From 4822fa012f9b1ddcfe962da4b66b5521ded12a8e Mon Sep 17 00:00:00 2001
From: Kaitlyn Johnson <kej38@georgetown.edu>
Date: Fri, 25 Oct 2024 14:27:43 -0400
Subject: [PATCH] fix handling of subpops from merge, modify vignette
 temporarily

---
 R/get_stan_data.R         | 4 ++--
 vignettes/wwinference.Rmd | 1 +
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/get_stan_data.R b/R/get_stan_data.R
index 2329f8e2..75d84950 100644
--- a/R/get_stan_data.R
+++ b/R/get_stan_data.R
@@ -559,8 +559,8 @@ get_stan_data <- function(input_count_data,
     # This dist_matrix will not be used, only needed for stan data specs.
     dist_matrix <- matrix(
       0,
-      nrow = subpop_data$n_subpops - 1,
-      ncol = subpop_data$n_subpops - 1
+      nrow = length(ww_vals$subpop_pops) - 1,
+      ncol = length(ww_vals$subpop_pops) - 1
     )
   }
   if (!(corr_structure_switch %in% c(0, 1, 2))) {
diff --git a/vignettes/wwinference.Rmd b/vignettes/wwinference.Rmd
index 39835926..19112c10 100644
--- a/vignettes/wwinference.Rmd
+++ b/vignettes/wwinference.Rmd
@@ -334,6 +334,7 @@ compile the model. This can be done using the `compile_model()` function
 
 
 ```{r compile-model}
+# temporarily compile from local to make troubleshooting faster/easier
 model <- wwinference::compile_model(
   model_filepath = here::here(file.path(
     "inst", "stan", "wwinference.stan"