[R] error of betadiver in vegan

[David Winsemius]

On Jul 12, 2013, at 1:47 AM, Elaine Kuo wrote:

> 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.

Elaine;

This problem has literally been addressed hundreds of times on R-help:

http://markmail.org/search/?q=list%3Aorg.r-project.r-help+%22Error%3A+cannot+allocate+vector+of+size%22

And it's either been asked or answered 54 times on StackOverflow:

http://stackoverflow.com/search?q=[r]+%22Error%3A+cannot+allocate+vector+of+size%22

Th lack of contiguous RAM is small enought that the problem should be manageable after reading a few of the solutions offered.

-- 
David.


> 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 <jari.oksanen at oulu.fi> 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
-- 

David Winsemius
Alameda, CA, USA