From 2802ace9efde63335878c4868296845f03ab0bdb Mon Sep 17 00:00:00 2001
From: Alexander Christensen <alexpaulchristensen@gmail.com>
Date: Thu, 11 Jul 2024 12:39:20 -0500
Subject: [PATCH] Update network.compare.R

---
 R/network.compare.R | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/R/network.compare.R b/R/network.compare.R
index f9c0419c..54249717 100644
--- a/R/network.compare.R
+++ b/R/network.compare.R
@@ -246,12 +246,13 @@ network.compare <- function(
   return(
     t(data.frame(
       "statistic" = empirical_values,
-      "p.value" = colMeans(
-        sweep(
-          x = abs(permutated_values), MARGIN = 2,
-          STATS = empirical_values, FUN = ">="
-        ), na.rm = TRUE
-      )
+      "p.value" = c(
+        mean(permutated_values[,1] <= empirical_values[1]),
+        mean(permutated_values[,2] <= empirical_values[2]),
+        mean(abs(permutated_values[,3]) >= empirical_values[3])
+      ),
+      "M_permutated" = colMeans(permutated_values),
+      "SD_permutated" = apply(permutated_values, 2, sd)
     ))
   )