tocher {biotools} | R Documentation |

## 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 |

`algorithm` |
a character indicating the algorithm to be used for clustering objects.
It must be one of the two: |

`x` |
an object of class |

`...` |
optional further arguments from |

### 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 |

`class` |
a numeric vector indicating the class (the cluster) of each object in |

`criterion` |
a numeric vector containing the clustering criteria - the greatest amongst
the smallest distances involving each object in |

`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 <anderson.agro@hotmail.com>

### 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)
```

*biotools*version 4.2 Index]