Displaying 4 results from an estimated 4 matches for "mdist".
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2003 Jun 09
1
estimate the number of clusters
...estimate the number of clusters in a microarray
dataset.
Initially, I used the iris data to test my piece of code as follows:
library(cluster)
data(iris)
mydata<-iris[,1:4]
maxk<-15 # at most 15 clusters
myindex<-rep(0,maxk) # hold the si values for each k clusters
mdist<-1-cor(t(mydata)) #dissimlarity
mdist<-as.dist(mdist)
for(k in 2:maxk)
{
hc<-diana(mdist,diss =TRUE, stand = FALSE)
si<-silhouette.default(cutree(as.hclust(hc),k=k),mdist)
myindex<-summary(si)$avg.width
}
myk<-rev(order(myindex))[1] #select the number of k clusters w...
2007 Oct 03
2
Speeding up simulation of mean nearest neighbor distances
...o simulate the mean 1st through nth
nearest neighbor distances for a random spatial pattern using the
functions nndist() and runifpoint() from spatsat. It works, but runs
relatively slowly - would appreciate suggestions on how to speed up
this function. Thanks. --Dale
library(spatstat)
sim.nth.mdist <- function(nth,nsim) {
D <- matrix(ncol=nth, nrow=nsim)
for (i in 1:nsim) {
rpp <- runifpoint(22, win=owin(c(0,1),c(0,1)), giveup=1000)
for (k in 1:nth) D[i,k] <- mean(nndist(rpp ,k=k))
}
D
}
sim.nth.mdist(5,100)
2004 Aug 19
3
Do you know if you can map a large minimum spanning tree in R?
...tats/programming software such as SAS, however no longer have access to
SAS so I've turned to R. I also have tried using MapInfo with the data
exported from R, but have found that not so intuitive to learn on the
fly.
Back to R - I'm using W2K, and have managed to graph the tree using
plot(mdist,graph="nsca") where mdist is the output matrix from my mst
command, however this is not terribly map-like, so I'm looking for a
better display that can be embedded in a document.
Any assistance gratefully received!
Fiona.
> Fiona Wade
> Project Manager
> MARA
> F&A
&g...
2010 Feb 21
1
How to: Compare Two dendrograms (Hierarchical Clusterings) ?
Hello all,
I wish to compare two dendrograms (representing Hierarchical Clusterings).
My problems are several:
1) how do I manually create a dendrogram object ?
That is, how can I reconstruct it as an "hclust" object that creates such a
dendrogram, when all I have is the dendrogram image (but don't have the
underlaying distance matrix that produced it) ?
I see that there is a