reran analysis to get up to date stuff

r-analysis/EffectsOfEnrollmentDelay.qmd

@@ -744,7 +744,7 @@ ggplot(counterfact_predicted_ib, aes(x=p_predicted_default)) +
         ,x="Probability Domain 'p'"
         ,y="Probability Density"
     )
-ggsave(paste0(image_dist_diff_analysis,"p_no_intervention.png"))
+ggsave(paste0(image_dist_diff_analysis,"/p_no_intervention.png"))
 
 ggplot(counterfact_predicted_ib, aes(x=p_predicted_intervention)) +
     geom_density() + 
@@ -849,7 +849,7 @@ ggplot(pddf_ib, aes(x=value,)) +
     ) + 
     geom_vline(aes(xintercept = 0), color = "skyblue", linetype="dashed") +
     theme(strip.text.x = element_text(size = 8))
-ggsave(paste0(image_dist_diff_analysis,"p_delay_intervention_histdiff_by_group.png"))
+ggsave(paste0(image_dist_diff_analysis,"/p_delay_intervention_histdiff_by_group.png"))
 ```
 
 
@@ -1046,7 +1046,7 @@ quant_df <- data.frame(
 )
 # Convert to LaTeX
 table <- xtable(quant_df,
-    digits = rep(3, ncol(d) + 1),
+    digits = rep(3, ncol(quant_df) + 1),
     floating = FALSE,
     latex.environments = NULL,
     booktabs = TRUE

r-analysis/EffectsOfEnrollmentDelay.rmarkdown

@@ -39,7 +39,6 @@ image_dist_diff_analysis <- paste0(image_root,"/dist_diff_analysis")
 image_trial_details <-paste0(image_root,"/trials_details")
 image_parameters_by_groups <-paste0(image_root,"/betas/parameters_by_group")
 image_parameters_across_groups <-paste0(image_root,"/betas/parameter_across_groups")
-
 ```
 
 ```{r}
@@ -1073,9 +1072,23 @@ quants <- quantile(pddf_ib$value, probs = seq(0,1,0.05), type=4)
 
 # Convert to a data frame
 quant_df <- data.frame(
-  Percentile = names(quants),
+  #Percentile = names(quants),
   Value = quants
 )
+# Convert to LaTeX
+table <- xtable(quant_df,
+    digits = rep(3, ncol(d) + 1),
+    floating = FALSE,
+    latex.environments = NULL,
+    booktabs = TRUE
+)
+
+# Write to file
+write_lines(
+    print(table, include.rownames = FALSE),
+    paste0(image_root,"/distdiff_5percentile_table.tex")
+)
+
 kable(quant_df)
 
 proportion_increase <- mean(pddf_ib$value >= 0)
@@ -1101,6 +1114,59 @@ simulated_percentages <- (simulated_terminations_intervention - simulated_termin
 The simulation above shows that this results in a percentage-point change in terminations of about 
 `r simulated_percentages * 100`.
 
+## fixed effects distributions
+
+
+
+```{r}
+#Get dataframe with only the rows of interest
+filtdata <- as.data.frame(extract(fit, pars="status_diff"))
+#rename columns
+dimnames(filtdata)[[2]] <- beta_list$groups
+#create area plot with appropriate title
+mcmc_areas(filtdata,prob = 0.8, prob_outer = 0.95) +
+    ggtitle("Differences in Fixed Effects | By ICD-10 Category", 
+            subtitle = "Moving from 'Active, not recruiting' to 'Recruiting'"
+        ) +
+    geom_vline(xintercept=seq(-0.25,0.5,0.25),color="grey",alpha=0.750)  
+ggsave(paste0(image_parameters_across_groups,"/fixed_effects_anr_vs_rec_by_group.png"))
+    
+d <- pivot_longer(filtdata, everything()) |> 
+    group_by(name) |> 
+    summarize(
+        mean = mean(value),
+        `P(≥0)` = mean(value >= 0),
+        `2.5%` = quantile(value, probs = 0.025),
+        `5%` = quantile(value, probs = 0.05),
+        `25%` = quantile(value, probs = 0.25),
+        `50% median` = quantile(value, probs = 0.5),
+        `75%` = quantile(value, probs = 0.75),
+        `95%` = quantile(value, probs = 0.95),
+        `97.5%` = quantile(value, probs = 0.975)
+    )
+
+# Rename the name column
+names(d)[1] <- "ICD-10 Category"
+
+# Convert to LaTeX
+table <- xtable(d,
+    digits = rep(3, ncol(d) + 1),
+    floating = FALSE,
+    latex.environments = NULL,
+    booktabs = TRUE
+)
+
+
+# Write to file
+write_lines(
+    print(table, include.rownames = FALSE),
+    paste0(image_parameters_across_groups,"/fixed_effects_anr_vs_rec_by_group.tex")
+)
+
+
+
+```
+
 
 
 

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameter_across_groups/fixed_effects_anr_vs_rec_by_group.tex

@@ -1,5 +1,5 @@
 % latex table generated in R 4.4.2 by xtable 1.8-4 package
-% Sat Feb  1 22:53:42 2025
+% Sun Feb  2 01:37:36 2025
 \begin{table}[ht]
 \centering
 \begin{tabular}{lrrrrrrrrr}