[R] transpose dataset to PC-ORD?

[Jean Eid]

I do not know exactly what you are looking for but it seems that you are 
writing the column names (which become row names) when transposing the 
data. So to fix this try using write.table(..., sep=",", row.names=F)


Jean


Daniel Gruner wrote:
> Hello:
>
> I need to take a species-sample matrix and transpose it to the format 
> used by PC-ORD for analysis. Unfortunately, the number of species is 
> very large (>5000), and so this operation cannot be performed simply 
> in an application like Excel, which has a 255 column limit. So, I 
> wrote relatively simple code in R that I hoped would do this 
> (appended below). But there are glitches.
>
> The format needed for PC-ORD (where "NA" shows an empty cell):
>
> NA,3,sites,NA
> NA,3,species,NA
> NA,Q,Q,Q
> NA,sp1,sp2,sp3
> site1,1,0,0
> site2,0,1,2
> site3,0,3,0
>
> 2 cells in first row indicate number of samples (rows), the second 
> column indicates number of species (columns), the third row indicates 
> variable type (Q = quantitative), and the fourth row shows column 
> headers (species names). So, one can create a transposable matrix in 
> a spreadsheet where 5000+ species are the rows:
>
> NA,NA,NA,NA,site1,site2,site3
> 3,3,Q,sp1,1,0,0
> sites,species,Q,sp2,0,1,3
> NA,NA,Q,sp3,0,2,0
>
>
> It is important that the data file written out is totally clean and 
> ready to go for PC-ORD, because I cannot open and edit it in a 
> spreadsheet. However, the code performs the transpose operation and 
> writes the file, but now the former row IDs are the first row in the 
> new file (NA,1,2,3), and the 4 leading spaces are "X, X.1, X.2, 
> X.3".  I'd like to delete the first row and delete the first 4 values 
> of column1, without deleting the column.
>
> NA,1,2,3
> X,3,islands,NA
> X.1,3,speciesNA
> X.2,Q,Q,Q
> X.3,sp1,sp2,sp3
> site1,1,0,0
> site2,0,1,2
> site3,0,3,0
>
> I have tried various tricks that I will not list/belabor here 
> (various col.names, row.names, header, Extract, etc commands). Any 
> further hints on code that will either stop R from adding these, or 
> strip them at the end?
>
> (PS, yes, I can learn how to my multivariate analyses in R and skip 
> PC-ORD, but I am time limited on this one, and it seems that this 
> code could be very useful in numerous ways)
>
> Many thanks for the help,
> Dan Gruner
> (Windows XP, R vers2.2)
>
>
>
> ##transpose datasets to convert to PC-ORD format
>
> data<-read.csv("data.csv", header=TRUE, as.is=T,
>     strip.white=T, na.strings="NA")
> data<-as.matrix(data)
> data.trans <- t(data)
> write.csv(data.trans, file = "datatransp.csv",
>     quote = F, na = "")
>
>
>
> *******************************
>
> Daniel S. Gruner, Postdoctoral Scholar
> Bodega Marine Lab, University of California -- Davis
> PO Box 247, 2099 Westside Rd
> Bodega Bay, CA 94923-0247
> (o) 707.875.2022  (f) 707.875.2009   (m) 707.338.5722
> email:  dsgruner_at_ucdavis.edu
> http://www.bml.ucdavis.edu/facresearch/gruner.html
> http://www.hawaii.edu/ant/
>
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