diff --git a/R/extend_vegan.R b/R/extend_vegan.R index 2da390ba..ab6e82e4 100644 --- a/R/extend_vegan.R +++ b/R/extend_vegan.R @@ -1,5 +1,5 @@ ################################################################################ -# Define S3 methods for scores (originally defined by vegan-package) +# Define S3 methods for scores (originally defined by vegan-package) # to work for other ordination results # vegan:::scores.default ################################################################################ @@ -247,10 +247,10 @@ estimate_richness <- function(physeq, split=TRUE, measures=NULL){ outlist <- c(outlist, list(invsimpson = diversity(OTU, index="invsimpson"))) } if( "Fisher" %in% measures ){ - fisher = tryCatch(fisher.alpha(OTU, se=TRUE), + fisher = tryCatch(fisher.alpha(OTU), warning=function(w){ warning("phyloseq::estimate_richness: Warning in fisher.alpha(). See `?fisher.fit` or ?`fisher.alpha`. Treat fisher results with caution") - suppressWarnings(fisher.alpha(OTU, se=TRUE)[, c("alpha", "se")]) + suppressWarnings(fisher.alpha(OTU)) } ) if(!is.null(dim(fisher))){