ClinicalTrialsEstimation.Rproj

@@ -1,13 +0,0 @@
-Version: 1.0
-
-RestoreWorkspace: Default
-SaveWorkspace: Default
-AlwaysSaveHistory: Default
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: Sweave
-LaTeX: pdfLaTeX

r-analysis/EffectsOfEnrollmentDelay.qmd

@@ -28,13 +28,6 @@ options(mc.cores = parallel::detectCores())
 
 #test installation, shouldn't get any errors
 #example(stan_model, package = "rstan", run.dontrun = TRUE)
-
-
-image_root <- "./output/EffectsOfEnrollmentDelay"
-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}
@@ -218,8 +211,8 @@ counterfact_base <- data_formatter(df_counterfact_base)
 
 categories <- df$category_id
 
-x <- as.matrix(train$x)
+x <- train$x
-y <- as.vector(train$y)
+y <- train$y
 
 x_cf_base <- counterfact_base$x
 y_cf_base <- counterfact_base$y
@@ -237,14 +230,14 @@ cf_categories <- df_counterfact_base$category_id
 ################################# FIT MODEL #########################################
 inherited_cols <- c(
     "elapsed_duration"
-    ,"identical_brands"
+    #,"identical_brands"
-    ,"brand_name_counts"
+    #,"brand_name_counts"
     ,"h_sdi_val"
     ,"hm_sdi_val"
     ,"m_sdi_val"
     ,"lm_sdi_val"
     ,"l_sdi_val"
-    ,"status_NYR"
+    ,"status_NYR"# TODO: may need to remove
     ,"status_EBI"
     ,"status_Rec"
     ,"status_ANR"
@@ -403,30 +396,27 @@ parameter_mcmc_areas <- function(
 Plan: select all snapshots that are the first to have closed enrollment (Rec -> ANR)
 ```{r}
 #delay intervention
-intervention_enrollment <- x_cf_base[c(inherited_cols)]
+intervention_enrollment <- x_cf_base[c(inherited_cols,"brand_name_counts", "identical_brands")]
 intervention_enrollment["status_ANR"] <- 0
 intervention_enrollment["status_Rec"] <- 1
 ```
 
 ```{r}
-
 counterfact_delay <- list(
-    D = ncol(x),
+    D = ncol(x),#
     N = nrow(x),
     L = n_categories$count,
-    y = y,
+    y = as.vector(y),
     ll = as.vector(categories),
-    x = x,
+    x = as.matrix(x),
     mu_mean = 0,
     mu_stdev = 0.05,
-    sigma_location = -2.1,
+    sigma_shape = 4,
-    sigma_scale = 0.2,
+    sigma_rate = 20,
     Nx = nrow(x_cf_base),
     llx = as.vector(cf_categories),
     counterfact_x_tilde = as.matrix(intervention_enrollment),
-    counterfact_x = as.matrix(x_cf_base),
+    counterfact_x = as.matrix(x_cf_base)
-    status_indexes = c(11,12) #subtract anr from recruiting to get movement from anr to recruiting
-
 )
 ```
 
@@ -434,24 +424,14 @@ counterfact_delay <- list(
 fit <- stan(
     file='Hierarchal_Logistic.stan', 
     data = counterfact_delay,
-    chains = 8,
+    chains = 4,
-    iter = 12000,
+    iter = 5000,
-    warmup = 4000,
     seed = 11021585
     )
 ```
 
 
-## Fit Results
-```{r}
-print(check_hmc_diagnostics(fit))
-print(get_bfmi(fit))
-```
-
 
-```{r}
-print(fit)
-```
 
 
 
@@ -493,7 +473,7 @@ ggplot(data=df3, aes(x=count, fill=final_status)) +
     geom_histogram(binwidth=1) +
     ggtitle("Histogram of snapshots per trial (matched trials)") +
     xlab("Snapshots per trial")
-ggsave(paste0(image_trial_details,"/HistSnapshots.png"))
+ggsave("./Images/HistSnapshots.png")
 
 #Plot duration for terminated vs completed
 df4 <- dbGetQuery(
@@ -516,7 +496,7 @@ ggplot(data=df4, aes(x=duration,fill=overall_status)) +
     ggtitle("Histogram of trial durations") +
     xlab("duration")+
     facet_wrap(~overall_status)
-ggsave(paste0(image_trial_details,"/HistTrialDurations_Faceted.png"))
+ggsave("./Images/HistTrialDurations_Faceted.png")
 
 df5 <- dbGetQuery(
     con,
@@ -547,7 +527,7 @@ ggplot(data=df5, aes(x=duration,y=snapshot_count,color=overall_status)) +
     ggtitle("Comparison of duration, status, and snapshot_count") +
     xlab("duration") +
     ylab("snapshot count") 
-ggsave(paste0(image_trial_details,"/SnapshotsVsDurationVsTermination.png"))
+ggsave("./Images/SnapshotsVsDurationVsTermination.png")
 
 dbDisconnect(con)
 
@@ -556,28 +536,34 @@ group_trials_by_category <- as.data.frame(aggregate(category_id ~ nct_id, df, ma
 group_trials_by_category <- as.data.frame(group_trials_by_category)
 
 ggplot(data = group_trials_by_category, aes(x=category_id)) +
-    geom_bar(binwidth=1,color="black",fill="lightblue") +
+    geom_bar(binwidth=1,color="black",fill="seagreen") +
     scale_x_continuous(breaks=scales::pretty_breaks(n=22)) + 
     labs(
         title="bar chart of trial categories"
         ,x="Category ID"
         ,y="Count"
     )
-ggsave(paste0(image_trial_details,"/CategoryCounts.png"))
+ggsave("./Images/CategoryCounts.png")
     
 
 
 summary(df5)
 
-cor_dur_count <- cor(df5$duration,df5$snapshot_count)
+cor(df5$duration,df5$snapshot_count)
-count_snapshots <- sum(df5$snapshot_count)
+sum(df5$snapshot_count)
 ```
 
-the correlation value is `r cor_dur_count` between duration and snapshot count.
-There are `r count_snapshots` snapshots in total.
 
 
 
+## Fit Results
+
+
+```{r}
+################################# ANALYZE #####################################
+print(fit)
+```
+
 # Parameter Distributions
 
 
@@ -588,13 +574,13 @@ There are `r count_snapshots` snapshots in total.
 gx <- c()
 
 #grab parameters for every category with more than 8 observations
-for (i in category_count$category_id[category_count$n >= 0]) {
+for (i in category_count$category_id[category_count$n >= 8]) {
     print(i)
     
     #Print parameter distributions
     gi <- group_mcmc_areas("beta",beta_list,fit,i) #add way to filter groups
     ggsave(
-        paste0(image_parameters_by_groups,"/group_",i,"_",gi$name,".png")
+        paste0("./Images/DirectEffects/Parameters/group_",i,"_",gi$name,".png")
         ,plot=gi$plot
         )
     gx <- c(gx,gi)
@@ -606,10 +592,7 @@ for (i in category_count$category_id[category_count$n >= 0]) {
       ,booktabs = TRUE
       ,zap=getOption("digits")
       )
-    write_lines(
+    write_lines(table,paste0("./latex_output/DirectEffects/group_",gi$name,".tex"))
-        table,
-        paste0(image_parameters_by_groups,"/group_table_",i,"_",gi$name,".tex")
-    )
 }
 ```
 
@@ -624,7 +607,7 @@ for (i in c(1,2,3,9,10,11,12)) {
     #Print parameter distributions
     pi <- parameter_mcmc_areas("beta",beta_list,fit,i) #add way to filter groups
     ggsave(
-        paste0(image_parameters_across_groups,"/parameters_",i,"_",pi$name,".png")
+        paste0("./Images/DirectEffects/Parameters/parameters_",i,"_",pi$name,".png")
         ,plot=pi$plot
         )
     px <- c(px,pi)
@@ -636,10 +619,7 @@ for (i in c(1,2,3,9,10,11,12)) {
       ,booktabs = TRUE
       ,zap=getOption("digits")
       )
-    write_lines(
+    write_lines(table,paste0("./latex_output/DirectEffects/parameters_",i,"_",pi$name,".tex"))
-        table,
-        paste0(image_parameters_across_groups,"/parameters_tables_",i,"_",pi$name,".tex")
-    )
     
 }
 ```
@@ -650,8 +630,13 @@ Note these have 95% outer CI and 80% inner (shaded)
 
 
 
+```{r}
+print(px[4]$plot + px[7]$plot)
+ggsave("./Images/DirectEffects/Parameters/2+3_generic_and_uspdc.png")
+```
+
 
-# Counterfactuals calculation
+# Counterfactuals
 
 ```{r}
 generated_ib <- gqs(
@@ -661,7 +646,7 @@ generated_ib <- gqs(
     seed=11021585
     )
 ```
-# Priors
+
 ```{r}
 df_ib_p <- data.frame(
     p_prior=as.vector(extract(generated_ib, pars="p_prior")$p_prior)
@@ -672,10 +657,7 @@ df_ib_prior <- data.frame(
     mu_prior = as.vector(extract(generated_ib, pars="mu_prior")$mu_prior)
     ,sigma_prior = as.vector(extract(generated_ib, pars="sigma_prior")$sigma_prior)
 )
-```
-
 
-```{r}
 #p_prior
 ggplot(df_ib_p, aes(x=p_prior)) +
     geom_density() + 
@@ -685,7 +667,7 @@ ggplot(df_ib_p, aes(x=p_prior)) +
         ,x="Probability Domain 'p'"
         ,y="Probability Density"
     )
-ggsave(paste0(image_dist_diff_analysis,"/prior_p.png"))
+ggsave("./EffectsOfEnrollmentDelay/Images/DirectEffects/prior_p.png")
 
 #p_posterior
 ggplot(df_ib_p, aes(x=p_predicted)) +
@@ -696,7 +678,7 @@ ggplot(df_ib_p, aes(x=p_predicted)) +
         ,x="Probability Domain 'p'"
         ,y="Probability Density"
     )
-ggsave(paste0(image_dist_diff_analysis,"/posterior_p.png"))
+ggsave("./EffectsOfEnrollmentDelay/Images/DirectEffects/posterior_p.png")
 
 #mu_prior
 ggplot(df_ib_prior) +
@@ -707,7 +689,7 @@ ggplot(df_ib_prior) +
         ,x="Mu"
         ,y="Probability"
     )
-ggsave(paste0(image_dist_diff_analysis,"/prior_mu.png"))
+ggsave("./EffectsOfEnrollmentDelay/Images/DirectEffects/prior_mu.png")
 
 #sigma_posterior
 ggplot(df_ib_prior) +
@@ -718,11 +700,16 @@ ggplot(df_ib_prior) +
         ,x="Sigma"
         ,y="Probability"
     )
-ggsave(paste0(image_dist_diff_analysis,"/prior_sigma.png"))
+ggsave("./EffectsOfEnrollmentDelay/Images/DirectEffects/prior_sigma.png")
 ```
 
 
 
+```{r}
+check_hmc_diagnostics(fit)
+```
+
+
 
 
 
@@ -744,7 +731,7 @@ 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("./EffectsOfEnrollmentDelay/Images/DirectEffects/default_p_generic_intervention_base.png")
 
 ggplot(counterfact_predicted_ib, aes(x=p_predicted_intervention)) +
     geom_density() + 
@@ -754,7 +741,7 @@ ggplot(counterfact_predicted_ib, aes(x=p_predicted_intervention)) +
         ,x="Probability Domain 'p'"
         ,y="Probability Density"
     )
-ggsave(paste0(image_dist_diff_analysis,"/p_delay_intervention.png"))
+ggsave("./EffectsOfEnrollmentDelay/Images/DirectEffects/default_p_generic_intervention_interv.png")
 
 ggplot(counterfact_predicted_ib, aes(x=predicted_difference)) +
     geom_density() + 
@@ -764,7 +751,7 @@ ggplot(counterfact_predicted_ib, aes(x=predicted_difference)) +
         ,x="Difference in 'p' under treatment"
         ,y="Probability Density"
     )
-ggsave(paste0(image_dist_diff_analysis,"/p_delay_intervention_distdiff_1.png"))
+ggsave("./EffectsOfEnrollmentDelay/Images/DirectEffects/default_p_generic_intervention_distdiff.png")
 ```
 
 
@@ -786,16 +773,16 @@ category_names <- sapply(1:length(beta_list$groups),
 pddf_ib <- data.frame(extract(generated_ib, pars="predicted_difference")$predicted_difference) |>
     pivot_longer(X1:X168) #CHANGE_NOTE: moved from X169 to X168
 
+#TODO: Fix Category names
 pddf_ib["entry_idx"] <- as.numeric(gsub("\\D","",pddf_ib$name))
 pddf_ib["category"] <-  sapply(pddf_ib$entry_idx, function(i) df$category_id[i])
 pddf_ib["category_name"] <- sapply(
     pddf_ib$category, 
     function(i) category_names[i]
     )
-```
   
 
-```{r}
+
 ggplot(pddf_ib, aes(x=value,)) +
     geom_density(adjust=1/5) +
     labs(
@@ -805,11 +792,9 @@ ggplot(pddf_ib, aes(x=value,)) +
         ,y = "Probability Density"
     ) + 
     geom_vline(aes(xintercept = 0), color = "skyblue", linetype="dashed") 
-ggsave(paste0(image_dist_diff_analysis,"/p_delay_intervention_distdiff_styled.png"))
+    #todo: add median, mean, 40/60 quantiles as well as 
-```
+ggsave("./EffectsOfEnrollmentDelay/Images/DirectEffects/p_delay_intervention_distdiff_styled.png")
-
 
-```{r}
 ggplot(pddf_ib, aes(x=value,)) +
     geom_density(adjust=1/5) +
     facet_wrap(
@@ -827,11 +812,8 @@ 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_distdiff_by_group.png"))
+ggsave("./EffectsOfEnrollmentDelay/Images/DirectEffects/p_delay_intervention_distdiff_by_group.png")
-```
-
 
-```{r}
 ggplot(pddf_ib, aes(x=value,)) +
     geom_histogram(bins=300) +
     facet_wrap(
@@ -849,7 +831,7 @@ 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("./EffectsOfEnrollmentDelay/Images/DirectEffects/p_delay_intervention_histdiff_by_group.png")
 ```
 
 
@@ -865,8 +847,6 @@ p3 <- ggplot(pddf_ib, aes(x=value,)) +
     ) + 
     geom_vline(aes(xintercept = 0), color = "skyblue", linetype="dashed") 
 
-density_hight <- max(density(pddf_ib$value)$y)
-
 stats <- list(
  p5 = quantile(pddf_ib$value, 0.05),
  p10 = quantile(pddf_ib$value, 0.10),
@@ -877,8 +857,7 @@ stats <- list(
  p90 = quantile(pddf_ib$value, 0.90),
  p95 = quantile(pddf_ib$value, 0.95),
  max_height = max(ggplot_build(p3)$data[[1]]$count),
- y_offset = -max(ggplot_build(p3)$data[[1]]$count) * 0.05,
+ y_offset = -max(ggplot_build(p3)$data[[1]]$count) * 0.05
- y_offset_density = -density_hight * 0.15
 )
 
 p3 + 
@@ -928,69 +907,7 @@ p3 +
    x = stats$mean,
    y = stats$y_offset * 1.5
  ), aes(x = x, y = y))
-ggsave(paste0(image_dist_diff_analysis,"/p_delay_intervention_histdiff_boxplot.png"))
+ggsave("./EffectsOfEnrollmentDelay/Images/DirectEffects/p_delay_intervention_histdiff_boxplot.png")
-```
-
-
-```{r}
-p4 <- ggplot(pddf_ib, aes(x = value)) +
-  geom_density() +
-    labs(
-        title = "Distribution of predicted differences"
-        ,subtitle = "Intervention: Delay close of enrollment"
-        ,x = "Difference in probability due to intervention"
-        ,y = "Probability Density"
-        ,caption = "Vertical marks: 5/10/25/50/75/90/95th percentiles. Dot shows mean."
-    ) + 
-    geom_vline(aes(xintercept = 0), color = "skyblue", linetype="dashed") +
- geom_segment(data = data.frame(
-   x = c(stats$q1, stats$q3, stats$med),
-   xend = c(stats$q1, stats$q3, stats$med),
-   y = rep(stats$y_offset_density, 3), 
-   yend = rep(stats$y_offset_density * 2, 3)
- ), aes(x = x, xend = xend, y = y, yend = yend)) +
- geom_segment(data = data.frame(
-   x = rep(stats$q1, 2),
-   xend = rep(stats$q3, 2),
-   y = c(stats$y_offset_density, stats$y_offset_density * 2),
-   yend = c(stats$y_offset_density, stats$y_offset_density * 2)
- ), aes(x = x, xend = xend, y = y, yend = yend)) +
- # Inner whiskers (Q1->P10, Q3->P90)
- geom_segment(data = data.frame(
-   x = c(stats$q1, stats$q3),
-   xend = c(stats$p10, stats$p90),
-   y = rep(stats$y_offset_density * 1.5, 2),
-   yend = rep(stats$y_offset_density * 1.5, 2)
- ), aes(x = x, xend = xend, y = y, yend = yend)) +
- # Crossbars at P10/P90
- geom_segment(data = data.frame(
-   x = c(stats$p10, stats$p90),
-   xend = c(stats$p10, stats$p90),
-   y = stats$y_offset_density * 1.3,
-   yend = stats$y_offset_density * 1.7
- ), aes(x = x, xend = xend, y = y, yend = yend)) +
- # Outer whiskers (P10->P5, P90->P95)
- geom_segment(data = data.frame(
-   x = c(stats$p10, stats$p90),
-   xend = c(stats$p5, stats$p95),
-   y = rep(stats$y_offset_density * 1.5, 2),
-   yend = rep(stats$y_offset_density * 1.5, 2)
- ), aes(x = x, xend = xend, y = y, yend = yend)) +
- # Crossbars at P5/P95
- geom_segment(data = data.frame(
-   x = c(stats$p5, stats$p95),
-   xend = c(stats$p5, stats$p95),
-   y = stats$y_offset_density * 1.3,
-   yend = stats$y_offset_density * 1.7
- ), aes(x = x, xend = xend, y = y, yend = yend)) +
- # Mean dot
- geom_point(data = data.frame(
-   x = stats$mean,
-   y = stats$y_offset_density * 1.5
- ), aes(x = x, y = y))
-ggsave(paste0(image_dist_diff_analysis,"/p_delay_intervention_distdiff_boxplot.png"))
-
-p4
 ```
 
 ```{r}
@@ -1003,7 +920,7 @@ p4
         y = "Cumulative Proportion"
     ) 
 
-ggsave(paste0(image_dist_diff_analysis,"/p_delay_intervention_cumulative_distdiff.png"))
+ggsave("./EffectsOfEnrollmentDelay/Images/DirectEffects/p_delay_intervention_cumulative_distdiff.png")
 ```
 
 
@@ -1041,29 +958,13 @@ 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(quant_df) + 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)
 ```
 
-about `r proportion_increase * 100` percent probability increase in the probability of terminations
+There seems to be some trials that are highly suceptable to this enrollment delay. Specifically, there were some 
 
 ```{r}
 n = length(counterfact_predicted_ib$p_predicted_intervention)
@@ -1074,59 +975,10 @@ simulated_terminations_base <-mean(rbinom(n,k,as.vector(counterfact_predicted_ib
 simulated_percentages <- (simulated_terminations_intervention - simulated_terminations_base)/k
 ```
 
-The simulation above shows that this results in a percentage-point change in terminations of about 
+The simulation above shows that this results in a percentage-point increase 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")
-)
-
-
-
-```
 
 
 # Diagnostics
@@ -1134,10 +986,8 @@ write_lines(
 ```{r}
 #| eval: true
 #trace plots
-image_diagnostics <- paste0(image_root,"/diagnostics")
-
 plot(fit, pars=c("mu"), plotfun="trace")
-ggsave(paste0(image_diagnostics,"/trace_plot_mu.png"))
+ggsave("./EffectsOfEnrollmentDelay/Images/diagnostics/trace_plot_mu.png")
 
 
 for (i in 1:3) {
@@ -1155,7 +1005,7 @@ for (i in 1:3) {
              scale_colour_ghibli_d("KikiMedium")
     )
     mu_range <- paste0(4*i-3,"-",4*i)
-    filename <- paste0(image_diagnostics,"/trace_rank_plot_mu_",mu_range,".png")
+    filename <- paste0("./EffectsOfEnrollmentDelay/Images/diagnostics/trace_rank_plot_mu_",mu_range,".png")
     ggsave(filename)
 }
 ```
@@ -1163,7 +1013,7 @@ for (i in 1:3) {
 ```{r}
 #| eval: true
 plot(fit, pars=c("sigma"), plotfun="trace")
-ggsave(paste0(image_diagnostics,"/traceplot_sigma.png"))
+ggsave("./EffectsOfEnrollmentDelay/Images/diagnostics/traceplot_sigma.png")
 
 for (i in 1:3) {
     print(
@@ -1180,7 +1030,7 @@ for (i in 1:3) {
              scale_colour_ghibli_d("KikiMedium")
     )
     sigma_range <- paste0(4*i-3,"-",4*i)
-    filename <- paste0(image_diagnostics,"/trace_rank_plot_sigma_",sigma_range,".png")
+    filename <- paste0("./EffectsOfEnrollmentDelay/Images/diagnostics/trace_rank_plot_sigma_",sigma_range,".png")
     ggsave(filename)
 }
 ```
@@ -1199,7 +1049,7 @@ posterior <- as.array(fit)
 color_scheme_set("darkgray")
 div_style <- parcoord_style_np(div_color = "green", div_size = 0.05, div_alpha = 0.4)
 mcmc_parcoord(posterior, regex_pars = "mu", np=nuts_prmts, np_style = div_style, alpha = 0.05)
-ggsave(paste0(image_diagnostics,"/parcoord_mu.png"))
+ggsave("./EffectsOfEnrollmentDelay/Images/diagnostics/parcoord_mu.png")
 ```
 
 ```{r}
@@ -1218,7 +1068,7 @@ for (i in 1:3) {
         )
     )
     mu_range <- paste0(4*i-3,"-",4*i)
-    filename <- paste0(image_diagnostics,"/correlation_plot_mu_",mu_range,".png")
+    filename <- paste0("./EffectsOfEnrollmentDelay/Images/diagnostics/correlation_plot_mu_",mu_range,".png")
     ggsave(filename)
 }
 
@@ -1229,7 +1079,7 @@ for (i in 1:3) {
 ```{r}
 #| eval: true
 mcmc_parcoord(posterior,regex_pars = "sigma", np=nuts_prmts, alpha=0.05)
-ggsave(paste0(image_diagnostics,"/parcoord_sigma.png"))
+ggsave("./EffectsOfEnrollmentDelay/Images/diagnostics/parcoord_sigma.png")
 ```
 
 ```{r}
@@ -1249,7 +1099,7 @@ for (i in 1:3) {
         )
     )
     sigma_range <- paste0(4*i-3,"-",4*i)
-    filename <- paste0(image_diagnostics,"/correlation_plot_sigma_",sigma_range,".png")
+    filename <- paste0("./EffectsOfEnrollmentDelay/Images/diagnostics/correlation_plot_sigma_",sigma_range,".png")
     ggsave(filename)
 }
 ```
@@ -1273,7 +1123,7 @@ for (i in 1:3) {
     )
     
     beta_range <- paste0("k_",k,"_i_",4*i-3,"-",4*i)
-    filename <- paste0(image_diagnostics,"/correlation_plot_beta_",beta_range,".png")
+    filename <- paste0("./EffectsOfEnrollmentDelay/Images/diagnostics/correlation_plot_beta_",beta_range,".png")
     ggsave(filename)
 }}
 ```
@@ -1283,4 +1133,11 @@ for (i in 1:3) {
 
 
 
-  
+# TODO
+- [ ] Double check data flow. (Write summary of this in human readable form)
+    - Is it the data we want from the database 
+        - Training
+        - Counterfactual Evaluation
+            - choose a single snapshot per trial.
+    - Is the model in STAN well specified.
+- [ ] work on LOO validation of model

r-analysis/Hierarchal_Logistic.stan

@@ -19,15 +19,13 @@ data {
   array[N] row_vector[D] x; // independent variables
   real mu_mean; //hyperprior
   real<lower=0> mu_stdev; //hyperprior
-  real sigma_location; //hyperprior
+  real sigma_shape; //hyperprior
-  real<lower=0> sigma_scale; //hyperprior
+  real sigma_rate; //hyperprior
   //counterfactuals
   int<lower=0> Nx;
   array[Nx] int<lower=1, upper=L> llx;//vec of categories
   array[Nx] row_vector[D] counterfact_x_tilde; // Posterior Prediction intervention
   array[Nx] row_vector[D] counterfact_x; // Posterior Prediction intervention
-  //the two statuses to catch relative difference
-  array[2] int status_indexes; //the two status indexes to compare (order is x[1] - x[2])
 }
 parameters {
   array[D] real mu;
@@ -35,7 +33,7 @@ parameters {
   array[L] vector[D] beta;
 }
 model {
-  sigma ~ lognormal(sigma_location,sigma_scale); //hyperprior for stdev: shape and inverse scale
+  sigma ~ gamma(sigma_shape,sigma_rate); //hyperprior for stdev: shape and inverse scale
   mu ~ normal(mu_mean, mu_stdev); //hyperprior for mean //TODO: convert to mvnormal
   for (l in 1:L) {
     beta[l] ~ normal(mu, sigma);
@@ -60,20 +58,13 @@ generated quantities {
     real p_predicted_intervention[Nx]; //predicted p_values
     real predicted_difference[Nx]; //difference in predicted values
 
-    //collect array of relative status differences between
-    array[L] real status_diff;
-    //GENERATE RELATIVE DIFFERENCES BETWEEN STATUSES
-    for (l in 1:L) {
-      status_diff[l] = beta[l,status_indexes[1]] - beta[l,status_indexes[2]];
-    }
-
     //GENERATE PRIOR PREDICTIONS
     {
         vector[D] beta_prior[L];//local var
         //sample parameters
         for (d in 1:D) {
             mu_prior[d] = normal_rng(mu_mean,mu_stdev);
-            sigma_prior[d] = lognormal_rng(sigma_location,sigma_scale);
+            sigma_prior[d] = gamma_rng(sigma_shape,sigma_rate);
         }
         for (l in 1:L) {
             for (d in 1:D) {

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

@@ -1,34 +0,0 @@
-% latex table generated in R 4.4.2 by xtable 1.8-4 package
-% Sun Feb  2 01:37:36 2025
-\begin{table}[ht]
-\centering
-\begin{tabular}{lrrrrrrrrr}
-  \hline
-ICD-10 Category & mean & P(≥0) & 2.5\% & 5\% & 25\% & 50\% median & 75\% & 95\% & 97.5\% \\ 
-  \hline
-Blood \& Immune system & 0.061 & 0.624 & -0.333 & -0.267 & -0.071 & 0.061 & 0.194 & 0.388 & 0.454 \\ 
-  Circulatory & 0.037 & 0.577 & -0.362 & -0.293 & -0.094 & 0.038 & 0.170 & 0.363 & 0.426 \\ 
-  Congential & 0.063 & 0.628 & -0.332 & -0.264 & -0.068 & 0.063 & 0.195 & 0.391 & 0.456 \\ 
-  Contact with Healthcare & 0.063 & 0.627 & -0.335 & -0.267 & -0.070 & 0.064 & 0.194 & 0.390 & 0.454 \\ 
-  Digestive & 0.060 & 0.621 & -0.339 & -0.270 & -0.071 & 0.059 & 0.192 & 0.388 & 0.454 \\ 
-  Ear and Mastoid & 0.063 & 0.625 & -0.332 & -0.263 & -0.069 & 0.064 & 0.196 & 0.393 & 0.457 \\ 
-  Endocrine, Nutritional, and Metabolic & 0.177 & 0.820 & -0.201 & -0.137 & 0.045 & 0.173 & 0.304 & 0.505 & 0.573 \\ 
-  External Causes & 0.063 & 0.625 & -0.330 & -0.266 & -0.070 & 0.064 & 0.194 & 0.392 & 0.460 \\ 
-  Eye and Adnexa & 0.061 & 0.624 & -0.333 & -0.265 & -0.069 & 0.062 & 0.192 & 0.386 & 0.452 \\ 
-  Genitourinary & 0.063 & 0.627 & -0.337 & -0.270 & -0.070 & 0.065 & 0.195 & 0.389 & 0.456 \\ 
-  Infections \& Parasites & 0.135 & 0.772 & -0.223 & -0.163 & 0.013 & 0.134 & 0.257 & 0.438 & 0.498 \\ 
-  Injury etc. & 0.063 & 0.625 & -0.337 & -0.268 & -0.069 & 0.062 & 0.196 & 0.392 & 0.459 \\ 
-  Mental \& Behavioral & 0.142 & 0.767 & -0.239 & -0.175 & 0.010 & 0.140 & 0.270 & 0.469 & 0.537 \\ 
-  Musculoskeletal & 0.159 & 0.794 & -0.218 & -0.156 & 0.027 & 0.156 & 0.286 & 0.482 & 0.550 \\ 
-  Neoplasms & 0.211 & 0.902 & -0.107 & -0.056 & 0.099 & 0.208 & 0.320 & 0.489 & 0.546 \\ 
-  Nervous System & 0.009 & 0.524 & -0.383 & -0.315 & -0.120 & 0.011 & 0.140 & 0.327 & 0.389 \\ 
-  Perinatal Period & 0.062 & 0.626 & -0.338 & -0.270 & -0.068 & 0.062 & 0.194 & 0.390 & 0.457 \\ 
-  Pregancy, Childbirth, \& Puerperium & 0.061 & 0.622 & -0.336 & -0.270 & -0.071 & 0.061 & 0.194 & 0.392 & 0.458 \\ 
-  Respiratory & 0.061 & 0.622 & -0.335 & -0.269 & -0.072 & 0.061 & 0.195 & 0.391 & 0.458 \\ 
-  Skin \& Subcutaneaous tissue & 0.104 & 0.704 & -0.283 & -0.220 & -0.027 & 0.103 & 0.234 & 0.429 & 0.494 \\ 
-  Special Purposes & 0.062 & 0.625 & -0.335 & -0.268 & -0.070 & 0.062 & 0.194 & 0.391 & 0.456 \\ 
-  Symptoms, Signs etc. & 0.062 & 0.625 & -0.332 & -0.265 & -0.069 & 0.062 & 0.194 & 0.390 & 0.456 \\ 
-   \hline
-\end{tabular}
-\end{table}
-

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameter_across_groups/parameters_tables_10_status_EBI.tex

@@ -1,10 +0,0 @@
-c("Blood & Immune system", "Circulatory", "Congential", "Contact with Healthcare", "Digestive", "Ear and Mastoid", "Endocrine, Nutritional, and Metabolic", "External Causes", "Eye and Adnexa", "Genitourinary", "Infections & Parasites", "Injury etc.", "Mental & Behavioral", "Musculoskeletal", "Neoplasms", "Nervous System", "Perinatal Period", "Pregancy, Childbirth, & Puerperium", "Respiratory", "Skin & Subcutaneaous tissue", "Special Purposes", "Symptoms, Signs etc.")
-c(-0.00287140656905416, -0.0020229135961933, -0.00252250078632693, -0.00209236160817254, -0.00233302952373521, -0.00216616648896081, -0.00681543732790809, -0.00273617241938979, -0.00219896995482389, -0.00310971192809426, -0.00900529540694934, -0.00252589644802287, -0.00444905498743218, -0.00275503221432378, -0.00295173909211749, -0.00517241124667845, -0.00201260276746087, -0.00257497154836192, -0.00242272398017638, -0.00267620974013439, -0.00248385412497201, -0.00206395314166231)
-c(`2.5%` = -0.275944463803495, `2.5%` = -0.272921161056328, `2.5%` = -0.272430725186905, `2.5%` = -0.272911375314851, `2.5%` = -0.27286212768348, `2.5%` = -0.276406977245084, `2.5%` = -0.277987677303119, `2.5%` = -0.270429258845101, `2.5%` = -0.272173859797933, `2.5%` = -0.270957011640022, `2.5%` = -0.281051472827658, `2.5%` = -0.274123164780341, `2.5%` = -0.273927630545993, `2.5%` = -0.272259113214428, `2.5%` = -0.271867873121147, `2.5%` = -0.275526164264352, `2.5%` = -0.275736741086972, `2.5%` = -0.274025059638234, 
-`2.5%` = -0.271895651649722, `2.5%` = -0.274439135854432, `2.5%` = -0.272777026543343, `2.5%` = -0.274505781494588)
-c(`97.5%` = 0.268525663885088, `97.5%` = 0.269687555821123, `97.5%` = 0.263988376114375, `97.5%` = 0.268376674723849, `97.5%` = 0.271595831106391, `97.5%` = 0.27398054865504, `97.5%` = 0.26497995981819, `97.5%` = 0.264914777867797, `97.5%` = 0.268729163024419, `97.5%` = 0.266687930004995, `97.5%` = 0.260632526818398, `97.5%` = 0.270701536658997, `97.5%` = 0.264287404395679, `97.5%` = 0.266631371530776, `97.5%` = 0.265171319133342, `97.5%` = 0.267696135908434, `97.5%` = 0.269792405742312, `97.5%` = 0.267738792080357, 
-`97.5%` = 0.270026733830649, `97.5%` = 0.267892275489918, `97.5%` = 0.266305005411752, `97.5%` = 0.271501986023693)
-c(`5%` = -0.228422342352796, `5%` = -0.225192615705392, `5%` = -0.225155935562034, `5%` = -0.227577347541465, `5%` = -0.226336678780408, `5%` = -0.227963356496732, `5%` = -0.230488468962024, `5%` = -0.226216509362732, `5%` = -0.224813386072165, `5%` = -0.224824888562106, `5%` = -0.232874112114568, `5%` = -0.227479714082238, `5%` = -0.227858560023144, `5%` = -0.22530608055078, `5%` = -0.226179910621409, `5%` = -0.228284369418676, `5%` = -0.228444224989461, `5%` = -0.226622261032726, `5%` = -0.224288571128251, 
-`5%` = -0.227590395464131, `5%` = -0.225531022618535, `5%` = -0.227689137616937)
-c(`95%` = 0.2234974899362, `95%` = 0.222074828728455, `95%` = 0.218357594565282, `95%` = 0.22222430007764, `95%` = 0.222289991457749, `95%` = 0.223327488400761, `95%` = 0.216270931014924, `95%` = 0.220095617146775, `95%` = 0.221009192368411, `95%` = 0.218989193656767, `95%` = 0.213804656879867, `95%` = 0.222889299900387, `95%` = 0.220133939553423, `95%` = 0.21899037055656, `95%` = 0.218796743068272, `95%` = 0.220217569663176, `95%` = 0.224044557893232, `95%` = 0.220936167501407, `95%` = 0.222159099161132, 
-`95%` = 0.220911069519647, `95%` = 0.220781640962889, `95%` = 0.223599356920508)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameter_across_groups/parameters_tables_11_status_Rec.tex

@@ -1,10 +0,0 @@
-c("Blood & Immune system", "Circulatory", "Congential", "Contact with Healthcare", "Digestive", "Ear and Mastoid", "Endocrine, Nutritional, and Metabolic", "External Causes", "Eye and Adnexa", "Genitourinary", "Infections & Parasites", "Injury etc.", "Mental & Behavioral", "Musculoskeletal", "Neoplasms", "Nervous System", "Perinatal Period", "Pregancy, Childbirth, & Puerperium", "Respiratory", "Skin & Subcutaneaous tissue", "Special Purposes", "Symptoms, Signs etc.")
-c(0.00652882287222823, -0.0121276026193075, 0.00806097077518296, 0.00921072076176892, 0.00511136013511625, 0.00923452323640744, 0.0756452851959799, 0.00901967004583639, 0.00596509106734287, 0.00869308015726206, 0.0234704825434495, 0.00891347968211811, 0.0410008650026277, 0.0493113026890666, -0.0318651891745962, -0.0230137010884716, 0.00907668265519354, 0.0082773304353959, 0.00672386515176627, 0.0229027326955782, 0.00903950397151059, 0.00840626979762671)
-c(`2.5%` = -0.26412401679988, `2.5%` = -0.284982548735974, `2.5%` = -0.262583809560454, `2.5%` = -0.259623047912961, `2.5%` = -0.267223017905891, `2.5%` = -0.262824783073146, `2.5%` = -0.182738362310984, `2.5%` = -0.261194421023313, `2.5%` = -0.264838971088612, `2.5%` = -0.263984097470059, `2.5%` = -0.233328888684629, `2.5%` = -0.260381735988535, `2.5%` = -0.219982381931615, `2.5%` = -0.209178899422793, `2.5%` = -0.272496159194591, `2.5%` = -0.293189864865698, `2.5%` = -0.259442015177563, `2.5%` = -0.265643699376373, 
-`2.5%` = -0.264848607612733, `2.5%` = -0.243262927814473, `2.5%` = -0.263583321279326, `2.5%` = -0.260710033426863)
-c(`97.5%` = 0.279506924359323, `97.5%` = 0.25166727687992, `97.5%` = 0.279367210952163, `97.5%` = 0.278659096264822, `97.5%` = 0.274044451638933, `97.5%` = 0.280562384576216, `97.5%` = 0.359198759844572, `97.5%` = 0.282464614440408, `97.5%` = 0.274146522142649, `97.5%` = 0.279840596472466, `97.5%` = 0.282219317765516, `97.5%` = 0.279650795194328, `97.5%` = 0.3146382824935, `97.5%` = 0.324504387608479, `97.5%` = 0.198395249398707, `97.5%` = 0.238015436387141, `97.5%` = 0.279664049019525, `97.5%` = 0.282472259620116, 
-`97.5%` = 0.280170359985892, `97.5%` = 0.296090615801029, `97.5%` = 0.278827396276502, `97.5%` = 0.276519814652463)
-c(`5%` = -0.217405377189081, `5%` = -0.235700053008877, `5%` = -0.215580888141684, `5%` = -0.212836780879927, `5%` = -0.220927862811969, `5%` = -0.215245283188846, `5%` = -0.139947007794807, `5%` = -0.214372400370517, `5%` = -0.216692707544591, `5%` = -0.215840640492215, `5%` = -0.190195428873606, `5%` = -0.214974248730335, `5%` = -0.175242262948575, `5%` = -0.166101667860902, `5%` = -0.228981038446028, `5%` = -0.246615923137647, `5%` = -0.214004181031889, `5%` = -0.218493362752846, `5%` = -0.21829426001738, 
-`5%` = -0.197184265526973, `5%` = -0.216831943794109, `5%` = -0.21336683632312)
-c(`95%` = 0.231060746721114, `95%` = 0.206639994505824, `95%` = 0.232261579219567, `95%` = 0.231058781781102, `95%` = 0.228526975656424, `95%` = 0.233653720301541, `95%` = 0.306122759153545, `95%` = 0.234530990151044, `95%` = 0.226800701259279, `95%` = 0.230966741806046, `95%` = 0.237452575327, `95%` = 0.23322865073513, `95%` = 0.264306220644107, `95%` = 0.274559112084226, `95%` = 0.161143364484194, `95%` = 0.195044859439803, `95%` = 0.232513302970324, `95%` = 0.233960896032084, `95%` = 0.232756864140852, 
-`95%` = 0.246925692056239, `95%` = 0.231685551132494, `95%` = 0.230370019187908)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameter_across_groups/parameters_tables_12_status_ANR.tex

@@ -1,10 +0,0 @@
-c("Blood & Immune system", "Circulatory", "Congential", "Contact with Healthcare", "Digestive", "Ear and Mastoid", "Endocrine, Nutritional, and Metabolic", "External Causes", "Eye and Adnexa", "Genitourinary", "Infections & Parasites", "Injury etc.", "Mental & Behavioral", "Musculoskeletal", "Neoplasms", "Nervous System", "Perinatal Period", "Pregancy, Childbirth, & Puerperium", "Respiratory", "Skin & Subcutaneaous tissue", "Special Purposes", "Symptoms, Signs etc.")
-c(-0.0543082831893662, -0.0491179148659016, -0.0550797452225853, -0.0532946953959887, -0.0546326964547788, -0.054263670489829, -0.101183732558573, -0.0537419015558274, -0.055296341966815, -0.0541521176630153, -0.111933746601916, -0.0536195743237358, -0.101358093383466, -0.109295568325447, -0.242704066590673, -0.0324576251191776, -0.0530684599999257, -0.0529707690770896, -0.0545919114607711, -0.0809466615050335, -0.0530673747164349, -0.0537090394695628)
-c(`2.5%` = -0.3460926221197, `2.5%` = -0.340513734259116, `2.5%` = -0.345063660691308, `2.5%` = -0.343936968361375, `2.5%` = -0.347086498849369, `2.5%` = -0.346730664863283, `2.5%` = -0.402573667581036, `2.5%` = -0.344748248866169, `2.5%` = -0.348019495991554, `2.5%` = -0.343259904607912, `2.5%` = -0.397011060181461, `2.5%` = -0.347299904964005, `2.5%` = -0.398857333530158, `2.5%` = -0.407252271853641, `2.5%` = -0.543673509898535, `2.5%` = -0.315411836398564, `2.5%` = -0.344614905885746, `2.5%` = -0.345987208689716, 
-`2.5%` = -0.34467924126698, `2.5%` = -0.37464941870207, `2.5%` = -0.346982193867717, `2.5%` = -0.34255968704254)
-c(`97.5%` = 0.23859370882391, `97.5%` = 0.247596369898235, `97.5%` = 0.236924146027621, `97.5%` = 0.239608837398885, `97.5%` = 0.23894631939739, `97.5%` = 0.238196795290067, `97.5%` = 0.180340815442861, `97.5%` = 0.240218974320717, `97.5%` = 0.235175513197134, `97.5%` = 0.237777766149638, `97.5%` = 0.156402075952097, `97.5%` = 0.242638519639189, `97.5%` = 0.182559370226462, `97.5%` = 0.170699887327904, `97.5%` = 0.0114150292406248, `97.5%` = 0.259944925352525, `97.5%` = 0.242795694071721, `97.5%` = 0.242602907693202, 
-`97.5%` = 0.239492781782234, `97.5%` = 0.204585540113804, `97.5%` = 0.238328250302865, `97.5%` = 0.240534823211121)
-c(`5%` = -0.295316756003101, `5%` = -0.29096401042673, `5%` = -0.294243091294835, `5%` = -0.293355784827148, `5%` = -0.296193852536529, `5%` = -0.294348519148639, `5%` = -0.347024621453625, `5%` = -0.293279771169653, `5%` = -0.297136938616546, `5%` = -0.2933097076324, `5%` = -0.347474604177594, `5%` = -0.294318945943837, `5%` = -0.344628024841975, `5%` = -0.352532667961251, `5%` = -0.488379411138948, `5%` = -0.266550224886603, `5%` = -0.293396519481707, `5%` = -0.295913858425759, `5%` = -0.294475437187543, 
-`5%` = -0.322719512364534, `5%` = -0.294234511411049, `5%` = -0.291661527567577)
-c(`95%` = 0.186170625673217, `95%` = 0.194446427538144, `95%` = 0.18316007227917, `95%` = 0.185398130082336, `95%` = 0.18656668417393, `95%` = 0.186918825584728, `95%` = 0.133329444707804, `95%` = 0.188140180351712, `95%` = 0.186846293810823, `95%` = 0.188406047073467, `95%` = 0.112535221760718, `95%` = 0.191176019972506, `95%` = 0.132004530075709, `95%` = 0.124477125901656, `95%` = -0.0267022930175043, `95%` = 0.205343484029368, `95%` = 0.187850282416095, `95%` = 0.190035921589226, `95%` = 0.188021330440522, 
-`95%` = 0.155090212003947, `95%` = 0.188333556494078, `95%` = 0.187492448246279)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameter_across_groups/parameters_tables_1_Elapsed Duration.tex

@@ -1,10 +0,0 @@
-c("Blood & Immune system", "Circulatory", "Congential", "Contact with Healthcare", "Digestive", "Ear and Mastoid", "Endocrine, Nutritional, and Metabolic", "External Causes", "Eye and Adnexa", "Genitourinary", "Infections & Parasites", "Injury etc.", "Mental & Behavioral", "Musculoskeletal", "Neoplasms", "Nervous System", "Perinatal Period", "Pregancy, Childbirth, & Puerperium", "Respiratory", "Skin & Subcutaneaous tissue", "Special Purposes", "Symptoms, Signs etc.")
-c(-0.0505321895701756, -0.0561236542390722, -0.0499660268658585, -0.0481574325504504, -0.0505967062178304, -0.0480668691756736, -0.0585983827703775, -0.047133883963608, -0.0507912436647474, -0.0478593490739956, -0.0816317285457012, -0.0482822682398582, -0.0774004055701482, -0.016726156695298, -0.315526037006588, -0.0578472700681722, -0.0475268941302727, -0.0480850373469818, -0.0494676291479126, -0.0931186973375372, -0.0479483938019099, -0.0486654863146441)
-c(`2.5%` = -0.351333711658477, `2.5%` = -0.358192918691032, `2.5%` = -0.350165746673952, `2.5%` = -0.348260904879301, `2.5%` = -0.355213104294602, `2.5%` = -0.349537890844496, `2.5%` = -0.356636178298712, `2.5%` = -0.348967122811696, `2.5%` = -0.356770047469594, `2.5%` = -0.348523219782961, `2.5%` = -0.369067201876791, `2.5%` = -0.352751358464831, `2.5%` = -0.384222770661754, `2.5%` = -0.310459552529128, `2.5%` = -0.642054194627079, `2.5%` = -0.359167198818045, `2.5%` = -0.351037786426624, `2.5%` = -0.35686171619278, 
-`2.5%` = -0.353960823288628, `2.5%` = -0.398212841275992, `2.5%` = -0.351411960176182, `2.5%` = -0.352062830672535)
-c(`97.5%` = 0.252996678658013, `97.5%` = 0.245199739323497, `97.5%` = 0.252568610015387, `97.5%` = 0.256300675128962, `97.5%` = 0.256220116158008, `97.5%` = 0.256880194696558, `97.5%` = 0.237496943950342, `97.5%` = 0.260731873495491, `97.5%` = 0.255694095814266, `97.5%` = 0.258199105421347, `97.5%` = 0.196240544658593, `97.5%` = 0.256780445660338, `97.5%` = 0.218570279154564, `97.5%` = 0.295751559042532, `97.5%` = -0.0498087194116947, `97.5%` = 0.238629751570793, `97.5%` = 0.258078396538427, `97.5%` = 0.259647869046876, 
-`97.5%` = 0.256663885447249, `97.5%` = 0.195728293212208, `97.5%` = 0.259664751280795, `97.5%` = 0.257403541589351)
-c(`5%` = -0.29803422118825, `5%` = -0.304624731177692, `5%` = -0.298500654906565, `5%` = -0.295625102451718, `5%` = -0.300950367218894, `5%` = -0.296909500653078, `5%` = -0.304028644400323, `5%` = -0.295898014297575, `5%` = -0.301053900765771, `5%` = -0.297395770121559, `5%` = -0.318536205133514, `5%` = -0.298729047781782, `5%` = -0.328832973524529, `5%` = -0.260408972551825, `5%` = -0.580798660746861, `5%` = -0.303098555574414, `5%` = -0.297724180258084, `5%` = -0.300789071762739, `5%` = -0.29885389568916, 
-`5%` = -0.341186799958823, `5%` = -0.297555789883245, `5%` = -0.297336353504652)
-c(`95%` = 0.199805705380915, `95%` = 0.193775727317953, `95%` = 0.20049984396355, `95%` = 0.203214802673669, `95%` = 0.202603902019158, `95%` = 0.203401989386427, `95%` = 0.187816936293634, `95%` = 0.205427481892033, `95%` = 0.200369696005793, `95%` = 0.203709821019864, `95%` = 0.149606773044668, `95%` = 0.201078718458991, `95%` = 0.168803960348435, `95%` = 0.23786658788661, `95%` = -0.0876108144400803, `95%` = 0.186931912303368, `95%` = 0.204472031901114, `95%` = 0.205112704275416, `95%` = 0.201106127451977, 
-`95%` = 0.145913702571692, `95%` = 0.204425554740135, `95%` = 0.202755710634796)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameter_across_groups/parameters_tables_2_asinh(Generic Brands).tex

@@ -1,10 +0,0 @@
-c("Blood & Immune system", "Circulatory", "Congential", "Contact with Healthcare", "Digestive", "Ear and Mastoid", "Endocrine, Nutritional, and Metabolic", "External Causes", "Eye and Adnexa", "Genitourinary", "Infections & Parasites", "Injury etc.", "Mental & Behavioral", "Musculoskeletal", "Neoplasms", "Nervous System", "Perinatal Period", "Pregancy, Childbirth, & Puerperium", "Respiratory", "Skin & Subcutaneaous tissue", "Special Purposes", "Symptoms, Signs etc.")
-c(-0.0374509867623648, -0.114801759701441, -0.0421991751741288, -0.0268927396537672, -0.0431305204973958, -0.0260913808525182, -0.147540114797909, -0.027116517230545, -0.0572148794918185, -0.0567196164994895, -0.0431781674057524, -0.0247442525263859, -0.148857275259831, 0.173176112299651, -0.745438348426778, 0.514928808041493, -0.0262970064646734, -0.0273698856833142, -0.0519713531203428, -0.0813059076860515, -0.0258722297716816, -0.0348374667962509)
-c(`2.5%` = -0.519252573751591, `2.5%` = -0.588446720987112, `2.5%` = -0.518375863151681, `2.5%` = -0.504192330494074, `2.5%` = -0.521537560181517, `2.5%` = -0.501531706057096, `2.5%` = -0.605455988019874, `2.5%` = -0.50319865217871, `2.5%` = -0.529409792355877, `2.5%` = -0.537648621232678, `2.5%` = -0.392971765289971, `2.5%` = -0.499643963973294, `2.5%` = -0.654106115127152, `2.5%` = -0.223573014616573, `2.5%` = -1.12441685579914, `2.5%` = 0.0216592886163218, `2.5%` = -0.492165903236766, `2.5%` = -0.506906607161406, 
-`2.5%` = -0.530569224373654, `2.5%` = -0.560352091813988, `2.5%` = -0.502878744623734, `2.5%` = -0.516492014350377)
-c(`97.5%` = 0.438156824615533, `97.5%` = 0.326892147498506, `97.5%` = 0.439646865645069, `97.5%` = 0.45479809614294, `97.5%` = 0.429980507934071, `97.5%` = 0.452354448697589, `97.5%` = 0.271710367913333, `97.5%` = 0.452356456142033, `97.5%` = 0.408657439741233, `97.5%` = 0.413237173559078, `97.5%` = 0.304781682760948, `97.5%` = 0.462872494668127, `97.5%` = 0.307321465786219, `97.5%` = 0.625146449622561, `97.5%` = -0.396240166662077, `97.5%` = 1.17318649525454, `97.5%` = 0.448797338514388, `97.5%` = 0.456641082563543, 
-`97.5%` = 0.416128814653975, `97.5%` = 0.375467600073314, `97.5%` = 0.455154502226114, `97.5%` = 0.445072841208461)
-c(`5%` = -0.43284681982114, `5%` = -0.498779889626974, `5%` = -0.434007392588596, `5%` = -0.417440686797088, `5%` = -0.43620401741364, `5%` = -0.415561086942261, `5%` = -0.520616290327113, `5%` = -0.415868472350007, `5%` = -0.445215274649135, `5%` = -0.450348871660559, `5%` = -0.335854611911698, `5%` = -0.417370214498537, `5%` = -0.55799947646926, `5%` = -0.165197877092618, `5%` = -1.05984134753029, `5%` = 0.0851401986791414, `5%` = -0.412294843116399, `5%` = -0.421537839042216, `5%` = -0.443110847973097, 
-`5%` = -0.472054693822914, `5%` = -0.4154217625395, `5%` = -0.430050287469576)
-c(`95%` = 0.353300713490598, `95%` = 0.251902327224973, `95%` = 0.353130963560884, `95%` = 0.367385797642419, `95%` = 0.346576238409847, `95%` = 0.364713198282056, `95%` = 0.20347262465658, `95%` = 0.366348980622731, `95%` = 0.328590570058774, `95%` = 0.329135185773538, `95%` = 0.24519101313148, `95%` = 0.372694013964094, `95%` = 0.231568717349548, `95%` = 0.544725565756189, `95%` = -0.449885315105183, `95%` = 1.03873143227049, `95%` = 0.364171369034129, `95%` = 0.369255306736876, `95%` = 0.335218886894626, 
-`95%` = 0.30207955992225, `95%` = 0.367493122771963, `95%` = 0.360231402349028)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameter_across_groups/parameters_tables_3_asinh(Competitors USPDC).tex

@@ -1,10 +0,0 @@
-c("Blood & Immune system", "Circulatory", "Congential", "Contact with Healthcare", "Digestive", "Ear and Mastoid", "Endocrine, Nutritional, and Metabolic", "External Causes", "Eye and Adnexa", "Genitourinary", "Infections & Parasites", "Injury etc.", "Mental & Behavioral", "Musculoskeletal", "Neoplasms", "Nervous System", "Perinatal Period", "Pregancy, Childbirth, & Puerperium", "Respiratory", "Skin & Subcutaneaous tissue", "Special Purposes", "Symptoms, Signs etc.")
-c(0.0177091826256191, -0.0174830982131017, 0.0197148498472504, 0.0267207484850693, 0.01865599931714, 0.0273355925564759, -0.0557624513358899, 0.0285704704444676, 0.0105781672515, 0.0120682740554864, 0.117270560237318, 0.0273743158412062, 0.0202098736769506, -0.0761301686125453, 0.14948178706425, 0.363548114620147, 0.027441418729276, 0.0271631725930479, 0.0175175823493799, 0.0472688930727053, 0.0278787334069728, 0.0236727211994869)
-c(`2.5%` = -0.321412408332877, `2.5%` = -0.360033194654434, `2.5%` = -0.317756875891385, `2.5%` = -0.310112746266069, `2.5%` = -0.321047087440019, `2.5%` = -0.307177857312271, `2.5%` = -0.406584875693101, `2.5%` = -0.302290577496734, `2.5%` = -0.329787608837027, `2.5%` = -0.325741416529682, `2.5%` = -0.15743258849236, `2.5%` = -0.31119118357692, `2.5%` = -0.317021340734379, `2.5%` = -0.431037121901406, `2.5%` = -0.095511016993371, `2.5%` = 0.02041143019079, `2.5%` = -0.305991043265743, `2.5%` = -0.30655610684263, 
-`2.5%` = -0.319852685329391, `2.5%` = -0.276270824232982, `2.5%` = -0.304861628467873, `2.5%` = -0.311752202314792)
-c(`97.5%` = 0.343837322664501, `97.5%` = 0.295622079182328, `97.5%` = 0.349107813430285, `97.5%` = 0.355203673240806, `97.5%` = 0.349024698020337, `97.5%` = 0.360808144158849, `97.5%` = 0.249517798279291, `97.5%` = 0.358750370961986, `97.5%` = 0.33508908205543, `97.5%` = 0.337658598779989, `97.5%` = 0.421101378052922, `97.5%` = 0.354555256028663, `97.5%` = 0.350403071909054, `97.5%` = 0.22676112069751, `97.5%` = 0.422731018753381, `97.5%` = 0.85608235301133, `97.5%` = 0.355759840642227, `97.5%` = 0.356934774044409, 
-`97.5%` = 0.341627016198812, `97.5%` = 0.376205200194986, `97.5%` = 0.358952915535868, `97.5%` = 0.352180233725197)
-c(`5%` = -0.25720973558682, `5%` = -0.294903363605129, `5%` = -0.257137304097466, `5%` = -0.248399306392637, `5%` = -0.25489751531943, `5%` = -0.247102777254339, `5%` = -0.339933290032092, `5%` = -0.242533928470576, `5%` = -0.263620928816618, `5%` = -0.263152155503003, `5%` = -0.112232006084965, `5%` = -0.246916752820145, `5%` = -0.255886271822305, `5%` = -0.360056361494536, `5%` = -0.0582870053082083, `5%` = 0.0634526303087552, `5%` = -0.245278803753055, `5%` = -0.246842321323342, `5%` = -0.256280286172, 
-`5%` = -0.217436243551559, `5%` = -0.244210801606863, `5%` = -0.250885342909289)
-c(`95%` = 0.285370104912777, `95%` = 0.243010994205006, `95%` = 0.289287710051617, `95%` = 0.297571077262736, `95%` = 0.291325959161563, `95%` = 0.299270475058976, `95%` = 0.200063580704579, `95%` = 0.298824142626635, `95%` = 0.27722780854366, `95%` = 0.278261424943046, `95%` = 0.365441233493439, `95%` = 0.297355276712413, `95%` = 0.290718931165702, `95%` = 0.178465709918192, `95%` = 0.373392398003416, `95%` = 0.753336516739962, `95%` = 0.297312097796899, `95%` = 0.297460388207995, `95%` = 0.285527407612361, 
-`95%` = 0.317952486884081, `95%` = 0.296773071637121, `95%` = 0.292674820916317)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameter_across_groups/parameters_tables_9_status_NYR.tex

@@ -1,10 +0,0 @@
-c("Blood & Immune system", "Circulatory", "Congential", "Contact with Healthcare", "Digestive", "Ear and Mastoid", "Endocrine, Nutritional, and Metabolic", "External Causes", "Eye and Adnexa", "Genitourinary", "Infections & Parasites", "Injury etc.", "Mental & Behavioral", "Musculoskeletal", "Neoplasms", "Nervous System", "Perinatal Period", "Pregancy, Childbirth, & Puerperium", "Respiratory", "Skin & Subcutaneaous tissue", "Special Purposes", "Symptoms, Signs etc.")
-c(-0.00521081730211856, 0.0102255609545677, -0.00496344785285301, -0.00412970481483706, -0.00482782618675194, -0.0050365287595942, -0.0244992731496998, -0.00474024131164134, -0.00556304034621756, -0.00514633902980756, 0.0549642831190738, -0.00505116955549756, 0.000222710855606745, -0.0139890440514832, -0.101150807225687, 0.00328213613579688, -0.00511716442489377, -0.00389750763874108, -0.00529064338687045, 0.00342256724316399, -0.00450674475013338, -0.00565678046765618)
-c(`2.5%` = -0.283907488368931, `2.5%` = -0.264718520415862, `2.5%` = -0.281159012081347, `2.5%` = -0.28202830088485, `2.5%` = -0.284419420868419, `2.5%` = -0.281327857726233, `2.5%` = -0.301921658351706, `2.5%` = -0.281271371584173, `2.5%` = -0.284249194010694, `2.5%` = -0.284012477531593, `2.5%` = -0.210012739588992, `2.5%` = -0.283029586218827, `2.5%` = -0.27410283519672, `2.5%` = -0.290631236010586, `2.5%` = -0.392051441442553, `2.5%` = -0.267503827888536, `2.5%` = -0.281737736791382, `2.5%` = -0.279312077145091, 
-`2.5%` = -0.282292027611709, `2.5%` = -0.271858847048387, `2.5%` = -0.282095546296768, `2.5%` = -0.283135697264375)
-c(`97.5%` = 0.273419332183028, `97.5%` = 0.291348978934726, `97.5%` = 0.271017033043418, `97.5%` = 0.274111097548879, `97.5%` = 0.273436192936731, `97.5%` = 0.269026268053048, `97.5%` = 0.248170504583118, `97.5%` = 0.271591216677986, `97.5%` = 0.273523419916202, `97.5%` = 0.274995321113636, `97.5%` = 0.342573757255475, `97.5%` = 0.272937984720548, `97.5%` = 0.274132679138622, `97.5%` = 0.258354914663837, `97.5%` = 0.156606469826098, `97.5%` = 0.279853103150131, `97.5%` = 0.270902691342387, `97.5%` = 0.272104479124203, 
-`97.5%` = 0.273263017556272, `97.5%` = 0.279847543183877, `97.5%` = 0.272441175448396, `97.5%` = 0.274036307386916)
-c(`5%` = -0.233812893025361, `5%` = -0.217746444191205, `5%` = -0.233921233193929, `5%` = -0.232257851816202, `5%` = -0.233567219181413, `5%` = -0.233477104858465, `5%` = -0.252962421653837, `5%` = -0.232486743487047, `5%` = -0.235070814746299, `5%` = -0.234533692066961, `5%` = -0.167107728841027, `5%` = -0.234659301068703, `5%` = -0.226762629571076, `5%` = -0.243190415663175, `5%` = -0.337956677281885, `5%` = -0.221951335704386, `5%` = -0.233061969747887, `5%` = -0.230188221811804, `5%` = -0.234247825650107, 
-`5%` = -0.223218309293191, `5%` = -0.235479873959263, `5%` = -0.234291225207645)
-c(`95%` = 0.225018049213407, `95%` = 0.240749705129402, `95%` = 0.223576635602984, `95%` = 0.22490531538246, `95%` = 0.225150662214719, `95%` = 0.222530040783611, `95%` = 0.200572258529045, `95%` = 0.224085208533272, `95%` = 0.223765301903729, `95%` = 0.224205184960909, `95%` = 0.289724198406613, `95%` = 0.224221721966219, `95%` = 0.226948329518661, `95%` = 0.212010272021156, `95%` = 0.117095735429865, `95%` = 0.231832837318039, `95%` = 0.222364411332351, `95%` = 0.223927230144499, `95%` = 0.223829194578265, 
-`95%` = 0.231111983676153, `95%` = 0.225668354476114, `95%` = 0.223106259041378)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameters_by_group/group_table_10_Respiratory.tex

@@ -1,6 +0,0 @@
-c("Elapsed Duration", "asinh(Competitors USPDC)", "asinh(Generic Brands)", "asinh(High SDI)", "asinh(High-Medium SDI)", "asinh(Low SDI)", "asinh(Low-Medium SDI)", "asinh(Medium SDI)", "status_ANR", "status_EBI", "status_NYR", "status_Rec")
-c(-0.0494676291479126, 0.0175175823493799, -0.0519713531203428, -0.141092626419518, -0.100269478864353, -0.0483011770497731, -0.0706566951944514, -0.0903067809957733, -0.0545919114607711, -0.00242272398017638, -0.00529064338687045, 0.00672386515176627)
-c(`2.5%` = -0.353960823288628, `2.5%` = -0.319852685329391, `2.5%` = -0.530569224373654, `2.5%` = -0.422086178248832, `2.5%` = -0.35533612512543, `2.5%` = -0.30969751701722, `2.5%` = -0.328762771558244, `2.5%` = -0.347450401239575, `2.5%` = -0.34467924126698, `2.5%` = -0.271895651649722, `2.5%` = -0.282292027611709, `2.5%` = -0.264848607612733)
-c(`97.5%` = 0.256663885447249, `97.5%` = 0.341627016198812, `97.5%` = 0.416128814653975, `97.5%` = 0.122884801270876, `97.5%` = 0.140134372918192, `97.5%` = 0.193515113672737, `97.5%` = 0.167756086960966, `97.5%` = 0.148714819749431, `97.5%` = 0.239492781782234, `97.5%` = 0.270026733830649, `97.5%` = 0.273263017556272, `97.5%` = 0.280170359985892)
-c(`5%` = -0.29885389568916, `5%` = -0.256280286172, `5%` = -0.443110847973097, `5%` = -0.3719291117473, `5%` = -0.309480163754538, `5%` = -0.2632490885577, `5%` = -0.281813066410411, `5%` = -0.302200597441508, `5%` = -0.294475437187543, `5%` = -0.224288571128251, `5%` = -0.234247825650107, `5%` = -0.21829426001738)
-c(`95%` = 0.201106127451977, `95%` = 0.285527407612361, `95%` = 0.335218886894626, `95%` = 0.0802166258592332, `95%` = 0.100605252625849, `95%` = 0.155768362847512, `95%` = 0.129300525656481, `95%` = 0.109558120218469, `95%` = 0.188021330440522, `95%` = 0.222159099161132, `95%` = 0.223829194578265, `95%` = 0.232756864140852)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameters_by_group/group_table_11_Digestive.tex

@@ -1,6 +0,0 @@
-c("Elapsed Duration", "asinh(Competitors USPDC)", "asinh(Generic Brands)", "asinh(High SDI)", "asinh(High-Medium SDI)", "asinh(Low SDI)", "asinh(Low-Medium SDI)", "asinh(Medium SDI)", "status_ANR", "status_EBI", "status_NYR", "status_Rec")
-c(-0.0505967062178304, 0.01865599931714, -0.0431305204973958, -0.164813949931452, -0.115970648900297, -0.0569474070992618, -0.0803009641524095, -0.102290027233277, -0.0546326964547788, -0.00233302952373521, -0.00482782618675194, 0.00511136013511625)
-c(`2.5%` = -0.355213104294602, `2.5%` = -0.321047087440019, `2.5%` = -0.521537560181517, `2.5%` = -0.440159920047502, `2.5%` = -0.373679807524352, `2.5%` = -0.324379242419328, `2.5%` = -0.338605161726642, `2.5%` = -0.358079997022996, `2.5%` = -0.347086498849369, `2.5%` = -0.27286212768348, `2.5%` = -0.284419420868419, `2.5%` = -0.267223017905891)
-c(`97.5%` = 0.256220116158008, `97.5%` = 0.349024698020337, `97.5%` = 0.429980507934071, `97.5%` = 0.0934098582169743, `97.5%` = 0.122782511673881, `97.5%` = 0.187764012771118, `97.5%` = 0.163449179706992, `97.5%` = 0.135463410274458, `97.5%` = 0.23894631939739, `97.5%` = 0.271595831106391, `97.5%` = 0.273436192936731, `97.5%` = 0.274044451638933)
-c(`5%` = -0.300950367218894, `5%` = -0.25489751531943, `5%` = -0.43620401741364, `5%` = -0.392282017795443, `5%` = -0.327592131875321, `5%` = -0.276552341418244, `5%` = -0.293674641980593, `5%` = -0.312900506044298, `5%` = -0.296193852536529, `5%` = -0.226336678780408, `5%` = -0.233567219181413, `5%` = -0.220927862811969)
-c(`95%` = 0.202603902019158, `95%` = 0.291325959161563, `95%` = 0.346576238409847, `95%` = 0.053045778552792, `95%` = 0.0838312787329803, `95%` = 0.149008753739683, `95%` = 0.122846563348083, `95%` = 0.0964502516045677, `95%` = 0.18656668417393, `95%` = 0.222289991457749, `95%` = 0.225150662214719, `95%` = 0.228526975656424)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameters_by_group/group_table_12_Skin & Subcutaneaous tissue.tex

@@ -1,6 +0,0 @@
-c("Elapsed Duration", "asinh(Competitors USPDC)", "asinh(Generic Brands)", "asinh(High SDI)", "asinh(High-Medium SDI)", "asinh(Low SDI)", "asinh(Low-Medium SDI)", "asinh(Medium SDI)", "status_ANR", "status_EBI", "status_NYR", "status_Rec")
-c(-0.0931186973375372, 0.0472688930727053, -0.0813059076860515, -0.115696459653843, -0.0668043254017594, 0.0225267378773846, -0.00783924736360468, -0.0287628443176525, -0.0809466615050335, -0.00267620974013439, 0.00342256724316399, 0.0229027326955782)
-c(`2.5%` = -0.398212841275992, `2.5%` = -0.276270824232982, `2.5%` = -0.560352091813988, `2.5%` = -0.369871784607321, `2.5%` = -0.303609657008891, `2.5%` = -0.217526831000879, `2.5%` = -0.243184811863137, `2.5%` = -0.259649581484174, `2.5%` = -0.37464941870207, `2.5%` = -0.274439135854432, `2.5%` = -0.271858847048387, `2.5%` = -0.243262927814473)
-c(`97.5%` = 0.195728293212208, `97.5%` = 0.376205200194986, `97.5%` = 0.375467600073314, `97.5%` = 0.133967945394652, `97.5%` = 0.165983963699542, `97.5%` = 0.265350540741357, `97.5%` = 0.230601337710681, `97.5%` = 0.207050118076093, `97.5%` = 0.204585540113804, `97.5%` = 0.267892275489918, `97.5%` = 0.279847543183877, `97.5%` = 0.296090615801029)
-c(`5%` = -0.341186799958823, `5%` = -0.217436243551559, `5%` = -0.472054693822914, `5%` = -0.32668730633076, `5%` = -0.26256729924706, `5%` = -0.178033167408505, `5%` = -0.204261113664472, `5%` = -0.222392523721118, `5%` = -0.322719512364534, `5%` = -0.227590395464131, `5%` = -0.223218309293191, `5%` = -0.197184265526973)
-c(`95%` = 0.145913702571692, `95%` = 0.317952486884081, `95%` = 0.30207955992225, `95%` = 0.093183366481975, `95%` = 0.125927251547133, `95%` = 0.224177921805955, `95%` = 0.189346878001297, `95%` = 0.165962633366688, `95%` = 0.155090212003947, `95%` = 0.220911069519647, `95%` = 0.231111983676153, `95%` = 0.246925692056239)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameters_by_group/group_table_13_Musculoskeletal.tex

@@ -1,6 +0,0 @@
-c("Elapsed Duration", "asinh(Competitors USPDC)", "asinh(Generic Brands)", "asinh(High SDI)", "asinh(High-Medium SDI)", "asinh(Low SDI)", "asinh(Low-Medium SDI)", "asinh(Medium SDI)", "status_ANR", "status_EBI", "status_NYR", "status_Rec")
-c(-0.016726156695298, -0.0761301686125453, 0.173176112299651, -0.0875007238905653, -0.0663531879724985, 0.0263716192287277, -0.00242271539233981, -0.0381494869327325, -0.109295568325447, -0.00275503221432378, -0.0139890440514832, 0.0493113026890666)
-c(`2.5%` = -0.310459552529128, `2.5%` = -0.431037121901406, `2.5%` = -0.223573014616573, `2.5%` = -0.340476599617661, `2.5%` = -0.305174376069712, `2.5%` = -0.214602193292334, `2.5%` = -0.238403789666391, `2.5%` = -0.273459885159963, `2.5%` = -0.407252271853641, `2.5%` = -0.272259113214428, `2.5%` = -0.290631236010586, `2.5%` = -0.209178899422793)
-c(`97.5%` = 0.295751559042532, `97.5%` = 0.22676112069751, `97.5%` = 0.625146449622561, `97.5%` = 0.167253531302005, `97.5%` = 0.166163888071297, `97.5%` = 0.270408213531531, `97.5%` = 0.239032427936572, `97.5%` = 0.196051431168698, `97.5%` = 0.170699887327904, `97.5%` = 0.266631371530776, `97.5%` = 0.258354914663837, `97.5%` = 0.324504387608479)
-c(`5%` = -0.260408972551825, `5%` = -0.360056361494536, `5%` = -0.165197877092618, `5%` = -0.295749142104736, `5%` = -0.263170921158664, `5%` = -0.174300938748019, `5%` = -0.199357322617647, `5%` = -0.232838007090428, `5%` = -0.352532667961251, `5%` = -0.22530608055078, `5%` = -0.243190415663175, `5%` = -0.166101667860902)
-c(`95%` = 0.23786658788661, `95%` = 0.178465709918192, `95%` = 0.544725565756189, `95%` = 0.123888229912759, `95%` = 0.128681125268866, `95%` = 0.228097063420235, `95%` = 0.196129167554776, `95%` = 0.155695563618615, `95%` = 0.124477125901656, `95%` = 0.21899037055656, `95%` = 0.212010272021156, `95%` = 0.274559112084226)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameters_by_group/group_table_14_Genitourinary.tex

@@ -1,6 +0,0 @@
-c("Elapsed Duration", "asinh(Competitors USPDC)", "asinh(Generic Brands)", "asinh(High SDI)", "asinh(High-Medium SDI)", "asinh(Low SDI)", "asinh(Low-Medium SDI)", "asinh(Medium SDI)", "status_ANR", "status_EBI", "status_NYR", "status_Rec")
-c(-0.0478593490739956, 0.0120682740554864, -0.0567196164994895, -0.126233602235583, -0.0888817238478321, -0.0319840844510598, -0.055198586240614, -0.0772497283445443, -0.0541521176630153, -0.00310971192809426, -0.00514633902980756, 0.00869308015726206)
-c(`2.5%` = -0.348523219782961, `2.5%` = -0.325741416529682, `2.5%` = -0.537648621232678, `2.5%` = -0.408043017285209, `2.5%` = -0.343971909458341, `2.5%` = -0.293935837353889, `2.5%` = -0.316931983669652, `2.5%` = -0.333641043439836, `2.5%` = -0.343259904607912, `2.5%` = -0.270957011640022, `2.5%` = -0.284012477531593, `2.5%` = -0.263984097470059)
-c(`97.5%` = 0.258199105421347, `97.5%` = 0.337658598779989, `97.5%` = 0.413237173559078, `97.5%` = 0.141325836240884, `97.5%` = 0.154268857189929, `97.5%` = 0.215841474017224, `97.5%` = 0.188621888649733, `97.5%` = 0.163079486802808, `97.5%` = 0.237777766149638, `97.5%` = 0.266687930004995, `97.5%` = 0.274995321113636, `97.5%` = 0.279840596472466)
-c(`5%` = -0.297395770121559, `5%` = -0.263152155503003, `5%` = -0.450348871660559, `5%` = -0.357452526309299, `5%` = -0.298995454954135, `5%` = -0.246714915420225, `5%` = -0.268903804112122, `5%` = -0.285856831702031, `5%` = -0.2933097076324, `5%` = -0.224824888562106, `5%` = -0.234533692066961, `5%` = -0.215840640492215)
-c(`95%` = 0.203709821019864, `95%` = 0.278261424943046, `95%` = 0.329135185773538, `95%` = 0.0975164848465818, `95%` = 0.11201114117772, `95%` = 0.174468036775523, `95%` = 0.148448833659993, `95%` = 0.122321755852338, `95%` = 0.188406047073467, `95%` = 0.218989193656767, `95%` = 0.224205184960909, `95%` = 0.230966741806046)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameters_by_group/group_table_17_Congential.tex

@@ -1,6 +0,0 @@
-c("Elapsed Duration", "asinh(Competitors USPDC)", "asinh(Generic Brands)", "asinh(High SDI)", "asinh(High-Medium SDI)", "asinh(Low SDI)", "asinh(Low-Medium SDI)", "asinh(Medium SDI)", "status_ANR", "status_EBI", "status_NYR", "status_Rec")
-c(-0.0499660268658585, 0.0197148498472504, -0.0421991751741288, -0.13476563953491, -0.0956058294147287, -0.0442534026160268, -0.0662861597218824, -0.0865335314057803, -0.0550797452225853, -0.00252250078632693, -0.00496344785285301, 0.00806097077518296)
-c(`2.5%` = -0.350165746673952, `2.5%` = -0.317756875891385, `2.5%` = -0.518375863151681, `2.5%` = -0.414723657705109, `2.5%` = -0.35057979600666, `2.5%` = -0.306304745881982, `2.5%` = -0.323256686118706, `2.5%` = -0.342841852065351, `2.5%` = -0.345063660691308, `2.5%` = -0.272430725186905, `2.5%` = -0.281159012081347, `2.5%` = -0.262583809560454)
-c(`97.5%` = 0.252568610015387, `97.5%` = 0.349107813430285, `97.5%` = 0.439646865645069, `97.5%` = 0.129542894513277, `97.5%` = 0.145184905982789, `97.5%` = 0.197603443786488, `97.5%` = 0.173229891076501, `97.5%` = 0.153760033992607, `97.5%` = 0.236924146027621, `97.5%` = 0.263988376114375, `97.5%` = 0.271017033043418, `97.5%` = 0.279367210952163)
-c(`5%` = -0.298500654906565, `5%` = -0.257137304097466, `5%` = -0.434007392588596, `5%` = -0.363849520269935, `5%` = -0.30377336167253, `5%` = -0.259427189054046, `5%` = -0.277378887591161, `5%` = -0.29778671716257, `5%` = -0.294243091294835, `5%` = -0.225155935562034, `5%` = -0.233921233193929, `5%` = -0.215580888141684)
-c(`95%` = 0.20049984396355, `95%` = 0.289287710051617, `95%` = 0.353130963560884, `95%` = 0.0859110309743907, `95%` = 0.105692185919512, `95%` = 0.15909647715405, `95%` = 0.13405804651131, `95%` = 0.114598752695363, `95%` = 0.18316007227917, `95%` = 0.218357594565282, `95%` = 0.223576635602984, `95%` = 0.232261579219567)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameters_by_group/group_table_18_Symptoms, Signs etc..tex

@@ -1,6 +0,0 @@
-c("Elapsed Duration", "asinh(Competitors USPDC)", "asinh(Generic Brands)", "asinh(High SDI)", "asinh(High-Medium SDI)", "asinh(Low SDI)", "asinh(Low-Medium SDI)", "asinh(Medium SDI)", "status_ANR", "status_EBI", "status_NYR", "status_Rec")
-c(-0.0486654863146441, 0.0236727211994869, -0.0348374667962509, -0.115895916505032, -0.0800513158310921, -0.023475914516512, -0.0466582461817656, -0.0684715865431922, -0.0537090394695628, -0.00206395314166231, -0.00565678046765618, 0.00840626979762671)
-c(`2.5%` = -0.352062830672535, `2.5%` = -0.311752202314792, `2.5%` = -0.516492014350377, `2.5%` = -0.394971716793324, `2.5%` = -0.333434811543346, `2.5%` = -0.286384363759695, `2.5%` = -0.304309764526848, `2.5%` = -0.325218632099741, `2.5%` = -0.34255968704254, `2.5%` = -0.274505781494588, `2.5%` = -0.283135697264375, `2.5%` = -0.260710033426863)
-c(`97.5%` = 0.257403541589351, `97.5%` = 0.352180233725197, `97.5%` = 0.445072841208461, `97.5%` = 0.154546638365113, `97.5%` = 0.162204869037247, `97.5%` = 0.222312513558577, `97.5%` = 0.200387773947608, `97.5%` = 0.175953830420771, `97.5%` = 0.240534823211121, `97.5%` = 0.271501986023693, `97.5%` = 0.274036307386916, `97.5%` = 0.276519814652463)
-c(`5%` = -0.297336353504652, `5%` = -0.250885342909289, `5%` = -0.430050287469576, `5%` = -0.345255477437627, `5%` = -0.288017242271703, `5%` = -0.239293183426376, `5%` = -0.258607586912473, `5%` = -0.280518378138114, `5%` = -0.291661527567577, `5%` = -0.227689137616937, `5%` = -0.234291225207645, `5%` = -0.21336683632312)
-c(`95%` = 0.202755710634796, `95%` = 0.292674820916317, `95%` = 0.360231402349028, `95%` = 0.109134691618903, `95%` = 0.123319005948664, `95%` = 0.182494091485978, `95%` = 0.158914432925447, `95%` = 0.135737605682531, `95%` = 0.187492448246279, `95%` = 0.223599356920508, `95%` = 0.223106259041378, `95%` = 0.230370019187908)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameters_by_group/group_table_1_Infections & Parasites.tex

@@ -1,6 +0,0 @@
-c("Elapsed Duration", "asinh(Competitors USPDC)", "asinh(Generic Brands)", "asinh(High SDI)", "asinh(High-Medium SDI)", "asinh(Low SDI)", "asinh(Low-Medium SDI)", "asinh(Medium SDI)", "status_ANR", "status_EBI", "status_NYR", "status_Rec")
-c(-0.0816317285457012, 0.117270560237318, -0.0431781674057524, -0.322939255980837, -0.0445097363713965, 0.0831185962473774, 0.054469735486804, 0.00439061656478571, -0.111933746601916, -0.00900529540694934, 0.0549642831190738, 0.0234704825434495)
-c(`2.5%` = -0.369067201876791, `2.5%` = -0.15743258849236, `2.5%` = -0.392971765289971, `2.5%` = -0.495385786097959, `2.5%` = -0.279907428049715, `2.5%` = -0.126136965980224, `2.5%` = -0.164686552393619, `2.5%` = -0.221766129169443, `2.5%` = -0.397011060181461, `2.5%` = -0.281051472827658, `2.5%` = -0.210012739588992, `2.5%` = -0.233328888684629)
-c(`97.5%` = 0.196240544658593, `97.5%` = 0.421101378052922, `97.5%` = 0.304781682760948, `97.5%` = -0.159810477185182, `97.5%` = 0.194502628737617, `97.5%` = 0.305301279386911, `97.5%` = 0.287025096307068, `97.5%` = 0.239372401831851, `97.5%` = 0.156402075952097, `97.5%` = 0.260632526818398, `97.5%` = 0.342573757255475, `97.5%` = 0.282219317765516)
-c(`5%` = -0.318536205133514, `5%` = -0.112232006084965, `5%` = -0.335854611911698, `5%` = -0.466181244375375, `5%` = -0.239813977632262, `5%` = -0.0931509430887361, `5%` = -0.13026348611388, `5%` = -0.18443291032113, `5%` = -0.347474604177594, `5%` = -0.232874112114568, `5%` = -0.167107728841027, `5%` = -0.190195428873606)
-c(`95%` = 0.149606773044668, `95%` = 0.365441233493439, `95%` = 0.24519101313148, `95%` = -0.184792569485545, `95%` = 0.15345194844924, `95%` = 0.266763338434242, `95%` = 0.246022644974912, `95%` = 0.199837947046417, `95%` = 0.112535221760718, `95%` = 0.213804656879867, `95%` = 0.289724198406613, `95%` = 0.237452575327)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameters_by_group/group_table_2_Neoplasms.tex

@@ -1,6 +0,0 @@
-c("Elapsed Duration", "asinh(Competitors USPDC)", "asinh(Generic Brands)", "asinh(High SDI)", "asinh(High-Medium SDI)", "asinh(Low SDI)", "asinh(Low-Medium SDI)", "asinh(Medium SDI)", "status_ANR", "status_EBI", "status_NYR", "status_Rec")
-c(-0.315526037006588, 0.14948178706425, -0.745438348426778, 0.0393966359152392, -0.0457348007757995, 0.064106280747042, -0.0140917847275379, -0.0473660509007094, -0.242704066590673, -0.00295173909211749, -0.101150807225687, -0.0318651891745962)
-c(`2.5%` = -0.642054194627079, `2.5%` = -0.095511016993371, `2.5%` = -1.12441685579914, `2.5%` = -0.194160502625767, `2.5%` = -0.277926578990489, `2.5%` = -0.162654732653132, `2.5%` = -0.246821463107613, `2.5%` = -0.281736932939805, `2.5%` = -0.543673509898535, `2.5%` = -0.271867873121147, `2.5%` = -0.392051441442553, `2.5%` = -0.272496159194591)
-c(`97.5%` = -0.0498087194116947, `97.5%` = 0.422731018753381, `97.5%` = -0.396240166662077, `97.5%` = 0.291104489058118, `97.5%` = 0.186629528620266, `97.5%` = 0.30340806969423, `97.5%` = 0.218889942875867, `97.5%` = 0.182247266485996, `97.5%` = 0.0114150292406248, `97.5%` = 0.265171319133342, `97.5%` = 0.156606469826098, `97.5%` = 0.198395249398707)
-c(`5%` = -0.580798660746861, `5%` = -0.0582870053082083, `5%` = -1.05984134753029, `5%` = -0.157477096682293, `5%` = -0.237601446017153, `5%` = -0.12601793998578, `5%` = -0.207070786292008, `5%` = -0.242358894302708, `5%` = -0.488379411138948, `5%` = -0.226179910621409, `5%` = -0.337956677281885, `5%` = -0.228981038446028)
-c(`95%` = -0.0876108144400803, `95%` = 0.373392398003416, `95%` = -0.449885315105183, `95%` = 0.246925701935553, `95%` = 0.146465971010273, `95%` = 0.261260827352338, `95%` = 0.178110810416068, `95%` = 0.144856415039965, `95%` = -0.0267022930175043, `95%` = 0.218796743068272, `95%` = 0.117095735429865, `95%` = 0.161143364484194)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameters_by_group/group_table_3_Blood & Immune system.tex

@@ -1,6 +0,0 @@
-c("Elapsed Duration", "asinh(Competitors USPDC)", "asinh(Generic Brands)", "asinh(High SDI)", "asinh(High-Medium SDI)", "asinh(Low SDI)", "asinh(Low-Medium SDI)", "asinh(Medium SDI)", "status_ANR", "status_EBI", "status_NYR", "status_Rec")
-c(-0.0505321895701756, 0.0177091826256191, -0.0374509867623648, -0.125776066126894, -0.0902292099576031, -0.036944329702934, -0.0591309519669422, -0.0793088083304893, -0.0543082831893662, -0.00287140656905416, -0.00521081730211856, 0.00652882287222823)
-c(`2.5%` = -0.351333711658477, `2.5%` = -0.321412408332877, `2.5%` = -0.519252573751591, `2.5%` = -0.406597880159647, `2.5%` = -0.344254022808293, `2.5%` = -0.297343859139922, `2.5%` = -0.315544785108668, `2.5%` = -0.331413856081863, `2.5%` = -0.3460926221197, `2.5%` = -0.275944463803495, `2.5%` = -0.283907488368931, `2.5%` = -0.26412401679988)
-c(`97.5%` = 0.252996678658013, `97.5%` = 0.343837322664501, `97.5%` = 0.438156824615533, `97.5%` = 0.142015362351499, `97.5%` = 0.154012266834766, `97.5%` = 0.207443984276725, `97.5%` = 0.181870296298027, `97.5%` = 0.158756949640892, `97.5%` = 0.23859370882391, `97.5%` = 0.268525663885088, `97.5%` = 0.273419332183028, `97.5%` = 0.279506924359323)
-c(`5%` = -0.29803422118825, `5%` = -0.25720973558682, `5%` = -0.43284681982114, `5%` = -0.356137939234695, `5%` = -0.299115224405783, `5%` = -0.252322537371494, `5%` = -0.269748806995291, `5%` = -0.286403912298463, `5%` = -0.295316756003101, `5%` = -0.228422342352796, `5%` = -0.233812893025361, `5%` = -0.217405377189081)
-c(`95%` = 0.199805705380915, `95%` = 0.285370104912777, `95%` = 0.353300713490598, `95%` = 0.0994967769999591, `95%` = 0.113509581613765, `95%` = 0.167490802315082, `95%` = 0.14240768840267, `95%` = 0.120221139002118, `95%` = 0.186170625673217, `95%` = 0.2234974899362, `95%` = 0.225018049213407, `95%` = 0.231060746721114)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameters_by_group/group_table_4_Endocrine, Nutritional, and Metabolic.tex

@@ -1,6 +0,0 @@
-c("Elapsed Duration", "asinh(Competitors USPDC)", "asinh(Generic Brands)", "asinh(High SDI)", "asinh(High-Medium SDI)", "asinh(Low SDI)", "asinh(Low-Medium SDI)", "asinh(Medium SDI)", "status_ANR", "status_EBI", "status_NYR", "status_Rec")
-c(-0.0585983827703775, -0.0557624513358899, -0.147540114797909, -0.0438548071229014, -0.0394212013879011, 0.0495779683778335, -0.000453054277997355, -0.0472027857512424, -0.101183732558573, -0.00681543732790809, -0.0244992731496998, 0.0756452851959799)
-c(`2.5%` = -0.356636178298712, `2.5%` = -0.406584875693101, `2.5%` = -0.605455988019874, `2.5%` = -0.295750042124458, `2.5%` = -0.273112681569153, `2.5%` = -0.186331398654033, `2.5%` = -0.236827961184312, `2.5%` = -0.283031319821082, `2.5%` = -0.402573667581036, `2.5%` = -0.277987677303119, `2.5%` = -0.301921658351706, `2.5%` = -0.182738362310984)
-c(`97.5%` = 0.237496943950342, `97.5%` = 0.249517798279291, `97.5%` = 0.271710367913333, `97.5%` = 0.217593297859276, `97.5%` = 0.19504307737622, `97.5%` = 0.294769414462677, `97.5%` = 0.239952858853215, `97.5%` = 0.184326204801509, `97.5%` = 0.180340815442861, `97.5%` = 0.26497995981819, `97.5%` = 0.248170504583118, `97.5%` = 0.359198759844572)
-c(`5%` = -0.304028644400323, `5%` = -0.339933290032092, `5%` = -0.520616290327113, `5%` = -0.254196188061864, `5%` = -0.232559443411886, `5%` = -0.147666860670196, `5%` = -0.197308104756834, `5%` = -0.242030280687931, `5%` = -0.347024621453625, `5%` = -0.230488468962024, `5%` = -0.252962421653837, `5%` = -0.139947007794807)
-c(`95%` = 0.187816936293634, `95%` = 0.200063580704579, `95%` = 0.20347262465658, `95%` = 0.173544980297132, `95%` = 0.155038635197841, `95%` = 0.25235933990905, `95%` = 0.196860730183825, `95%` = 0.146126493852613, `95%` = 0.133329444707804, `95%` = 0.216270931014924, `95%` = 0.200572258529045, `95%` = 0.306122759153545)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameters_by_group/group_table_5_Mental & Behavioral.tex

@@ -1,6 +0,0 @@
-c("Elapsed Duration", "asinh(Competitors USPDC)", "asinh(Generic Brands)", "asinh(High SDI)", "asinh(High-Medium SDI)", "asinh(Low SDI)", "asinh(Low-Medium SDI)", "asinh(Medium SDI)", "status_ANR", "status_EBI", "status_NYR", "status_Rec")
-c(-0.0774004055701482, 0.0202098736769506, -0.148857275259831, -0.034756624929762, -0.0209198662802634, 0.0737245631655913, 0.0355843232922172, -0.0257770506361907, -0.101358093383466, -0.00444905498743218, 0.000222710855606745, 0.0410008650026277)
-c(`2.5%` = -0.384222770661754, `2.5%` = -0.317021340734379, `2.5%` = -0.654106115127152, `2.5%` = -0.28447613031784, `2.5%` = -0.251665449535869, `2.5%` = -0.161795305781745, `2.5%` = -0.197888724987928, `2.5%` = -0.256373204834308, `2.5%` = -0.398857333530158, `2.5%` = -0.273927630545993, `2.5%` = -0.27410283519672, `2.5%` = -0.219982381931615)
-c(`97.5%` = 0.218570279154564, `97.5%` = 0.350403071909054, `97.5%` = 0.307321465786219, `97.5%` = 0.226059193399154, `97.5%` = 0.218536405219445, `97.5%` = 0.325200306839703, `97.5%` = 0.279312654411686, `97.5%` = 0.207355980521146, `97.5%` = 0.182559370226462, `97.5%` = 0.264287404395679, `97.5%` = 0.274132679138622, `97.5%` = 0.3146382824935)
-c(`5%` = -0.328832973524529, `5%` = -0.255886271822305, `5%` = -0.55799947646926, `5%` = -0.243764242401936, `5%` = -0.214018963569841, `5%` = -0.12427108412664, `5%` = -0.159713441998239, `5%` = -0.217062488812283, `5%` = -0.344628024841975, `5%` = -0.227858560023144, `5%` = -0.226762629571076, `5%` = -0.175242262948575)
-c(`95%` = 0.168803960348435, `95%` = 0.290718931165702, `95%` = 0.231568717349548, `95%` = 0.181638021717836, `95%` = 0.175300930108115, `95%` = 0.280768005851167, `95%` = 0.236582791839493, `95%` = 0.16844496482049, `95%` = 0.132004530075709, `95%` = 0.220133939553423, `95%` = 0.226948329518661, `95%` = 0.264306220644107)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameters_by_group/group_table_6_Nervous System.tex

@@ -1,6 +0,0 @@
-c("Elapsed Duration", "asinh(Competitors USPDC)", "asinh(Generic Brands)", "asinh(High SDI)", "asinh(High-Medium SDI)", "asinh(Low SDI)", "asinh(Low-Medium SDI)", "asinh(Medium SDI)", "status_ANR", "status_EBI", "status_NYR", "status_Rec")
-c(-0.0578472700681722, 0.363548114620147, 0.514928808041493, -0.179789393683086, -0.0908978444606774, 0.0485959237871361, -0.00145174053575294, -0.0416302406262986, -0.0324576251191776, -0.00517241124667845, 0.00328213613579688, -0.0230137010884716)
-c(`2.5%` = -0.359167198818045, `2.5%` = 0.02041143019079, `2.5%` = 0.0216592886163218, `2.5%` = -0.430812731714158, `2.5%` = -0.333639714164675, `2.5%` = -0.181367177838171, `2.5%` = -0.231956837333007, `2.5%` = -0.27766810096831, `2.5%` = -0.315411836398564, `2.5%` = -0.275526164264352, `2.5%` = -0.267503827888536, `2.5%` = -0.293189864865698)
-c(`97.5%` = 0.238629751570793, `97.5%` = 0.85608235301133, `97.5%` = 1.17318649525454, `97.5%` = 0.0570528188192439, `97.5%` = 0.140764053180901, `97.5%` = 0.287579065151981, `97.5%` = 0.231839325930911, `97.5%` = 0.196383580001578, `97.5%` = 0.259944925352525, `97.5%` = 0.267696135908434, `97.5%` = 0.279853103150131, `97.5%` = 0.238015436387141)
-c(`5%` = -0.303098555574414, `5%` = 0.0634526303087552, `5%` = 0.0851401986791414, `5%` = -0.386505748941182, `5%` = -0.290084333457996, `5%` = -0.143728029163889, `5%` = -0.193940136889492, `5%` = -0.237273417600727, `5%` = -0.266550224886603, `5%` = -0.228284369418676, `5%` = -0.221951335704386, `5%` = -0.246615923137647)
-c(`95%` = 0.186931912303368, `95%` = 0.753336516739962, `95%` = 1.03873143227049, `95%` = 0.0190438837776769, `95%` = 0.102564973004199, `95%` = 0.243855515697918, `95%` = 0.193187180905901, `95%` = 0.155692997386599, `95%` = 0.205343484029368, `95%` = 0.220217569663176, `95%` = 0.231832837318039, `95%` = 0.195044859439803)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameters_by_group/group_table_7_Eye and Adnexa.tex

@@ -1,6 +0,0 @@
-c("Elapsed Duration", "asinh(Competitors USPDC)", "asinh(Generic Brands)", "asinh(High SDI)", "asinh(High-Medium SDI)", "asinh(Low SDI)", "asinh(Low-Medium SDI)", "asinh(Medium SDI)", "status_ANR", "status_EBI", "status_NYR", "status_Rec")
-c(-0.0507912436647474, 0.0105781672515, -0.0572148794918185, -0.161324485000642, -0.11718865552377, -0.0580549952623519, -0.0821974616540054, -0.105025588883719, -0.055296341966815, -0.00219896995482389, -0.00556304034621756, 0.00596509106734287)
-c(`2.5%` = -0.356770047469594, `2.5%` = -0.329787608837027, `2.5%` = -0.529409792355877, `2.5%` = -0.44209572260938, `2.5%` = -0.373553837099913, `2.5%` = -0.325433458075037, `2.5%` = -0.344635367302557, `2.5%` = -0.361334615741075, `2.5%` = -0.348019495991554, `2.5%` = -0.272173859797933, `2.5%` = -0.284249194010694, `2.5%` = -0.264838971088612)
-c(`97.5%` = 0.255694095814266, `97.5%` = 0.33508908205543, `97.5%` = 0.408657439741233, `97.5%` = 0.101657962161228, `97.5%` = 0.11864634098921, `97.5%` = 0.186079165001043, `97.5%` = 0.157815589258783, `97.5%` = 0.131395254082946, `97.5%` = 0.235175513197134, `97.5%` = 0.268729163024419, `97.5%` = 0.273523419916202, `97.5%` = 0.274146522142649)
-c(`5%` = -0.301053900765771, `5%` = -0.263620928816618, `5%` = -0.445215274649135, `5%` = -0.391137998579351, `5%` = -0.328258365252273, `5%` = -0.276463334286846, `5%` = -0.297022738992198, `5%` = -0.315922917337871, `5%` = -0.297136938616546, `5%` = -0.224813386072165, `5%` = -0.235070814746299, `5%` = -0.216692707544591)
-c(`95%` = 0.200369696005793, `95%` = 0.27722780854366, `95%` = 0.328590570058774, `95%` = 0.0578686050827066, `95%` = 0.0817009261712685, `95%` = 0.147963763976249, `95%` = 0.119977584917821, `95%` = 0.0949818456263718, `95%` = 0.186846293810823, `95%` = 0.221009192368411, `95%` = 0.223765301903729, `95%` = 0.226800701259279)

r-analysis/output/EffectsOfEnrollmentDelay/betas/parameters_by_group/group_table_9_Circulatory.tex

@@ -1,6 +0,0 @@
-c("Elapsed Duration", "asinh(Competitors USPDC)", "asinh(Generic Brands)", "asinh(High SDI)", "asinh(High-Medium SDI)", "asinh(Low SDI)", "asinh(Low-Medium SDI)", "asinh(Medium SDI)", "status_ANR", "status_EBI", "status_NYR", "status_Rec")
-c(-0.0561236542390722, -0.0174830982131017, -0.114801759701441, -0.0489532404314588, -0.00995833322809683, 0.0764993233097176, 0.0602798840227049, 0.0304789175922322, -0.0491179148659016, -0.0020229135961933, 0.0102255609545677, -0.0121276026193075)
-c(`2.5%` = -0.358192918691032, `2.5%` = -0.360033194654434, `2.5%` = -0.588446720987112, `2.5%` = -0.297868077807792, `2.5%` = -0.240899712415657, `2.5%` = -0.162465078674946, `2.5%` = -0.17414438609744, `2.5%` = -0.201017363333911, `2.5%` = -0.340513734259116, `2.5%` = -0.272921161056328, `2.5%` = -0.264718520415862, `2.5%` = -0.284982548735974)
-c(`97.5%` = 0.245199739323497, `97.5%` = 0.295622079182328, `97.5%` = 0.326892147498506, `97.5%` = 0.210710410280741, `97.5%` = 0.229119750480018, `97.5%` = 0.332077723102122, `97.5%` = 0.312602029054938, `97.5%` = 0.277230334088767, `97.5%` = 0.247596369898235, `97.5%` = 0.269687555821123, `97.5%` = 0.291348978934726, `97.5%` = 0.25166727687992)
-c(`5%` = -0.304624731177692, `5%` = -0.294903363605129, `5%` = -0.498779889626974, `5%` = -0.256277233535303, `5%` = -0.202637633223219, `5%` = -0.125070759586198, `5%` = -0.13517180498734, `5%` = -0.163740873087956, `5%` = -0.29096401042673, `5%` = -0.225192615705392, `5%` = -0.217746444191205, `5%` = -0.235700053008877)
-c(`95%` = 0.193775727317953, `95%` = 0.243010994205006, `95%` = 0.251902327224973, `95%` = 0.165019140778464, `95%` = 0.188705917246998, `95%` = 0.287176225295342, `95%` = 0.267926957380469, `95%` = 0.233147083774771, `95%` = 0.194446427538144, `95%` = 0.222074828728455, `95%` = 0.240749705129402, `95%` = 0.206639994505824)

r-analysis/output/EffectsOfEnrollmentDelay/distdiff_5percentile_table.tex

@@ -1,33 +0,0 @@
-% latex table generated in R 4.4.2 by xtable 1.8-4 package
-% Sun Feb  2 01:37:17 2025
-\begin{table}[ht]
-\centering
-\begin{tabular}{r}
-  \hline
-Value \\ 
-  \hline
--0.226 \\ 
-  -0.013 \\ 
-  -0.005 \\ 
-  -0.001 \\ 
-  -0.000 \\ 
-  0.000 \\ 
-  0.000 \\ 
-  0.002 \\ 
-  0.005 \\ 
-  0.008 \\ 
-  0.011 \\ 
-  0.014 \\ 
-  0.018 \\ 
-  0.022 \\ 
-  0.027 \\ 
-  0.032 \\ 
-  0.039 \\ 
-  0.047 \\ 
-  0.057 \\ 
-  0.073 \\ 
-  0.272 \\ 
-   \hline
-\end{tabular}
-\end{table}
-