From d05f168b2a166a6098191a190fadac6335df85fc Mon Sep 17 00:00:00 2001
From: vmikk <vmikryukov@gmail.com>
Date: Thu, 1 Mar 2018 09:52:38 +0500
Subject: [PATCH 1/2] Fix specnumber for OTU proportions

---
 R/extend_vegan.R | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/R/extend_vegan.R b/R/extend_vegan.R
index 2da390ba..f4fae06c 100644
--- a/R/extend_vegan.R
+++ b/R/extend_vegan.R
@@ -233,10 +233,13 @@ estimate_richness <- function(physeq, split=TRUE, measures=NULL){
   # Initialize to NULL
   outlist = vector("list")
 	# Some standard diversity indices
-  estimRmeas = c("Chao1", "Observed", "ACE")
-	if( any(estimRmeas %in% measures) ){ 
+  if( "Observed" %in% measures ){
+    outlist <- c(outlist, list(Observed = specnumber(OTU)))
+  }
+  estimRmeas = c("Chao1", "ACE")
+  if( any(estimRmeas %in% measures) ){ 
     outlist <- c(outlist, list(t(data.frame(estimateR(OTU)))))
-	}
+  }
 	if( "Shannon" %in% measures ){
     outlist <- c(outlist, list(shannon = diversity(OTU, index="shannon")))
 	}

From 5995554ae055ef1cf87c68dd6262e7f8d3d7617a Mon Sep 17 00:00:00 2001
From: vmikk <vmikryukov@gmail.com>
Date: Thu, 1 Mar 2018 14:25:17 +0500
Subject: [PATCH 2/2] add importFrom vegan

---
 R/extend_vegan.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/extend_vegan.R b/R/extend_vegan.R
index f4fae06c..47164a64 100644
--- a/R/extend_vegan.R
+++ b/R/extend_vegan.R
@@ -179,6 +179,7 @@ setMethod("vegdist", "phyloseq", function(x, method = "bray", binary = FALSE,
 #' @importFrom vegan estimateR
 #' @importFrom vegan diversity
 #' @importFrom vegan fisher.alpha
+#' @importFrom vegan specnumber
 #' @export
 #' @examples 
 #' ## There are many more interesting examples at the phyloseq online tutorials.