diff --git a/99_HIDDEN_functions.R b/99_HIDDEN_functions.R
index 774927d4f07aa31d9a0c9989ad7a38580d881d15..45e59b9064e30d066e3847b004502770a21396f2 100644
--- a/99_HIDDEN_functions.R
+++ b/99_HIDDEN_functions.R
@@ -124,7 +124,7 @@ get.corXE <- function(comm, traits, envir, trait.sel="all", env.sel="all", stat=
 #perm.df = df traitCombination X permutations with the chosen statistic of correlation on permuteda data
 
 get.SES <- function(obs.df, perm.df, stat="RV") {
-  nperm <- dim(perm.df)[2]
+  #nperm <- dim(perm.df)[2]
   SES.out <- as.data.frame.table(perm.df) %>% 
     rename(Trait.comb=Var1, perm=Var2, coef=Freq ) %>% 
     group_by(Trait.comb) %>% 
@@ -134,12 +134,15 @@ get.SES <- function(obs.df, perm.df, stat="RV") {
                 mutate(Trait.comb=paste0("t", Trait.comb)) %>% 
                 rename(obs=Coef), 
               by=c("Trait.comb")) %>% 
-    summarize(q15 = quantile(coef, probs = 0.15865), 
+    summarize(q025 = quantile(coef, probs = 0.025), 
+              q15 = quantile(coef, probs = 0.15865), 
               q50 = quantile(coef, .5),
-              q84 = quantile(coef, 0.84135), 
+              q84 = quantile(coef, 0.84135),
+              q975 = quantile(coef, 0.975),
               mean.perm=mean(coef),
-              sd.perm=sd(coef), 
-              greater.than.obs=sum( (abs(coef)>=abs(obs))/n())) %>% 
+              sd.perm = sd(coef), 
+              greater.than.obs = sum( coef >= obs )/n(), 
+              smaller.than.obs = sum( coef <= obs )/n()) %>% 
     left_join(obs.df %>% 
                 filter(Test==stat) %>% 
                 dplyr::select(-pvalue, -Test) %>% 
@@ -149,10 +152,11 @@ get.SES <- function(obs.df, perm.df, stat="RV") {
     mutate(SES.np= ifelse(obs>=q50, (obs-q50)/(q84-q50), (obs-q50)/(q50-q15))) %>%
     mutate(SES=(obs-mean.perm)/sd.perm) %>% 
     arrange(desc(SES.np)) %>% 
-    mutate(conf.m=obs-1.65*(sd.perm/sqrt(nperm))) %>% 
-    mutate(conf.p=obs+1.65*(sd.perm/sqrt(nperm)))
+    mutate(conf.m=mean.perm - 1.96*(sd.perm)) %>% #/sqrt(nperm))) %>% 
+    mutate(conf.p=mean.perm + 1.96*(sd.perm)) #/sqrt(nperm)))
   return(SES.out)
 }
 
 
 
+