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Fix species richness for non-integer data (e.g., OTU proportions) #891

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Fix species richness for non-integer data (e.g., OTU proportions) #891

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d05f168
Fix specnumber for OTU proportions
vmikk Mar 1, 2018
5995554
add importFrom vegan
vmikk Mar 1, 2018
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10 changes: 7 additions & 3 deletions R/extend_vegan.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down Expand Up @@ -233,10 +234,13 @@ 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")))
}
Expand Down