diff --git a/confplotd.R b/confplotd.R
new file mode 100644
index 0000000..db68e4c
--- /dev/null
+++ b/confplotd.R
@@ -0,0 +1,31 @@
+# Requires plotrix library and split.file() output files.
+# See Burton-Kelly (2008) for complete documentation.
+confplotd <- function(path, pattern, vardis="Disparity", smoo=c(1:20), reps=1000, ext="-confplotd.txt", probs=c(0.025,0.975))
+    {
+    files<-list.files(path=path,pattern=pattern,full.names=TRUE);
+    for(i in files)
+        #Loop through files and assign variable names
+        {
+        x <- read.table(i,header=TRUE);
+        assign(i, x);
+        }
+    for(j in 1:length(files))
+        {
+        SOV <- get(files[j]);
+        bootSOV <- numeric(reps); #creates place for bootstrap values
+        for (k in 1:reps) {bootSOV[k] <- sum(diag(var(sample(SOV,replace=TRUE))))};
+        conf<-quantile(bootSOV,probs=probs);
+        toplot<-paste(smoo[j],mean(bootSOV),conf[2],conf[1]);
+        write.table(toplot,file=paste(substring(files[1],1, nchar(files[1])-4), ext, sep=""),quote=FALSE,append=TRUE, row.names=FALSE, col.names=FALSE)
+        }
+    tableback<-read.table(file=paste(substring(files[1],1,nchar(files[1])-4), ext, sep=""));
+    x<-unlist(tableback[1]);
+    y<-unlist(tableback[2]);
+    cui<-unlist(tableback[3]);
+    cli<-unlist(tableback[4]);
+    plotCI(x,y,ui=cui,li=cli,xlab=c("Smoothing"),ylab=vardis, ylim=c(0,0.025));
+    pdf(paste(substring(files[1],1,nchar(files[1])-4), ext, c(".pdf"), sep=""));
+    plotCI(x,y,ui=cui,li=cli,xlab=c("Smoothing"),ylab=vardis, ylim=c(0,0.025));
+    dev.off();
+    }
+
diff --git a/confplotv.R b/confplotv.R
new file mode 100644
index 0000000..7610d63
--- /dev/null
+++ b/confplotv.R
@@ -0,0 +1,31 @@
+# Requires plotrix library and split.file() output files.
+# See Burton-Kelly (2008) for complete documentation.
+confplotv <- function(path, pattern, vardis="Variation", smoo=c(1:20), reps=1000, ext="-confplotv.txt", probs=c(0.025,0.975))
+    {
+    files<-list.files(path=path,pattern=pattern,full.names=TRUE);
+    for(i in files)
+        #Loop through files and assign variable names
+        {
+        x <- read.table(i,header=TRUE,row.names=1);
+        assign(i, x);
+        }
+    for(j in 1:length(files))
+        {
+        SOV <- get(files[j]);
+        bootSOV <- numeric(reps); #creates place for bootstrap values
+        for (k in 1:reps) {bootSOV[k] <- sum(diag(var(sample(SOV,replace=TRUE))))};
+        conf<-quantile(bootSOV,probs=probs);
+        toplot<-paste(smoo[j],mean(bootSOV),conf[2],conf[1]);
+        write.table(toplot,file=paste(substring(files[1],1, nchar(files[1])-4), ext, sep=""),quote=FALSE,append=TRUE, row.names=FALSE, col.names=FALSE)
+        }
+    tableback<-read.table(file=paste(substring(files[1],1,nchar(files[1])-4), ext, sep=""));
+    x<-unlist(tableback[1]);
+    y<-unlist(tableback[2]);
+    cui<-unlist(tableback[3]);
+    cli<-unlist(tableback[4]);
+    plotCI(x,y,ui=cui,li=cli,xlab=c("Smoothing"),ylab=vardis, ylim=c(0,0.025));
+    pdf(paste(substring(files[1],1,nchar(files[1])-4), ext, c(".pdf"), sep=""));
+    plotCI(x,y,ui=cui,li=cli,xlab=c("Smoothing"),ylab=vardis, ylim=c(0,0.025));
+    dev.off();
+    }
+
diff --git a/confplotvbar.R b/confplotvbar.R
new file mode 100644
index 0000000..811fe83
--- /dev/null
+++ b/confplotvbar.R
@@ -0,0 +1,36 @@
+# Requires gplots, gregmisc package. split.file() output files.
+# See Burton-Kelly (2008) for complete documentation.
+confplotvbar<-function(path, pattern, vardis="Variation", barnames=c(1:20),xlabel="Genus", reps=1000, ext="-confplotvbar.txt", probs=c(0.025,0.975))
+    {
+    require(gplots);
+    files<-list.files(path=path,pattern=pattern,full.names=TRUE);
+    for(i in files)
+        #Loop through files and assign variable names [This is not necessary]
+        {
+        x <- read.table(i,header=TRUE);
+        assign(i, x);
+        }
+    for(j in 1:length(files))
+        {
+        SOV <- get(files[j]);
+        bootSOV <- numeric(reps);
+        #creates place for bootstrap values
+        for (k in 1:reps) {bootSOV[k] <- sum(diag(var(sample(SOV, replace=TRUE))))}; 
+        conf<-quantile(bootSOV,probs=probs);
+        toplot<-paste(barnames[j],mean(bootSOV), conf[2],conf[1],files[j]);
+        write.table(toplot,file=paste(substring(files[1],1, nchar(files[1])-4), ext, sep=""),quote=FALSE,append=TRUE, row.names=FALSE,col.names=FALSE)
+        }
+    tableback<-read.table(file=paste(substring(files[1],1, nchar(files[1])-4), ext, sep=""));
+    x<-unlist(tableback[1]);
+    y<-unlist(tableback[2]);
+    cui<-unlist(tableback[3]);
+    cli<-unlist(tableback[4]);
+    barplot2(height=y,names.arg=x,xlab=xlabel, ylab=vardis,ci.l=cli,ci.u=cui,plot.ci=TRUE);
+    pdf(paste(substring(files[1],1,nchar(files[1])-4), ext, c(".pdf"), sep=""));
+    barplot2(height=y,names.arg=x,xlab=xlabel,ylab=vardis,ci.l=cli,ci.u=cui,plot.ci=TRUE);
+    dev.off();
+    file.rename(paste(substring(files[1],1,nchar(files[1])-4), ext, sep=""),paste(path,"/confplotvbar-",pattern,".txt",sep=""));
+    file.rename(paste(substring(files[1],1,nchar(files[1])-4), ext, c(".pdf"), sep=""),paste(path,"/confplotvbar-", pattern,".pdf",sep=""));
+    # If using OS X, can announce when done
+    # system("say All done!");
+    }
\ No newline at end of file
diff --git a/euc.group.R b/euc.group.R
new file mode 100644
index 0000000..21346e5
--- /dev/null
+++ b/euc.group.R
@@ -0,0 +1,22 @@
+# Requires function cbind.all(). Single-column input files without column or row names.
+# See Burton-Kelly (2008) for complete documentation.
+
+euc.group <- function(path,pattern,ext="-eucgroup.euc",len=11)
+ {
+ file.list <- list.files(path=path,pattern=pattern,full.names=TRUE);
+#List files that match pattern.
+ for(i in file.list)
+ #Loop through files and assign variable names
+{
+                 x <- read.table(i);
+                 assign(i, x);
+  }
+ output <- cbind.all(get(file.list[1]));  #Initiate output
+ for (j in 2:length(file.list))
+ #Dump everything into that array
+  {
+  output <- cbind.all(output, get(file.list[j]));
+  }
+ write(t(as.matrix(output)),file=paste(substring(file.list[1],1, nchar(file.list[1])-4), ext, sep=""), ncolumns=dim(output)[2],sep="\t");
+ return(output);
+}
\ No newline at end of file