Fixed error in column order that invalidated results

The columns for competitor drugs were placed in the wrong spot.

r-analysis/EffectsOfEnrollmentDelay_rebased.qmd

@@ -239,14 +239,14 @@ cf_categories <- df_counterfact_base$category_id
 ################################# FIT MODEL #########################################
 inherited_cols <- c(
     "elapsed_duration"
-    #,"identical_brands"
-    #,"brand_name_counts"
+    ,"identical_brands"
+    ,"brand_name_counts"
     ,"h_sdi_val"
     ,"hm_sdi_val"
     ,"m_sdi_val"
     ,"lm_sdi_val"
     ,"l_sdi_val"
-    ,"status_NYR"# TODO: may need to remove
+    ,"status_NYR"
     ,"status_EBI"
     ,"status_Rec"
     ,"status_ANR"
@@ -406,7 +406,8 @@ Plan: select all snapshots that are the first to have closed
 enrollment (Rec -> ANR when comparing across snapshots), and then 
 ```{r}
 #delay intervention
-intervention_enrollment <- x_cf_base[c(inherited_cols,"brand_name_counts", "identical_brands")]
+intervention_enrollment <- x_cf_base[c(inherited_cols)]
+#TOFIX: ^^^ This ordering of columns is
 intervention_enrollment["status_ANR"] <- 0
 intervention_enrollment["status_Rec"] <- 1
 ```
@@ -581,7 +582,7 @@ sum(df5$snapshot_count)
 
 ```{r}
 ################################# ANALYZE #####################################
-print(fit)
+#print(fit)
 ```
 
 # Parameter Distributions
@@ -672,6 +673,7 @@ generated_ib <- gqs(
     )
 ```
 
+### Get priors
 ```{r}
 df_ib_p <- data.frame(
     p_prior=as.vector(extract(generated_ib, pars="p_prior")$p_prior)
@@ -687,10 +689,10 @@ df_ib_prior <- data.frame(
 ggplot(df_ib_p, aes(x=p_prior)) +
     geom_density() + 
     labs(
-        title="Implied Prior Distribution P"
+        title="implied prior distribution p"
         ,subtitle=""
-        ,x="Probability Domain 'p'"
-        ,y="Probability Density"
+        ,x="probability domain 'p'"
+        ,y="probability density"
     )
 ggsave(paste0(image_dist_diff_analysis,"/prior_p.png"))
 
@@ -698,9 +700,9 @@ ggsave(paste0(image_dist_diff_analysis,"/prior_p.png"))
 ggplot(df_ib_p, aes(x=p_predicted)) +
     geom_density() + 
     labs(
-        title="Implied Posterior Distribution P"
+        title="implied posterior distribution p"
         ,subtitle=""
-        ,x="Probability Domain 'p'"
+        ,x="probability domain 'p'"
         ,y="Probability Density"
     )
 ggsave(paste0(image_dist_diff_analysis,"/posterior_p.png"))
@@ -1219,4 +1221,4 @@ for (i in 1:3) {
 
 
 
-  
+