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Cluster Analysis

Source: R/cluster_analysis.R
cluster_analysis.Rd

Compute hierarchical or kmeans cluster analysis and return the group assignment for each observation as vector.

Usage

cluster_analysis(
  x,
  n = NULL,
  method = "kmeans",
  include_factors = FALSE,
  standardize = TRUE,
  verbose = TRUE,
  distance_method = "euclidean",
  hclust_method = "complete",
  kmeans_method = "Hartigan-Wong",
  dbscan_eps = 15,
  iterations = 100,
  ...
)

Arguments

x

A data frame (with at least two variables), or a matrix (with at least two columns).

n

Number of clusters used for supervised cluster methods. If NULL, the number of clusters to extract is determined by calling n_clusters(). Note that this argument does not apply for unsupervised clustering methods like dbscan, hdbscan, mixture, pvclust, or pamk.

method

Method for computing the cluster analysis. Can be "kmeans" (default; k-means using kmeans()), "hkmeans" (hierarchical k-means using factoextra::hkmeans()), pam (K-Medoids using cluster::pam()), pamk (K-Medoids that finds out the number of clusters), "hclust" (hierarchical clustering using hclust() or pvclust::pvclust()), dbscan (DBSCAN using dbscan::dbscan()), hdbscan (Hierarchical DBSCAN using dbscan::hdbscan()), or mixture (Mixture modeling using mclust::Mclust(), which requires the user to run library(mclust) before).

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.

standardize

Standardize the dataframe before clustering (default).

verbose

Toggle warnings and messages.

distance_method

Distance measure to be used for methods based on distances (e.g., when method = "hclust" for hierarchical clustering. For other methods, such as "kmeans", this argument will be ignored). Must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". See dist() and pvclust::pvclust() for more information.

hclust_method

Agglomeration method to be used when method = "hclust" or method = "hkmeans" (for hierarchical clustering). This should be one of "ward", "ward.D2", "single", "complete", "average", "mcquitty", "median" or "centroid". Default is "complete" (see hclust()).

kmeans_method

Algorithm used for calculating kmeans cluster. Only applies, if method = "kmeans". May be one of "Hartigan-Wong" (default), "Lloyd" (used by SPSS), or "MacQueen". See kmeans() for details on this argument.

dbscan_eps

The eps argument for DBSCAN method. See n_clusters_dbscan().

iterations

The number of replications.

...

Arguments passed to or from other methods.

Value

The group classification for each observation as vector. The returned vector includes missing values, so it has the same length as nrow(x).

Details

The print() and plot() methods show the (standardized) mean value for each variable within each cluster. Thus, a higher absolute value indicates that a certain variable characteristic is more pronounced within that specific cluster (as compared to other cluster groups with lower absolute mean values).

Clusters classification can be obtained via print(x, newdata = NULL, ...).

Note

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

References

  • Maechler M, Rousseeuw P, Struyf A, Hubert M, Hornik K (2014) cluster: Cluster Analysis Basics and Extensions. R package.

See also

Examples

set.seed(33)
# K-Means ====================================================
rez <- cluster_analysis(iris[1:4], n = 3, method = "kmeans")
rez # Show results
#> # Clustering Solution
#> 
#> The 3 clusters accounted for 68.16% of the total variance of the original data.
#> 
#> Cluster | n_Obs | Sum_Squares | Sepal.Length | Sepal.Width | Petal.Length | Petal.Width
#> ---------------------------------------------------------------------------------------
#> 1       |    21 |       23.16 |        -1.32 |       -0.37 |        -1.13 |       -1.11
#> 2       |    33 |       17.33 |        -0.81 |        1.31 |        -1.28 |       -1.22
#> 3       |    96 |      149.26 |         0.57 |       -0.37 |         0.69 |        0.66
#> 
#>   Sum_Squares_Total Sum_Squares_Between Sum_Squares_Within        R2
#> 1               596            406.2488           189.7512 0.6816254
#> 
#> # You can access the predicted clusters via `predict()`.
#> 
predict(rez) # Get clusters
#>   [1] 2 1 1 1 2 2 2 2 1 1 2 2 1 1 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 1 1 2 2 2 1 1 2
#>  [38] 2 1 2 2 1 1 2 2 1 2 1 2 2 3 3 3 3 3 3 3 1 3 3 1 3 3 3 3 3 3 3 3 3 3 3 3 3
#>  [75] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 1 3 3 3 3 1 3 3 3 3 3 3 3 3 3 3 3 3
#> [112] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
#> [149] 3 3
summary(rez) # Extract the centers values (can use 'plot()' on that)
#>   Cluster Sepal.Length Sepal.Width Petal.Length Petal.Width
#> 1       1   -1.3232208  -0.3718921   -1.1334386  -1.1111395
#> 2       2   -0.8135055   1.3145538   -1.2825372  -1.2156393
#> 3       3    0.5690971  -0.3705265    0.6888118   0.6609378
if (requireNamespace("MASS", quietly = TRUE)) {
  cluster_discrimination(rez) # Perform LDA
}
#> # Accuracy of Cluster Group Classification via Linear Discriminant Analysis (LDA)
#> 
#>  Group Accuracy
#>      1  100.00%
#>      2   71.43%
#>      3  100.00%
#> 
#> Overall accuracy of classification: 96.00%
#> 

# Hierarchical k-means (more robust k-means)
if (require("factoextra", quietly = TRUE)) {
  rez <- cluster_analysis(iris[1:4], n = 3, method = "hkmeans")
  rez # Show results
  predict(rez) # Get clusters
}
#> Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa
#>   [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#>  [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 3 3 3 2 2 2 3 2 2 2 2 2 2 2 2 3 2 2 2 2 3 2 2 2
#>  [75] 2 3 3 3 2 2 2 2 2 2 2 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 3 3 3 3 2 3 3 3 3
#> [112] 3 3 2 2 3 3 3 3 2 3 2 3 2 3 3 2 3 3 3 3 3 3 2 2 3 3 3 2 3 3 3 2 3 3 3 2 3
#> [149] 3 2

# Hierarchical Clustering (hclust) ===========================
rez <- cluster_analysis(iris[1:4], n = 3, method = "hclust")
rez # Show results
#> # Clustering Solution
#> 
#> The 3 clusters accounted for 74.35% of the total variance of the original data.
#> 
#> Cluster | n_Obs | Sum_Squares | Sepal.Length | Sepal.Width | Petal.Length | Petal.Width
#> ---------------------------------------------------------------------------------------
#> 1       |    49 |       40.12 |        -1.00 |        0.90 |        -1.30 |       -1.25
#> 2       |    24 |       18.65 |        -0.40 |       -1.36 |         0.06 |       -0.04
#> 3       |    77 |       94.08 |         0.76 |       -0.15 |         0.81 |        0.81
#> 
#>   Sum_Squares_Total Sum_Squares_Between Sum_Squares_Within        R2
#> 1               596            443.1431           152.8569 0.7435286
#> 
#> # You can access the predicted clusters via `predict()`.
#> 
predict(rez) # Get clusters
#>   [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#>  [38] 1 1 1 1 2 1 1 1 1 1 1 1 1 3 3 3 2 3 2 3 2 3 2 2 3 2 3 3 3 3 2 2 2 3 3 3 3
#>  [75] 3 3 3 3 3 2 2 2 2 3 3 3 3 2 3 2 2 3 2 2 2 3 3 3 2 2 3 3 3 3 3 3 2 3 3 3 3
#> [112] 3 3 3 3 3 3 3 3 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
#> [149] 3 3

# K-Medoids (pam) ============================================
if (require("cluster", quietly = TRUE)) {
  rez <- cluster_analysis(iris[1:4], n = 3, method = "pam")
  rez # Show results
  predict(rez) # Get clusters
}
#>   [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#>  [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 3 3 3 2 3 3 3 3 3 3 3 3 2 3 3 3 3 3 3 3 3
#>  [75] 3 2 2 2 3 3 3 3 3 3 3 3 2 3 3 3 3 3 3 3 3 3 3 3 3 3 2 3 2 2 2 2 3 2 2 2 2
#> [112] 2 2 3 2 2 2 2 2 3 2 3 2 3 2 2 3 3 2 2 2 2 2 3 3 2 2 2 3 2 2 2 3 2 2 2 3 2
#> [149] 2 3

# PAM with automated number of clusters
if (require("fpc", quietly = TRUE)) {
  rez <- cluster_analysis(iris[1:4], method = "pamk")
  rez # Show results
  predict(rez) # Get clusters
}
#>   [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#>  [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
#>  [75] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
#> [112] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
#> [149] 2 2

# DBSCAN ====================================================
if (require("dbscan", quietly = TRUE)) {
  # Note that you can assimilate more outliers (cluster 0) to neighbouring
  # clusters by setting borderPoints = TRUE.
  rez <- cluster_analysis(iris[1:4], method = "dbscan", dbscan_eps = 1.45)
  rez # Show results
  predict(rez) # Get clusters
}
#> 
#> Attaching package: ‘dbscan’
#> The following object is masked from ‘package:fpc’:
#> 
#>     dbscan
#> The following object is masked from ‘package:stats’:
#> 
#>     as.dendrogram
#>   [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#>  [38] 1 1 1 1 0 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
#>  [75] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
#> [112] 2 2 2 2 2 2 0 0 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
#> [149] 2 2

# Mixture ====================================================
if (require("mclust", quietly = TRUE)) {
  library(mclust) # Needs the package to be loaded
  rez <- cluster_analysis(iris[1:4], method = "mixture")
  rez # Show results
  predict(rez) # Get clusters
}
#> Package 'mclust' version 6.1.1
#> Type 'citation("mclust")' for citing this R package in publications.
#>   [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#>  [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
#>  [75] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
#> [112] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
#> [149] 2 2