DendSer {DendSer} | R Documentation |

## Implements dendrogram seriation

### Description

Implements dendrogram seriation.

### Usage

```
DendSer(h, ser_weight, cost = costBAR, node_op = NULL, costArg = NULL,
maxloops = NULL, saveinfo = FALSE, direction = NULL, GW=NULL,...)
```

### Arguments

`h` |
An object of class hclust |

`ser_weight` |
Used by cost function to evaluate ordering. For cost=costLS, this is a vector of object weights. Otherwise is a dist or symmetric matrix. |

`cost` |
Function used to evaluate permutation.Current choices are costLS, costPL, costLPL, costED, costARc, costBAR. |

`node_op` |
Function used to reorder branches at a dendrogram node. DendSer picks default depending on cost function. NULL means use default depending on cost. |

`costArg` |
Other args for cost function. |

`maxloops` |
Maximum number of iterations allowed. NULL means use default depending on cost. |

`saveinfo` |
Logical, whether info associated with search is saved. |

`direction` |
Order of visiting nodes. Values are "up" or "down", for nodes in order of increasing or decreasing height.NULL means use default depending on cost. |

`GW` |
Logical, initial GW step or not. NULL means use default depending on cost. |

`...` |
Not used. |

### Details

costED uses the Gruvaeus and Wainer 1972 algorithm, as provided by package gclus.

### Value

Numeric vector giving an optimal dendrogram order

### Author(s)

Catherine Hurley & Denise Earle

### References

Gruvaeus, G. \& Wainer, H. (1972), “Two additions to hierarchical cluster analysis”, British Journal of Mathematical and Statistical Psychology, 25, 200-206.

### See Also

### Examples

```
require(DendSer)
d<- dist(iris[,-5])
h <- hclust(d,method="average")
ob<- DendSer(h,d)
opl<- DendSer(h,d,cost=costPL)
plotAsColor(d,ob)
w <- rowSums(iris[,-5])
ow <- DendSer(h,w,cost=costLS) # arranges cases by size, within hclust
stars(iris[ow,-5],labels=NULL, col.stars=cutree(h,3)[ow]) # and color by cluster
#stars(iris[ow,-5],labels=NULL, col.stars=iris[ow,5]) # or by species
```

*DendSer*version 1.0.2 Index]