Dear all,
We have a problem with a large dataset that we want to cluster. The
dataset is in a long format: 1154024 rows with presence data. Each row
has the name of the species and the location. We have 1381 species and
6354 locations.
The main problem is that we need the data in wide format (one
Dear Thierry,
the 'mefa' package should do this, and I am also interested in the
testing of the package for such a large number of species. I have used
it before with 75K records, but only with ~160 species and 1052 sites.
So please let me know if it worked!
You can do the clustering like this (S
Thierry,
Search of CRAN with "sparse clustering" yielded cluster.dist {cba},
defined as "Clustering a Sparse Symmetric Distance Matrix". There were
also sparse PCA packages and sparse matrix classes. I have no experience
with these procedures.
As additional background, you might like to s
"ONKELINX, Thierry" <[EMAIL PROTECTED]>
writes:
> Dear all,
>
> We have a problem with a large dataset that we want to cluster. The
> dataset is in a long format: 1154024 rows with presence data. Each row
> has the name of the species and the location. We have 1381 species and
> 6354 locations.
>
This method for converting long to wide format seems to work well with
pretty large datasets and it uses only base functions.
# this function will return a site*species matrix
# based on the formula variable. Data does not need
# to be grouped, the xtabs function will take care of
# summing any
table)
mx <-as.matrix(tbl)
if (relativize==T) {mx<-mx/rowSums(mx)}
return(mx)
}
"Christian A. Parker" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
10/07/2008 11:04 AM
To
"ONKELINX, Thierry" <[EMAIL PROTECTED]>
cc
r-sig-ecology@r-project.org
Subject
te: Tue, 7 Oct 2008 09:56:15 -0400
> CC: [EMAIL PROTECTED]; r-sig-ecology@r-project.org
> Subject: Re: [R-sig-eco] Clustering large data
>
> Thierry,
>
> Search of CRAN with "sparse clustering" yielded cluster.dist {cba},
> defined as "Clustering a Sparse S
Sent by: [EMAIL PROTECTED]
10/07/2008 11:04 AM
To
"ONKELINX, Thierry" <[EMAIL PROTECTED]>
cc
r-sig-ecology@r-project.org
Subject
Re: [R-sig-eco] Clustering large data
This method for converting long to wide format seems to work well with
pretty large datasets and it uses onl
data.
~ John Tukey
-Oorspronkelijk bericht-
Van: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Namens Peter Solymos
Verzonden: dinsdag 7 oktober 2008 15:51
Aan: r-sig-ecology@r-project.org
Onderwerp: Re: [R-sig-eco] Clustering large data
Dear Thierry,
the 'mefa' package should do this, and I am al
pronkelijk bericht-
Van: hadley wickham [mailto:[EMAIL PROTECTED]
Verzonden: vrijdag 10 oktober 2008 14:40
Aan: ONKELINX, Thierry
CC: Peter Solymos; r-sig-ecology@r-project.org
Onderwerp: Re: [R-sig-eco] Clustering large data
> Thanks for your responses. The biggest problem seems to be cast() for
ROTECTED]
10/10/2008 10:12 AM
To
"hadley wickham" <[EMAIL PROTECTED]>
cc
r-sig-ecology@r-project.org
Subject
Re: [R-sig-eco] Clustering large data
Hi Hadley,
R ran out of memory. I got the "can't allocate vector of xxx mb" type of
error.
I did something lik
> Thanks for your responses. The biggest problem seems to be cast() for
> the reshape package which could not handle the dataset. Peter's solution
> using the mefa package worked fine. I found an other solution: table()
> which works fine to crosstabulate presence-only data.
Exactly what error did
a given body of
data.
~ John Tukey
-Oorspronkelijk bericht-
Van: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Namens hadley wickham
Verzonden: vrijdag 10 oktober 2008 14:40
Aan: ONKELINX, Thierry
CC: r-sig-ecology@r-project.org
Onderwerp: Re: [R-sig-eco] Clustering large data
> Thanks for
ment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of
> data.
> ~ John Tukey
&
body of
data.
~ John Tukey
-----Oorspronkelijk bericht-----
Van: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Namens hadley wickham
Verzonden: vrijdag 10 oktober 2008 14:40
Aan: ONKELINX, Thierry
CC: r-sig-ecology@r-project.org
Onderwerp: Re: [R-sig-eco] Clustering large data
Thanks for your respo
d from a given body of
data.
~ John Tukey
-Oorspronkelijk bericht-
Van: Dave Roberts [mailto:[EMAIL PROTECTED]
Verzonden: vrijdag 24 oktober 2008 20:11
Aan: r-sig-ecology@r-project.org
CC: ONKELINX, Thierry
Onderwerp: Re: [R-sig-eco] Clustering large data
Thierry and Hadley,
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