Re: [R] hierarchical clustering of large dataset

2012-03-10 Thread Hans Ekbrand
On Fri, Mar 09, 2012 at 08:26:01PM -0500, Massimo Di Stefano wrote: > my target is to have 'groups of species' based on the similarity of theyr > environmental parameters, and build a dendrogram like [2] > > [2] http://massimo-timecapsule.whoi.edu//data/img/manova_clust_matlab.png > Il giorno M

Re: [R] hierarchical clustering of large dataset

2012-03-09 Thread Massimo Di Stefano
i'll try to describe the data, here [1] there is a subdatset (255 rows) 6 columns (a to f) the last columns contains the Identification Number (ID) for a particular species. the ID in f are 20 different species and it should be my 'label': 16001 11012 25011 13011 11029 11027 10022 10024 20009 11

Re: [R] hierarchical clustering of large dataset

2012-03-09 Thread Peter Langfelder
On Fri, Mar 9, 2012 at 1:50 PM, Massimo Di Stefano wrote: > Peter, > > really thanks  for your answer. > > > > install.packages("flashClust") > library(flashClust) > data <- read.csv('/Users/epifanio/Desktop/cluster/x.txt') > data <- na.omit(data) > data <- scale(data) >> mydata >                

Re: [R] hierarchical clustering of large dataset

2012-03-09 Thread Massimo Di Stefano
Peter, really thanks for your answer. install.packages("flashClust") library(flashClust) data <- read.csv('/Users/epifanio/Desktop/cluster/x.txt') data <- na.omit(data) data <- scale(data) > mydata a bc d e 1 -0.207709346 -6.61855

Re: [R] hierarchical clustering of large dataset

2012-03-09 Thread Peter Langfelder
On Thu, Mar 8, 2012 at 4:41 AM, Massimo Di Stefano wrote: > > Hello All, > > i've a set of observations that is in the form : > > a,    b,    c,    d,    e,    f > 67.12,    4.28,    1.7825,    30,    3,    16001 > 67.12,    4.28,    1.7825,    30,    3,    16001 > 66.57,    4.28,    1.355,    30,

Re: [R] hierarchical clustering of large dataset

2012-03-09 Thread Sarah Goslee
2012/3/9 Uwe Ligges : > I think the main issue of the OP is that he geneartes a 55000x55000 distance > matrix and has to calculate on it. Beside immense main memory consumption > this may take ages to complete with hierarchical clustering. Indeed. I missed that in the original email. If a non-hie

Re: [R] hierarchical clustering of large dataset

2012-03-09 Thread Uwe Ligges
I think the main issue of the OP is that he geneartes a 55000x55000 distance matrix and has to calculate on it. Beside immense main memory consumption this may take ages to complete with hierarchical clustering. Uwe Ligges On 08.03.2012 15:02, Sarah Goslee wrote: See inline: On Thu, Mar 8,

Re: [R] hierarchical clustering of large dataset

2012-03-08 Thread Sarah Goslee
See inline: On Thu, Mar 8, 2012 at 7:41 AM, Massimo Di Stefano wrote: > > Hello All, > > i've a set of observations that is in the form : > > a,    b,    c,    d,    e,    f > 67.12,    4.28,    1.7825,    30,    3,    16001 > 67.12,    4.28,    1.7825,    30,    3,    16001 > 66.57,    4.28,    

[R] hierarchical clustering of large dataset

2012-03-08 Thread Massimo Di Stefano
Hello All, i've a set of observations that is in the form : a,b,c,d,e,f 67.12,4.28,1.7825,30,3,16001 67.12,4.28,1.7825,30,3,16001 66.57,4.28,1.355,30,3,16001 66.2,4.28,1.3459,13,3,16001 66.2,4