n_clusters: Find number of clusters in your data

In parameters: Processing of Model Parameters

Find number of clusters in your data

Description

Similarly to n_factors() for factor / principal component analysis, n_clusters() is the main function to find out the optimal numbers of clusters present in the data based on the maximum consensus of a large number of methods.

Essentially, there exist many methods to determine the optimal number of clusters, each with pros and cons, benefits and limitations. The main n_clusters function proposes to run all of them, and find out the number of clusters that is suggested by the majority of methods (in case of ties, it will select the most parsimonious solution with fewer clusters).

Note that we also implement some specific, commonly used methods, like the Elbow or the Gap method, with their own visualization functionalities. See the examples below for more details.

Usage

n_clusters(
  x,
  standardize = TRUE,
  include_factors = FALSE,
  package = c("easystats", "NbClust", "mclust"),
  fast = TRUE,
  nbclust_method = "kmeans",
  n_max = 10,
  ...
)

n_clusters_elbow(
  x,
  standardize = TRUE,
  include_factors = FALSE,
  clustering_function = stats::kmeans,
  n_max = 10,
  ...
)

n_clusters_gap(
  x,
  standardize = TRUE,
  include_factors = FALSE,
  clustering_function = stats::kmeans,
  n_max = 10,
  gap_method = "firstSEmax",
  ...
)

n_clusters_silhouette(
  x,
  standardize = TRUE,
  include_factors = FALSE,
  clustering_function = stats::kmeans,
  n_max = 10,
  ...
)

n_clusters_dbscan(
  x,
  standardize = TRUE,
  include_factors = FALSE,
  method = c("kNN", "SS"),
  min_size = 0.1,
  eps_n = 50,
  eps_range = c(0.1, 3),
  ...
)

n_clusters_hclust(
  x,
  standardize = TRUE,
  include_factors = FALSE,
  distance_method = "correlation",
  hclust_method = "average",
  ci = 0.95,
  iterations = 100,
  ...
)

Arguments

x	A data frame.
standardize	Standardize the dataframe before clustering (default).
include_factors	Logical, if TRUE, factors are converted to numerical values in order to be included in the data for determining the number of clusters. By default, factors are removed, because most methods that determine the number of clusters need numeric input only.
package	Package from which methods are to be called to determine the number of clusters. Can be "all" or a vector containing "easystats", "NbClust", "mclust", and "M3C".
fast	If FALSE, will compute 4 more indices (sets index = "allong" in NbClust). This has been deactivated by default as it is computationally heavy.
nbclust_method	The clustering method (passed to NbClust::NbClust() as method).
n_max	Maximal number of clusters to test.
...	Arguments passed to or from other methods. For instance, when bootstrap = TRUE, arguments like type or parallel are passed down to bootstrap_model(). Further non-documented arguments are digits, p_digits, ci_digits and footer_digits to set the number of digits for the output. If s_value = TRUE, the p-value will be replaced by the S-value in the output (cf. Rafi and Greenland 2020). pd adds an additional column with the probability of direction (see bayestestR::p_direction() for details). groups can be used to group coefficients. It will be passed to the print-method, or can directly be used in print(), see documentation in print.parameters_model(). Furthermore, see 'Examples' for this function. For developers, whose interest mainly is to get a "tidy" data frame of model summaries, it is recommended to set pretty_names = FALSE to speed up computation of the summary table.
clustering_function, gap_method	Other arguments passed to other functions. clustering_function is used by fviz_nbclust() and can be kmeans, cluster::pam, cluster::clara, cluster::fanny, and more. gap_method is used by cluster::maxSE to extract the optimal numbers of clusters (see its method argument).
method, min_size, eps_n, eps_range	Arguments for DBSCAN algorithm.
distance_method	The distance method (passed to dist()). Used by algorithms relying on the distance matrix, such as hclust or dbscan.
hclust_method	The hierarchical clustering method (passed to hclust()).
ci	Confidence Interval (CI) level. Default to 0.95 (⁠95%⁠).
iterations	The number of bootstrap replicates. This only apply in the case of bootstrapped frequentist models.

Note

There is also a plot()-method implemented in the see-package.

Examples

library(parameters)

# The main 'n_clusters' function ===============================
if (require("mclust", quietly = TRUE) && require("NbClust", quietly = TRUE) &&
  require("cluster", quietly = TRUE) && require("see", quietly = TRUE)) {
  n <- n_clusters(iris[, 1:4], package = c("NbClust", "mclust")) # package can be "all"
  n
  summary(n)
  as.data.frame(n) # Duration is the time elapsed for each method in seconds
  plot(n)

  # The following runs all the method but it significantly slower
  # n_clusters(iris[1:4], standardize = FALSE, package = "all", fast = FALSE)
}



x <- n_clusters_elbow(iris[1:4])
x
as.data.frame(x)
plot(x)



#
# Gap method --------------------
if (require("see", quietly = TRUE) &&
  require("cluster", quietly = TRUE) &&
  require("factoextra", quietly = TRUE)) {
  x <- n_clusters_gap(iris[1:4])
  x
  as.data.frame(x)
  plot(x)
}


#
# Silhouette method --------------------------
if (require("factoextra", quietly = TRUE)) {
  x <- n_clusters_silhouette(iris[1:4])
  x
  as.data.frame(x)
  plot(x)
}


#
if (require("dbscan", quietly = TRUE)) {
  # DBSCAN method -------------------------
  # NOTE: This actually primarily estimates the 'eps' parameter, the number of
  # clusters is a side effect (it's the number of clusters corresponding to
  # this 'optimal' EPS parameter).
  x <- n_clusters_dbscan(iris[1:4], method = "kNN", min_size = 0.05) # 5 percent
  x
  head(as.data.frame(x))
  plot(x)

  x <- n_clusters_dbscan(iris[1:4], method = "SS", eps_n = 100, eps_range = c(0.1, 2))
  x
  head(as.data.frame(x))
  plot(x)
}


#
# hclust method -------------------------------
if (require("pvclust", quietly = TRUE)) {
  # iterations should be higher for real analyses
  x <- n_clusters_hclust(iris[1:4], iterations = 50, ci = 0.90)
  x
  head(as.data.frame(x), n = 10) # Print 10 first rows
  plot(x)
}

parameters documentation built on Oct. 18, 2024, 5:13 p.m.