chclust | R Documentation |

Constrained hierarchical clustering.

```
chclust(d, method = "coniss")
## S3 method for class 'chclust'
plot(x, labels = NULL, hang = 0.1, axes = TRUE,
xvar=1:(length(x$height)+1), xlim=NULL, ylim=NULL,
x.rev = FALSE, y.rev=FALSE, horiz=FALSE, ...)
bstick(n, ...)
## S3 method for class 'chclust'
bstick(n, ng=10, plot=TRUE, ...)
```

`d` |
a dissimilarity structure as produced, for example, by |

`method` |
the agglomeration method to be used. This should be (an unambiguous abbreviation of) either "coniss" or "conslink". |

`x` , `n` |
a constrained cluster object of class |

`xvar` |
numeric vector containing x-coordinates for the leaves of the dendrogram (see |

`x.rev` , `y.rev` |
logical flags to reverse the x- or y-axis (and dendrogram labels). Defaults to |

`horiz` |
logical indicating if the dendrogram should be drawn horizontally or not. Note that y-axis still refers to the dendrogram height even after rotating. |

`xlim` , `ylim` |
optional x- and y-limits of the plot, passed to the underlying plto function. The defaults for these show the full dendrogram. |

`labels` , `hang` , `axes` |
further arguments as in |

`ng` |
number of groups to display. |

`plot` |
logical to plot a broken stick model. Defaults to |

`...` |
further graphical arguments. Use |

`chclust`

performs a constrained hierarchical clustering of a distance matrix, with clusters constrained by sample order. Returns an object of class `chclust`

which can be plotted and interrogated. See Grimm (1987), Gordon & Birks (1972) and Birks & Gordon (1985) for discusssiom of the coniss and conslink algorithms. The resulting dendrogram can be plotted with `plot`

. This is an extension of `plot`

method for hclust that allows the dendrogram to be plotted horizontally or vertically (default). `plot`

also accepts a numeric vector coordinates for x-axis positions of the leaves of the dendrogram. These could, for example, be the stratigraphic depths of core samples or geographic distances along a line transect.

`bstick.chclust`

compares the dispersion of a hierarchical classification to that obtained from a broken stick model and displays the results graphically. See Bennett (1996) for details. `bstick`

is a generic function and the default method is defined in package `vegan`

. If package `vegan`

is installed the function may be called using `vegan::bstick`

, otherwise use `bstick.chclust`

.

Function `chclust`

returns an object of class `chclust`

, derived from `hclust`

.

Steve Juggins

Bennett, K. (1996) Determination of the number of zones in a biostratigraphic sequence. *New Phytologist*, **132**, 155-170.

Birks, H.J.B. & Gordon, A.D. (1985) *Numerical Methods in Quaternary Pollen Analysis* Academic Press, London.

Gordon, A.D. & Birks, H.J.B. (1972) Numerical methods in Quaternary palaeoecology I. Zonation of pollen diagrams. *New Phytologist*, **71**, 961-979.

Grimm, E.C. (1987) CONISS: A FORTRAN 77 program for stratigraphically constrained cluster analysis by the method of incremental sum of squares. *Computers & Geosciences*, **13**, 13-35.

`hclust`

, `cutree`

, `dendrogram`

.

```
data(RLGH)
diss <- dist(sqrt(RLGH$spec/100))
clust <- chclust(diss)
bstick(clust, 10)
# Basic diagram
plot(clust, hang=-1)
# Rotated through 90 degrees
plot(clust, hang=-1, horiz=TRUE)
# Rotated and observations plotted according to sample depth.
plot(clust, xvar=RLGH$depths$Depth, hang=-1, horiz=TRUE, x.rev=TRUE)
# Conslink for comparison
clust <- chclust(diss, method = "conslink")
plot(clust, hang=-1)
```

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.