tocher {biotools}

Tocher's Clustering

Description

tocher performs the Tocher (Rao, 1952) optimization clustering from a distance matrix. The cophenetic distance matrix for a Tocher's clustering can also be computed using the methodology proposed by Silva \& Dias (2013).

Usage

## S3 method for class 'dist'
tocher(d, algorithm = c("original", "sequential"))
## S3 method for class 'tocher'
print(x, ...)
## S3 method for class 'tocher'
cophenetic(x)

Arguments

d

an object of class "dist".

algorithm

a character indicating the algorithm to be used for clustering objects. It must be one of the two: "original" (default) or "sequential". The latter is the method proposed by Vasconcelos et al. (2007), and sometimes called "modified" Tocher.

x

an object of class "tocher".

...

optional further arguments from print.

Value

An object of class tocher. A list of

call

the call which produced the result.

algorithm

character; the algorithm that has been used as input.

clusters

a list of length k (the number of clusters), containing the labels of the objects in d for each cluster.

class

a numeric vector indicating the class (the cluster) of each object in d.

criterion

a numeric vector containing the clustering criteria - the greatest amongst the smallest distances involving each object in d. If algorithm = "original", this vector contains an unique value, i.e., the same criterion is used for every clustering step.

distClust

a matrix of distances within (diagonal) and between (off-diagonal) clusters.

d

the input object.

Warning

Clustering a large number of objects (say 300 or more) can be time demanding.

Author(s)

Anderson Rodrigo da Silva <[e-mail]>

References

Cruz, C.D.; Ferreira, F.M.; Pessoni, L.A. (2011) Biometria aplicada ao estudo da diversidade genetica. Visconde do Rio Branco: Suprema.

Rao, R.C. (1952) Advanced statistical methods in biometric research. New York: John Wiley & Sons.

Sharma, J.R. (2006) Statistical and biometrical techniques in plant breeding. Delhi: New Age International.

Silva, A.R. & Dias, C.T.S. (2013) A cophenetic correlation coefficient for Tocher's method. Pesquisa Agropecuaria Brasileira, 48:589-596.

Vasconcelos, E.S.; Cruz, C.D.; Bhering, L.L.; Resende Junior, M.F.R. (2007) Alternative methodology for the cluster analysis. Pesquisa Agropecuaria Brasileira, 42:1421-1428.

See Also

dist, D2.dist, cophenetic, distClust, hclust

Examples

# example 1
data(garlicdist)
(garlic <- tocher(garlicdist))
garlic$distClust  # cluster distances

# example 2
data(USArrests)
(usa <- tocher(dist(USArrests)))
usa$distClust

# cophenetic correlation
cophUS <- cophenetic(usa)
cor(cophUS, dist(USArrests))

# using the sequential algorithm
(usa2 <- tocher(dist(USArrests), algorithm = "sequential"))
usa2$criterion

# example 3
data(eurodist)
(euro <- tocher(eurodist))
euro$distClust

# End (not run)