[R] variables - data-structure

[Gabor Grothendieck]

Helmut Kudrnovsky <hellik <at> web.de> writes:

: 
: dear R-friends,
: 
: i`ve got a large dataset of  vegetation-samples with about 500 
: variables(=species) in the following format:
: 
: 1 spec1
: 1 spec23
: 1 spec54
: 1 spec63
: 2 spec1
: 2 spec2
: 2 spec253
: 2 spec300
: 2 spec423
: 3 spec20
: 3 spec88
: 3 spec121
: 3 spec200
: 3 spec450
: .
: .
: 
: this means:  sample 1 (grassland) with the species (=spec) 1, 23, 54, 63
: 
: is it possible to get a following data-structure for further analysis?
: 
: 		1	2	3	......
: spec1		1	1	0
: spec2		0	1	0
: spec3
: ...
: spec253	0	1	0
: ...
: spec450	0	0	1
: 
: with thanks from the snowy tirol
: helli



If your intention is to use this as a community matrix with the R
vegan package then I think you require the transpose of the above,
namely (assuming DF contains your data frame):

comm <- with(DF, table(sample, species)) 

library(vegan)
diversity(comm)
specaccum(comm, method = "random")

etc.