Of course,
manually checking the number of clusters that are cut at a specific height
(e.g. by abline())
is one possibility. However, this only makes sense for single trees, but is
not a feasible
approach for multiple model runs when hundreds of trees are built with many
cluster branches.

Thus, I'd be nice if somebody knows a more programatic approach or another
package
that allows cutting "centroid"-trees.

/Johannes


On Fri, Jul 11, 2014 at 4:19 PM, David L Carlson <dcarlson@tamu.edu> wrote:

>  The easiest workaround is the one you included in your original posting.
> Specify k= and not h=. Examine the dendrogram and decide how many clusters
> are at the level you want. You could add guidelines to the dendrogram with
> abline() to make it easier to see the number of clusters at various heights.
>
>
>
> plot(hc)
>
> abline(h=c(20, 40, 60, 80, 100, 120), lty=3)
>
>
>
> David C
>
>
>
> *From:* Johannes Radinger [mailto:johannesradinger@gmail.com]
> *Sent:* Friday, July 11, 2014 3:24 AM
> *To:* David L Carlson; R help
> *Subject:* Re: [R] Cutting hierarchical cluster tree at specific height
> fails
>
>
>
> Hi,
>
>
>
> @David: Thanks for the explanation why this does not work. This of
>
> course makes theoretically sense.
>
>
>
> However in a recent discussion
>
> (
> http://stats.stackexchange.com/questions/107448/spatial-distance-between-cluster-means
> )
>
> it was stated that "the 'reversals problem' of  centroid method is
>
> not a serious reason to deactivate the option of 'tree cut'". Instead
>
> a warning message should be provided rather than a deactivation.
>
>
>
> So does anyone know how a tree that was created with "centroid" can still
>
> be cut at a specific height? I tried the package "dynamicTreeCut", but this
>
> also relies on cutree and consequently raises an error when used for
> cutting
>
> "centroid" trees.
>
>
>
> Does anyone know a work around and can provide a minimum working example?
>
>
>
> /Johannes
>
>
>
> On Wed, Jul 9, 2014 at 4:58 PM, David L Carlson <dcarlson@tamu.edu> wrote:
>
> To cut the tree, the clustering algorithm must produce consistently
> increasing height values with no reversals. You used one of the two options
> in hclust that does not do this. Note the following from the hclust manual
> page:
>
> "Note however, that methods "median" and "centroid" are not leading to a
> monotone distance measure, or equivalently the resulting dendrograms can
> have so called inversions (which are hard to interpret)."
>
> The cutree manual page:
>
> "Cutting trees at a given height is only possible for ultrametric trees
> (with monotone clustering heights)."
>
> Use a different method (but not median).
>
> -------------------------------------
> David L Carlson
> Department of Anthropology
> Texas A&M University
> College Station, TX 77840-4352
>
>
> -----Original Message-----
> From: r-help-bounces@r-project.org [mailto:r-help-bounces@r-project.org]
> On Behalf Of Johannes Radinger
> Sent: Wednesday, July 9, 2014 7:07 AM
> To: R help
> Subject: [R] Cutting hierarchical cluster tree at specific height fails
>
> Hi,
>
> I'd like to cut a hierachical cluster tree calculated with hclust at a
> specific height.
> However ever get following error message:
> "Error in cutree(hc, h = 60) :
>   the 'height' component of 'tree' is not sorted (increasingly)"
>
>
> Here is a working example to show that when specifing a height in  cutree()
> the code fails. In contrast, specifying the number of clusters in cutree()
> works.
> What is the exact problem and how can I solve it?
>
> x <- c(rnorm(100,50,10),rnorm(100,200,25),rnorm(100,80,15))
> y <- c(rnorm(100,50,10),rnorm(100,200,25),rnorm(100,150,25))
> df <- data.frame(x,y)
> plot(df)
>
> hc <- hclust(dist(df,method = "euclidean"), method="centroid")
> plot(hc)
>
> df$memb <- cutree(hc, h = 60) # this does not work
> df$memb <- cutree(hc, k = 3) # this works!
>
> plot(df$x,df$y,col=df$memb)
>
>
> Thank you for your hints!
>
> Best regards,
> Johannes
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
>

	[[alternative HTML version deleted]]

