Hello everyone!
I'm having a problem in casting a data frame with the reshape package. I
have an original data set of species abundances in replicate samples at
certain sites, with the following form:
SITE SPECIES Replicate1 Replicate2 Replicate3
I A 1 3 0
I B 2 5 1
I C 1 0 2
II A 4 2 0
II C 1 0 0
II D 6 3 3
Please notice that site II does not have species B and has a new species D,
the remaining two are shared with site I.
I need to get these data in the form of a matrix like:
SITE.REPLICATE A B C D
I.1 1 2 1 NA
I.2 3 5 0 NA
I.3 0 1 2 NA
II.1 4 NA 1 6
II.2 2 NA 0 3
II.3 0 NA 0 3
Using the above "toy data" in R, everything works fine using melt and recast
as follows (lets call test to may initial matrix):
> testm <- melt (test, id.var=c("SITE","SPECIES"))
> testc <- cast(testm, ...~SPECIES)
> testc
SITE variable A B C D
1 I Replicate1 1 2 1 NA
2 I Replicate2 3 5 0 NA
3 I Replicate3 0 1 2 NA
4 II Replicate1 4 NA 1 6
5 II Replicate2 2 NA 0 3
6 II Replicate3 0 NA 0 3
However, when I use the same code in my real data set which is considerably
larger (73 sites and 7 replicates for site, resulting in a molten matrix of
14469 x 4), the cast function does some kind of aggregation (in fact it
advices of an aggregation using the default fun.aggregate) that I was not
able to understand. I also tried to split my original data frame in order to
get molten matrices smaller than 5500x4, but I got the same problem.
Could anyone help me with this?
(I use R 2.8.1 for Windows)
Thank you very very much in advance!
Cheers,
Dulce
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