modify test files after main change

NOAA-FIMS · Aug 26, 2024 · c30a0c4 · c30a0c4
1 parent 676a80d
commit c30a0c4
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Showing 2 changed files with 288 additions and 653 deletions.
diff --git a/tests/testthat/helper-integration-tests-setup.R b/tests/testthat/helper-integration-tests-setup.R
@@ -78,7 +78,7 @@ setup_and_run_FIMS <- function(iter_id,
   # recruit deviations should enter the model in normal space.
   # The log is taken in the likelihood calculations
   # alternative setting: recruitment$log_devs <- rep(0, length(om_input$logR.resid))
-  recruitment$log_devs <- methods::new(ParameterVector, om_input$logR.resid, om_input$nyr)
+  recruitment$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
@@ -254,6 +254,7 @@ setup_and_run_FIMS <- function(iter_id,
   return(list(
     parameters = parameters,
     obj = obj,
+    opt = opt,
     report = report,
     sdr_report = sdr_report,
     sdr_fixed = sdr_fixed,