Hello,
Thanks for Jari's comment.
It worked well after correction.
However, an error jumped out for the code below.
"Error: cannot allocate vector of size 90.6 Mb"
Please kindly advise how to modify it.
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)
## The beta sim index (Lennon 2001)
d <- betadiver(dataR, "sim")
On Fri, Jul 12, 2013 at 2:13 PM, Jari Oksanen <[email protected]> wrote:
> 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
>
> ______________________________________________
> [email protected] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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