updating table output

r-analysis/EffectsOfEnrollmentDelay.qmd

@@ -1083,7 +1083,7 @@ The simulation above shows that this results in a percentage-point change in ter
 #Get dataframe with only the rows of interest
 filtdata <- as.data.frame(extract(fit, pars="status_diff"))
 #rename columns
-dimnames(filtdata)[[2]] <- beta_list$groups
+dimnames(filtdata)[[2]] <- sprintf("%02d %s", seq_along(beta_list$groups), 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", 
@@ -1092,9 +1092,10 @@ mcmc_areas(filtdata,prob = 0.8, prob_outer = 0.95) +
     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()) |> 
+fixed_effects_table <- pivot_longer(filtdata, everything()) |> 
     group_by(name) |> 
     summarize(
+        `sample size` = 0,
         mean = mean(value),
         `P(≥0)` = mean(value >= 0),
         `2.5%` = quantile(value, probs = 0.025),
@@ -1106,18 +1107,26 @@ d <- pivot_longer(filtdata, everything()) |>
         `97.5%` = quantile(value, probs = 0.975)
     )
 
+# Convert the indexing to be consecutive by using a temporary vector
+sample_sizes <- rep(0, 22)  # Create vector of zeros
+sample_sizes[category_count$category_id] <- category_count$n
+
+# Now assign the whole vector at once
+fixed_effects_table["sample size"] <- sample_sizes
 # Rename the name column
-names(d)[1] <- "ICD-10 Category"
+names(fixed_effects_table)[1] <- "ICD-10 Category"
 
 # Convert to LaTeX
-table <- xtable(d,
-    digits = rep(3, ncol(d) + 1),
+table <- xtable(fixed_effects_table,
+    digits = rep(3, ncol(fixed_effects_table) + 1),
     floating = FALSE,
-    latex.environments = NULL,
+    align = "lccccccccccc",
+    latex.environments = "tabularx",
     booktabs = TRUE
 )
 
 
+
 # Write to file
 write_lines(
     print(table, include.rownames = FALSE),

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

@@ -1,33 +1,33 @@
 % latex table generated in R 4.4.2 by xtable 1.8-4 package
-% Sun Feb  2 01:37:36 2025
+% Mon Feb  3 23:56:27 2025
 \begin{table}[ht]
 \centering
-\begin{tabular}{lrrrrrrrrr}
+\begin{tabular}{ccccccccccc}
   \hline
-ICD-10 Category & mean & P(≥0) & 2.5\% & 5\% & 25\% & 50\% median & 75\% & 95\% & 97.5\% \\ 
+ICD-10 Category & sample size & 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 \\ 
+01 Infections \& Parasites & 20.000 & 0.135 & 0.772 & -0.223 & -0.163 & 0.013 & 0.134 & 0.257 & 0.438 & 0.498 \\ 
+  02 Neoplasms & 49.000 & 0.211 & 0.902 & -0.107 & -0.056 & 0.099 & 0.208 & 0.320 & 0.489 & 0.546 \\ 
+  03 Blood \& Immune system & 1.000 & 0.061 & 0.624 & -0.333 & -0.267 & -0.071 & 0.061 & 0.194 & 0.388 & 0.454 \\ 
+  04 Endocrine, Nutritional, and Metabolic & 10.000 & 0.177 & 0.820 & -0.201 & -0.137 & 0.045 & 0.173 & 0.304 & 0.505 & 0.573 \\ 
+  05 Mental \& Behavioral & 8.000 & 0.142 & 0.767 & -0.239 & -0.175 & 0.010 & 0.140 & 0.270 & 0.469 & 0.537 \\ 
+  06 Nervous System & 8.000 & 0.009 & 0.524 & -0.383 & -0.315 & -0.120 & 0.011 & 0.140 & 0.327 & 0.389 \\ 
+  07 Eye and Adnexa & 11.000 & 0.061 & 0.624 & -0.333 & -0.265 & -0.069 & 0.062 & 0.192 & 0.386 & 0.452 \\ 
+  08 Ear and Mastoid & 0.000 & 0.063 & 0.625 & -0.332 & -0.263 & -0.069 & 0.064 & 0.196 & 0.393 & 0.457 \\ 
+  09 Circulatory & 3.000 & 0.037 & 0.577 & -0.362 & -0.293 & -0.094 & 0.038 & 0.170 & 0.363 & 0.426 \\ 
+  10 Respiratory & 7.000 & 0.061 & 0.622 & -0.335 & -0.269 & -0.072 & 0.061 & 0.195 & 0.391 & 0.458 \\ 
+  11 Digestive & 12.000 & 0.060 & 0.621 & -0.339 & -0.270 & -0.071 & 0.059 & 0.192 & 0.388 & 0.454 \\ 
+  12 Skin \& Subcutaneaous tissue & 9.000 & 0.104 & 0.704 & -0.283 & -0.220 & -0.027 & 0.103 & 0.234 & 0.429 & 0.494 \\ 
+  13 Musculoskeletal & 17.000 & 0.159 & 0.794 & -0.218 & -0.156 & 0.027 & 0.156 & 0.286 & 0.482 & 0.550 \\ 
+  14 Genitourinary & 2.000 & 0.063 & 0.627 & -0.337 & -0.270 & -0.070 & 0.065 & 0.195 & 0.389 & 0.456 \\ 
+  15 Pregancy, Childbirth, \& Puerperium & 0.000 & 0.061 & 0.622 & -0.336 & -0.270 & -0.071 & 0.061 & 0.194 & 0.392 & 0.458 \\ 
+  16 Perinatal Period & 0.000 & 0.062 & 0.626 & -0.338 & -0.270 & -0.068 & 0.062 & 0.194 & 0.390 & 0.457 \\ 
+  17 Congential & 3.000 & 0.063 & 0.628 & -0.332 & -0.264 & -0.068 & 0.063 & 0.195 & 0.391 & 0.456 \\ 
+  18 Symptoms, Signs etc. & 1.000 & 0.062 & 0.625 & -0.332 & -0.265 & -0.069 & 0.062 & 0.194 & 0.390 & 0.456 \\ 
+  19 Injury etc. & 0.000 & 0.063 & 0.625 & -0.337 & -0.268 & -0.069 & 0.062 & 0.196 & 0.392 & 0.459 \\ 
+  20 External Causes & 0.000 & 0.063 & 0.625 & -0.330 & -0.266 & -0.070 & 0.064 & 0.194 & 0.392 & 0.460 \\ 
+  21 Contact with Healthcare & 0.000 & 0.063 & 0.627 & -0.335 & -0.267 & -0.070 & 0.064 & 0.194 & 0.390 & 0.454 \\ 
+  22 Special Purposes & 0.000 & 0.062 & 0.625 & -0.335 & -0.268 & -0.070 & 0.062 & 0.194 & 0.391 & 0.456 \\ 
    \hline
 \end{tabular}
 \end{table}