R help - Feb 2013 - cutreeDynamic error

I am having difficulty getting the dynamic tree cut package to work.

Given the data table "myddtable"
LengthPlaceColorAge5HRed224ABlue205WGreen243GRed222GBlue236WGreen255ARed194H
Blue23
I created a similarity matrix using DAISY and Gower metric and specified
Place and Color columns as characters (since they are categorical variables)
> dd.daisy<-daisy(myddtable, metric = "gower", stand = FALSE,
type list(character=c("Place","Color")))
Then I clustered using DIANA
dd.diana<-diana(dd.daisy)
I am trying to cutreeDynamic {dynamicTreeCut} as follows

cutreeDynamic(dd.diana, cutHeight = 2, minClusterSize = 1, method
"hybrid",+ distM = dd.daisy,+ deepSplit
(ifelse(method=="hybrid", 1, FALSE)),+ maxCoreScatter NULL, minGap =
NULL,+ maxAbsCoreScatter = NULL,
minAbsGap = NULL,+ maxDistToLabel = cutHeight,+
respectSmallClusters = TRUE, + verbose = 2, indent
= 0)

But get the following error:

Warning in if (class(dendro) != "hclust") stop("Argument dendro
must
have class hclust.") :
the condition has length > 1 and only the first element will be
usedError in cutreeDynamic(dd.diana, cutHeight = 2, minClusterSize 1, method =
"hybrid", :
Argument dendro must have class hclust.

Is this trying to tell me I cannot use this with DIANA but only with hclust
because I thought it could be used with any of the hierarchical methods?

I hope someone can please tell me what I am doing wrong.

Thank you.


-- 
******************************************************************


*Joanna Papakonstantinou, Ph.D.*

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So I realized I had to convert my dd.daisy to a matrix and used:
ddmatrix.daisy<-as.matrix(dd.daisy)
and then I passed that in as the distM:
> cutreeDynamic(as.hclust(dd.diana), cutHeight = NULL, minClusterSize = 2,
method = "hybrid", distM = ddmatrix.daisy,deepSplit
(ifelse(method=="hybrid", 1, FALSE)),maxCoreScatter = NULL, minGap =
NULL,
maxAbsCoreScatter = NULL, minAbsGap = NULL,useMedoids = FALSE,
maxDistToLabel = cutHeight,respectSmallClusters = TRUE, verbose = 2, indent
= 0)

However, now I am getting a different error:

 Detecting clusters...
..cutHeight not given, setting it to 0.847  ===>  99% of the (truncated)
height range in dendro.
Error in ifelse(method == "hybrid", 1, FALSE) : object
'method' not found

Anny suggestions on how to fix this?

Joanna

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