Description Usage Arguments Details Value Author(s) References Examples
pvalues are calculated for each branch of the cluster dendrogram to indicate
the stability of a specific partition. clusterBoot
will yield the same
clusters as the cluster
function (i.e. standard hierarchical
clustering) with additional pvalues. Two kindes of pvalues are reported:
bootstrap probabilities (BP) and approximately unbiased (AU) probabilities
(see Details section for more information).
1 2 3 4 5 6 7 8 9 10 11 12 
x 

along 
Along which dimension to cluster. 1 = constructs, 2= elements. 
align 
Whether the constructs should be aligned before clustering
(default is 
dmethod 
The distance measure to be used. This must be one of
"euclidean", "maximum", "manhattan", "canberra", "binary"
or "minkowski". Any unambiguous substring can be given.
For additional information on the different types type

cmethod 
The agglomeration method to be used. This should be (an
unambiguous abbreviation of) one of 
p 
Power of the Minkowski metric. Not yet passed on to pvclust! 
nboot 
the number of bootstrap replications. The default is

r 
numeric vector which specifies the relative sample sizes of bootstrap replications. For original sample size n and bootstrap sample size n', this is defined as r=n'/n. 
seed 
Random seed for bootstrapping. Can be set for reproducibility (see

... 
Arguments to pass on to 
In standard (hierarchical) cluster analysis the question arises which of the
idientified structures are significant or just emerged by chance. Over the
last decade several methods have been developed to test structures for
robustness. One line of research in this area is based on resampling. The
idea is to resample the rows or columns of the data matrix and to build the
dendrogram for each bootstrap sample (Felsenstein, 1985). The pvalues
indicates the pecentage of times a specific structure is identified across
the bootstrap samples. It was shown that the pvalue is biased (Hillis &
Bull, 1993; Zharkikh & Li, 1995). In the literature several methods for bias
correction have been proposed. In clusterBoot
a method based on the
multiscale bootstrap is used to derive corrected (approximately
unbiased) pvalues (Shimodaira, 2002, 2004). In conventional bootstrap
analysis the size of the bootstrap sample is identical to the orginal sample
size. Multiscale bootstrap varies the bootstrap sample size in order to infer
a correction formula for the biased pvalue on the basis of the variation of
the results for the different sample sizes (Suzuki & Shimodaira, 2006).
align: Aligning will reverse constructs if necessary to yield a maximal similarity between constructs. In a first step the constructs are clustered including both directions. In a second step the direction of a construct that yields smaller distances to the adjacent constructs is preserved and used for the final clustering. As a result, every construct is included once but with an orientation that guarantees optimal clustering. This approach is akin to the procedure used in FOCUS (Jankowicz & Thomas, 1982).
A pvclust object as returned by the function pvclust
Mark Heckmann
Felsenstein, J. (1985). Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution, 39(4), 783. doi:10.2307/2408678
Hillis, D. M., & Bull, J. J. (1993). An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis. Systematic Biology, 42(2), 182192.
Jankowicz, D., & Thomas, L. (1982). An Algorithm for the Cluster Analysis of Repertory Grids in Human Resource Development. Personnel Review, 11(4), 1522. doi:10.1108/eb055464.
Shimodaira, H. (2002) An approximately unbiased test of phylogenetic tree selection. Syst, Biol., 51, 492508.
Shimodaira,H. (2004) Approximately unbiased tests of regions using multistep multiscale bootstrap resampling. Ann. Stat., 32, 26162614.
Suzuki, R., & Shimodaira, H. (2006). Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics, 22(12), 15401542. doi:10.1093/bioinformatics/btl117
Zharkikh, A., & Li, W.H. (1995). Estimation of confidence in phylogeny: the completeandpartial bootstrap technique. Molecular Phylogenetic Evolution, 4(1), 4463.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16  ## Not run:
# pvclust must be loaded
library(pvclust)
# pvalues for construct dendrogram
s < clusterBoot(boeker)
plot(s)
pvrect(s, max.only=FALSE)
# pvalues for element dendrogram
s < clusterBoot(boeker, along=2)
plot(s)
pvrect(s, max.only=FALSE)
## End(Not run)

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