R help - Jul 2013 - error of betadiver in vegan

Hello,

I am using betadiver (vegan) to calculate beta diversity.
However, an error message shows

Error in ifelse(x > 0, 1, 0) :
  (list) object cannot be coerced to type 'double'


R version: 3.0.0

Please kindly advise how to solve the issue.
Also, please kindly tell if any more information is in need.
Thank you.

Elaine


code
# Non-Passerine table
dataNP_1 <-read.dbf("H:/temp_D/stage_4_R_2748/NP_1-10.dbf", as.is =
FALSE)
dataNP_2 <-read.dbf("H:/temp_D/stage_4_R_2748/NP_11-19.dbf", as.is
= FALSE)
dataNP<-merge(dataNP_1,dataNP_2,by=c("GID"),all=T)

.. skip...

# Non-Passerine and Passerine table (2748 species)
dataR<-merge(dataP,dataNP,by=c("GID"),all=T)
dim(dataR)
str(dataR)

library(vegan)

  ##  Raw  data
  R  <-  betadiver(dataR)

  ##  The  indices
  betadiver(help=TRUE)

  ##  The  beta sim  index (Lennon 2001)
  d  <-  betadiver(R,  "sim")

	[[alternative HTML version deleted]]

Elaine Kuo <elaine.kuo.tw <at> gmail.com> writes:
> 
> Hello,
> 
> I am using betadiver (vegan) to calculate beta diversity.
> However, an error message shows
> 
> Error in ifelse(x > 0, 1, 0) :
>   (list) object cannot be coerced to type 'double'
...snip...
>   ##  Raw  data
>   R  <-  betadiver(dataR)
> 
>   ##  The  indices
>   betadiver(help=TRUE)
> 
>   ##  The  beta sim  index (Lennon 2001)
>   d  <-  betadiver(R,  "sim")
> 
Elaine,

Look carefully what you do here: betadiver needs data as input -- not beta
diversities. Your last command is equal to this oneliner:

d <- betadiver(betadiver(dataR), "sim")

This is guaranteed to fail. Use instead

d <- betadiver(dataR, "sim")

Cheers, Jari Oksanen