AgglomerativeClustering: Performs clustering according to the agglomerative algorithm

In rgudhi: An Interface to the GUDHI Library for Topological Data Analysis

Performs clustering according to the agglomerative algorithm

Description

Recursively merges pair of clusters of sample data; uses linkage distance. This is a wrapper around the Python class sklearn.cluster.AgglomerativeClustering.

Super classes

rgudhi::PythonClass -> rgudhi::SKLearnClass -> rgudhi::BaseClustering -> AgglomerativeClustering

Methods

Public methods

• AgglomerativeClustering$new()

• AgglomerativeClustering$clone()

Inherited methods

• rgudhi::PythonClass$get_python_class()
• rgudhi::PythonClass$set_python_class()
• rgudhi::SKLearnClass$apply()
• rgudhi::SKLearnClass$fit()
• rgudhi::SKLearnClass$fit_transform()
• rgudhi::SKLearnClass$get_params()
• rgudhi::SKLearnClass$set_params()
• rgudhi::SKLearnClass$transform()

---

Method new()

The AgglomerativeClustering class constructor.

Usage

AgglomerativeClustering$new(
  n_clusters = 2L,
  affinity = c("euclidean", "l1", "l2", "manhattan", "cosine", "precomputed"),
  memory = NULL,
  connectivity = NULL,
  compute_full_tree = "auto",
  linkage = c("ward", "complete", "average", "single"),
  distance_threshold = NULL,
  compute_distances = FALSE
)

Arguments

n_clusters

An integer value specifying the number of clusters to find. It must be NULL if distance_threshold is not NULL. Defaults to 2L.

affinity

A string specifying the metric used to compute the linkage. Can be "euclidean", "l1", "l2", "manhattan", "cosine" or "precomputed". If linkage is "ward", only "euclidean" is accepted. If "precomputed", a distance matrix (instead of a similarity matrix) is needed as input for the ⁠$fit()⁠ method. Defaults to "euclidean".

memory

A string specifying the path to the caching directory. Defaults to NULL in which case no caching is done.

connectivity

Either a numeric matrix or an object of class stats::dist or an object coercible into a function by rlang::as_function() specifying for each sample the neighboring samples following a given structure of the data. This can be a connectivity matrix itself or a function that transforms the data into a connectivity matrix. Defaults to NULL, i.e., the hierarchical clustering algorithm is unstructured.

compute_full_tree

Either a boolean value or the "auto" string specifying whether to prematurely stop the construction of the tree at n_clusters. This is useful to decrease computation time if the number of clusters is not small compared to the number of samples. This option is useful only when specifying a connectivity matrix. Note also that when varying the number of clusters and using caching, it may be advantageous to compute the full tree. It must be TRUE if distance_threshold is not NULL. Defaults to "auto", which is equivalent to TRUE when distance_threshold is not NULL or that n_clusters is inferior to the maximum between 100 and 0.02 * n_samples. Otherwise, "auto" is equivalent to FALSE.

linkage

A string specifying which linkage criterion to use. The linkage criterion determines which distance to use between sets of observation. The algorithm will merge the pairs of cluster that minimize this criterion.

• ward: minimizes the variance of the clusters being merged;

• average: uses the average of the distances of each observation of the two sets;

• complete: uses the maximum of the distances between all observations of the two sets.

• single: uses the minimum of the distances between all observations of the two sets. Defaults to "ward".

distance_threshold

A numeric value specifying the linkage distance threshold above which clusters will not be merged. If not NULL, n_clusters must be NULL and compute_full_tree must be TRUE. Defaults to NULL.

compute_distances

A boolean value specifying whether to compute distances between clusters even if distance_threshold is not used. This can be used to make dendrogram visualization, but introduces a computational and memory overhead. Defaults to FALSE.

Returns

An object of class AgglomerativeClustering.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

AgglomerativeClustering$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

cl <- AgglomerativeClustering$new()

rgudhi documentation built on March 31, 2023, 11:38 p.m.