R: Clusters a set of time series using aglomerative hierarchical...

sits_cluster_dendro {sits} | R Documentation

## Clusters a set of time series using aglomerative hierarchical clustering

### Description

Takes a SITS tibble and produces a sits tibble with an added "cluster" column. This is done in several steps: 1. Calculation of the dendrogram; 2. Get validity index for best cluster using the adjusted Rand Index; 3. Cut the dendrogram using the chosen validity index.

### Usage

    sits_cluster_dendro(
      samples = NULL,
      bands = NULL,
      dist_method = "dtw_basic",
      linkage = "ward.D2",
      k = NULL,
      colors = "RdYlGn",
      .plot = TRUE,
      ...
    )

### Arguments

`samples` | A tibble with input set of time series
`bands` | Bands to be used in the clustering
`dist_method` | String with one of the supported distances.
`linkage` | String with agglomeration method to be used. Can be any 'hclust' method (see 'hclust'). Default is 'ward.D2'.
`k` | Desired number of clusters (overrides default value)
`colors` | Color scheme as per 'sits_color_name' function.
`.plot` | Plot the dendrogram?
`...` | Additional parameters to be passed to dtwclust::tsclust() function.

### Value

A tibble with the clusters or clusters' members.

### Author(s)

Rolf Simoes, rolf.simoes@inpe.br

### References

"dtwclust" package (https://CRAN.R-project.org/package=dtwclust)

### Examples

    ## Not run:
    # Load the "dtwclust" package
    # library(dtwclust)
    # load a simple data set with two classes
    data(cerrado_2classes)
    # calculate the dendrogram and the best clusters
    clusters <- sits_cluster_dendro(cerrado_2classes, bands = c("NDVI", "EVI"))

    ## End(Not run)

[Package sits version 0.11.0 Index]