_input$L.obs$fleet1
diff --git a/vignettes/fims-demo.Rmd b/vignettes/fims-demo.Rmd
index 6bd5858a..eaf75c3e 100644
--- a/vignettes/fims-demo.Rmd
+++ b/vignettes/fims-demo.Rmd
@@ -283,18 +283,11 @@ recruitment$log_devs <- new(ParameterVector, c(
 In order to estimate *log_devs*, a new distribution needs to be created. This will be left commented out as we will proceed with not estimating log_devs.
 
 ```{r recruitment-distribution}
-recruitment_distribution <- new(TMBDnormDistribution)
-recruitment_distribution$log_sd <- new(ParameterVector, 1)
-recruitment_distribution$log_sd[1]$value <- log(0.4)
-recruitment_distribution$log_sd[1]$estimated = FALSE
-# set dimension of observations
-recruitment_distribution$x <- new(ParameterVector, nyears)
-recruitment_distribution$expected_values <- new(ParameterVector, nyears)
-for(i in 1:nyears){
-  recruitment_distribution$x[i]$value <- 0
-  recruitment_distribution$expected_values[i]$value <- 0
-}
-recruitment_distribution$set_distribution_links("random_effects", recruitment$log_devs$get_id())
+recruitment_distribution <- 
+  new_process_distribution(par = "log_devs", module = recruitment, family = gaussian(),
+                           sd = list(value = 0.4, estimated = FALSE),
+                           is_random_effect = FALSE)
+
 recruitment$estimate_log_devs = TRUE
 ```