BayesCVI (version 1.0.2)

B_STRPBM.IDX: BCVI-Starczewski and Pakhira-Bandyopadhyay-Maulik for crisp clustering indexes

Description

Compute Bayesian cluster validity index (BCVI) from two to kmax groups using Starczewski (STR) and/or Pakhira-Bandyopadhyay-Maulik (PBM) as the underlying cluster validity index (CVI) and Dirichlet prior parameters of the user's choice. The full detail of BCVI can be found in the paper Wiroonsri and Preedasawakul (2024).

Usage

B_STRPBM.IDX(x, kmax, method = "kmeans", indexlist = "all",
          nstart = 100, alpha = "default", mult.alpha = 1/2)

Value

BCVI

the dataframe where the first and the second columns are the number of groups k and BCVI\((k)\), respectively, for k from 2 to kmax.

VAR

the data frame where the first and the second columns are the number of groups k and the variance of \(p_k\), respectively, for k from 2 to kmax.

CVI

the data frame where the first and the second columns are the number of groups k and the original STR\((k)\) or PBM\((k)\), respectively, for k from 2 to kmax.

Arguments

x

a numeric data frame or matrix where each column is a variable to be used for cluster analysis and each row is a data point.

kmax

a maximum number of clusters to be considered.

method

a character string indicating which clustering method to be used ("kmeans", "hclust_complete", "hclust_average", "hclust_single"). The default is "kmeans".

indexlist

a character string indicating which cluster validity indexes to be computed ("all", "STR", "PBM"). More than one indexes can be selected.

nstart

a maximum number of initial random sets for kmeans for method = "kmeans". The default is 100.

alpha

Dirichlet prior parameters \(\alpha_2,...,\alpha_k\) where \(\alpha_k\) is the parameter corresponding to "the probability of having k groups" (selecting each \(\alpha_k\) between 0 to 30 is recommended and using the other parameter mult.alpha to be its multiplier. The default is "default".)

mult.alpha

the power \(s\) from \(n^s\) to be multiplied to the Dirichlet prior parameters alpha (selecting mult.alpha in [0,1) is recommended). The default is \(\frac{1}{2}\).

Author

Nathakhun Wiroonsri and Onthada Preedasawakul

Details

BCVI-STRPBM is defined as follows.

Let
$$r_k(\bf x) = \dfrac{CVI(k)-\min_j CVI(j)}{\sum_{i=2}^K (CVI(i)-\min_j CVI(j))} $$ where CVI is either STR or PBM index.
Assume that
$$f({\bf x}|{\bf p}) = C({\bf p}) \prod_{k=2}^Kp_k^{nr_k(x)}$$ represents the conditional probability density function of the dataset given \(\bf p\), where \(C({\bf p})\) is the normalizing constant. Assume further that \({\bf p}\) follows a Dirichlet prior distribution with parameters \({\bm \alpha} = (\alpha_2,\ldots,\alpha_K)\). The posterior distribution of \(\bf p\) still remains a Dirichlet distribution with parameters \((\alpha_2+nr_2({\bf x}),\ldots,\alpha_K+nr_K({\bf x}))\).

The BCVI is then defined as
$$BCVI(k) = E[p_k|{\bf x}] = \frac{\alpha_k + nr_k({\bf x})}{\alpha_0+n}$$ where \(\alpha_0 = \sum_{k=2}^K \alpha_k.\)

The variance of \(p_k\) can be computed as $$Var(p_k|{\bf x}) = \dfrac{(\alpha_k + nr_k(x))(\alpha_0 + n -\alpha_k-nr_k(x))}{(\alpha_0 + n)^2(\alpha_0 + n +1 )}.$$

References

M. K. Pakhira, S. Bandyopadhyay and U. Maulik, "Validity index for crisp and fuzzy clusters," Pattern Recogn 37(3):487–501 (2004).

A. Starczewski, "A new validity index for crisp clusters," Pattern Anal Applic 20, 687–700 (2017).

O. Preedasawakul, and N. Wiroonsri, A Bayesian Cluster Validity Index, Computational Statistics & Data Analysis, 202, 108053, 2025. tools:::Rd_expr_doi("10.1016/j.csda.2024.108053")

See Also

B2_data, B_TANG.IDX, B_WP.IDX, B_Wvalid, B_DB.IDX

Examples

library(BayesCVI)

# The data included in this package.
data = B2_data[,1:2]

# alpha
aalpha = c(5,5,5,20,20,20,0.5,0.5,0.5)

B.STRPBM = B_STRPBM.IDX(x = scale(data), kmax=10, method = "kmeans",
            indexlist = "all", nstart = 100, alpha = aalpha, mult.alpha = 1/2)

# plot the BCVI-STR

pplot = plot_BCVI(B.STRPBM$STR)
pplot$plot_index
pplot$plot_BCVI
pplot$error_bar_plot

# plot the BCVI-PBM

pplot = plot_BCVI(B.STRPBM$PBM)
pplot$plot_index
pplot$plot_BCVI
pplot$error_bar_plot