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.oksa...@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 ______________________________________________ R-help@r-project.org 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.
