R: Computes Hierarchical Clustering and Cut the Tree

hcut {factoextra} | R Documentation

## Computes Hierarchical Clustering and Cut the Tree

### Description

Computes hierarchical clustering (hclust, agnes, diana) and cut the tree into k clusters. It also accepts correlation based distance measure methods such as "pearson", "spearman" and "kendall".

### Usage

    hcut(x, k = 2, isdiss = inherits(x, "dist"), hc_func = c("hclust",
      "agnes", "diana"), hc_method = "ward.D2", hc_metric = "euclidean",
      stand = FALSE, graph = FALSE, ...)

### Arguments

`x` | a numeric matrix, numeric data frame or a dissimilarity matrix.
`k` | the number of clusters to be generated.
`isdiss` | logical value specifying wether x is a dissimilarity matrix.
`hc_func` | the hierarchical clustering function to be used. Default value is "hclust". Possible values is one of "hclust", "agnes", "diana". Abbreviation is allowed.
`hc_method` | the agglomeration method to be used (?hclust) for hclust() and agnes(): "ward.D", "ward.D2", "single", "complete", "average", ...
`hc_metric` | character string specifying the metric to be used for calculating dissimilarities between observations. Allowed values are those accepted by the function dist() [including "euclidean", "manhattan", "maximum", "canberra", "binary", "minkowski"] and correlation based distance measures ["pearson", "spearman" or "kendall"].
`stand` | logical value; default is FALSE. If TRUE, then the data will be standardized using the function scale(). Measurements are standardized for each variable (column), by subtracting the variable's mean value and dividing by the variable's standard deviation.
`graph` | logical value. If TRUE, the dendrogram is displayed.
`...` | not used.

### Value

an object of class "hcut" containing the result of the standard function used (read the documentation of hclust, agnes, diana).

It includes also:

- cluster: the cluster assignement of observations after cutting the tree

- nbclust: the number of clusters

- silinfo: the silhouette information of observations (if k > 1)

- size: the size of clusters

- data: a matrix containing the original or the standardized data (if stand = TRUE)

### See Also

`fviz_dend`, `hkmeans`, `eclust`

### Examples

    data(USArrests)

    # Compute hierarchical clustering and cut into 4 clusters
    res <- hcut(USArrests, k = 4, stand = TRUE)

    # Cluster assignements of observations
    res$cluster
    # Size of clusters
    res$size

    # Visualize the dendrogram
    fviz_dend(res, rect = TRUE)

    # Visualize the silhouette
    fviz_silhouette(res)

    # Visualize clusters as scatter plots
    fviz_cluster(res)

[Package factoextra version 1.0.5 Index]