On Wed, 2008-02-20 at 13:24 +0100, Alfonso Pérez Rodríguez wrote:
> Hello, I'm trying to obtain a species abundance curve with the
> function specaccum from vegan package. I've applied this function to
> my data and I've obtained something like this:
>
> Sites 1.000000 2.000000 3.000000 4.000000 5.0000000 6.0000000
> 7.00 Richness 6.510000 8.290000 9.150000 9.770000 10.3300000
> 10.7600000 sd 1.381662 1.350608 1.200799 1.117853 0.9749903
> 0.9333333 0.90
That is just the _printed_ representation of the resulting object. In R,
don't believe your eyes - what is printed is not always an accurate
reflection of the complete object!
>
> But the problem is that I want to export this data to an excel file,
> or a txt file, but I'm not able to do it because I can not asign this
> values to a data.frame or a matrix or something. When I try to
> transform in a data frame the program tell me:
>
> Error en as.data.frame.default(x[[i]], optional = TRUE,
> stringsAsFactors = stringsAsFactors) :
> cannot coerce class "specaccum" into a data.frame
>
> Then, what can I do? Thank you very much.
I'll start with a reproducible example, from ?specaccum
require("vegan")
data(BCI)
sp1 <- specaccum(BCI)
str(sp1)
The latter call yields:
List of 6
$ call : language specaccum(comm = BCI)
$ method : chr "exact"
$ sites : int [1:50] 1 2 3 4 5 6 7 8 9 10 ...
$ richness: num [1:50] 90.8 121.6 139.0 150.7 159.2 ...
$ sd : num [1:50] 6.93 7.19 7.00 6.64 6.25 ...
$ perm : NULL
- attr(*, "class")= chr "specaccum"
Note the class - "specaccum" - and R has no idea how to convert this to
a data frame or matrix - there is no as.data.frame.specaccum() and this
is because how do you combine 3 vectors of length 50 into a data frame
with other information that is of a different type and length? You
can't.
So, now your problem boils down to extracting the relevant information
from sp1 and writing that out as a data frame. This is very easy. Given
your email I presume you are interested in the 'sites', 'richness' and
'sd' components:
my.res <- with(sp1, data.frame(sites, richness, sd))
head(my.res)
The latter call yielding the first 6 lines of my.res (there are 50 in
total):
sites richness sd
1 1 90.7800 6.934811
2 2 121.6098 7.193362
3 3 139.0459 7.001993
4 4 150.7116 6.635769
5 5 159.2363 6.248117
6 6 165.8306 5.894738
Now just write out my.res using write.table()
write.table(my.res, file = "my.results.txt")
Which works for me.
Is that what you wanted?
HTH
G
>
>
>
>
> Alfonso Prez Rodrguez
> Instituto de Investigaciones Marinas
> C/ Eduardo Cabello n 6
> C.P. 36208 Vigo (Espaa)
> Tlf.- 986231930 Extensin 241
> e-mail: [EMAIL PROTECTED]
> [[alternative HTML version deleted]]
>
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--
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
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