fix tmbstan calls

NOAA-FIMS · May 22, 2024 · da27b84 · da27b84
1 parent 58c3bfc
commit da27b84
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Showing 3 changed files with 26 additions and 15 deletions.
diff --git a/tests/testthat/test-multivariate-prior.R b/tests/testthat/test-multivariate-prior.R
@@ -115,14 +115,18 @@ test_that("test multivariate prior", {
   expect_equal( log(.1) > ci[[3]][1] & log(.1) < ci[[3]][2], TRUE)
 })
 
+DataNLL$finalize(opt$par)
+GrowthMVPrior$finalize(opt$par)
+DataNLL$nll_vec
+GrowthMVPrior$nll_vec
 #Fully Bayesian
 test_that("test_tmbstan", {
   skip_on_ci("skip tmbstan")
   library(tmbstan)
   library(shinystan)
   library(ggplot2)
-  newobj <- tmbstan(obj, warmup = 1000, iter = 4000)
-  launch_shinystan(newobj)
+  fit <- tmbstan(obj, init = "best.last.par")
+  launch_shinystan(obj)
 })
 
 clear()

diff --git a/tests/testthat/test-predictive-prior.R b/tests/testthat/test-predictive-prior.R
@@ -96,12 +96,13 @@ test_that("test single prior",{
   expect_equal( log(.1) > ci[[3]][1] & log(.1) < ci[[3]][2], TRUE)
 })
 
-test_that( "test_tmbstan", {
-skip_on_ci(library(tmbstan))
-skip_on_ci(fit <- tmbstan(obj))
-skip_on_ci(library(shinystan))
-skip_on_ci(library(ggplot2))
-skip_on_ci(launch_shinystan(fit))
+test_that("test_tmbstan", {
+  skip_on_ci("skip tmbstan")
+  library(tmbstan)
+  library(shinystan)
+  library(ggplot2)
+  fit <- tmbstan(obj, init = "best.last.par")
+  launch_shinystan(obj)
 })
 
 clear()

diff --git a/tests/testthat/test-prior.R b/tests/testthat/test-prior.R
@@ -105,14 +105,20 @@ test_that("test single prior",{
   expect_equal( log(.1) > ci[[3]][1] & log(.1) < ci[[3]][2], TRUE)
 })
 
-test_that( "test_tmbstan", {
-skip_on_ci(library(tmbstan))
-skip_on_ci(fit <- tmbstan(obj))
-skip_on_ci(library(shinystan))
-skip_on_ci(library(ggplot2))
-skip_on_ci(launch_shinystan(fit))
+#Check nll output
+DataNLL$finalize(opt$par)
+GrowthKPrior$finalize(opt$par)
+DataNLL$nll_vec
+GrowthKPrior$nll_vec
+
+test_that("test_tmbstan", {
+  skip_on_ci("skip tmbstan")
+  library(tmbstan)
+  library(shinystan)
+  library(ggplot2)
+  fit <- tmbstan(obj, init = "best.last.par")
+  launch_shinystan(obj)
 })
-
 clear()
 # #update the von Bertalanffy object with updated parameters
 # vonB$finalize(rep$par.fixed)