Added more info to printed output (#7)

R/permChacko.R

@@ -69,12 +69,18 @@ permChacko <- function(x, n_perm = 1000L, verbosity = 0) {
     table_p_value <- NA
   }
   if (verbosity >= 1L) message("\nTest statistics")
-  statistics <- c(
-    "chisq_bar" = chisq_bar,
-    "analytic_p-value" = anal_p_value,
-    "numeric_p-value" = perm_p_value,
-    "tabular_p-value" = table_p_value
+  p_values <- c(
+    "analytic" = anal_p_value,
+    "numeric" = perm_p_value,
+    "tabular" = table_p_value
   )
-  class(statistics) <- "chacko_test"
-  return(statistics)
+  out <- list(
+    statistic = chisq_bar,
+    p_values = p_values,
+    n_perm = n_perm,
+    observed_data = x,
+    reduced_data = x_t
+  )
+  class(out) <- "chacko_test"
+  return(out)
 }

R/print.R

@@ -1,9 +1,22 @@
 #' @export
 print.chacko_test <- function(x, ...) {
-  cat("Chacko test for order-restriction with permutation test\n\n")
-  cat("Test statistic (chisq_bar):",  x[["chisq_bar"]], "\n")
-  cat("p-values:\n")
-  cat("  Analytic p-value:        ", x[["analytic_p-value"]], "\n")
-  cat("  Numeric p-value:         ", x[["numeric_p-value"]], "\n")
-  cat("  Tabular p-value:         ", x[["tabular_p-value"]], "\n")
+  p_values <- x[["p_values"]]
+  cat(
+    sprintf(
+      paste0(
+        "          Chacko Test for Order-restriction with Permutation Test\n\n",
+        "Null hypothesis       : %s\n",
+        "Alternative hypothesis: %s\n\n",
+        "Test statistic (chisq_bar): %f\n",
+        "p-values:\n",
+        "  Analytic p-value:         %f\n",
+        "  Numeric p-value:          %f (%d permutations)\n",
+        "  Tabular p-value:          %f\n\n"
+      ),
+      paste0("p", seq_along(x$observed_data), collapse = " == "),
+      paste0("p", seq_along(x$observed_data), collapse = " <= "),
+      x[["statistic"]], p_values[["analytic"]],
+      p_values[["numeric"]], x[["n_perm"]], p_values[["tabular"]]
+    )
+  )
 }