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Kernel k-means clustering using indices

Source: R/clustering.R
clustInd_kkmeans.Rd

Perform kernel kmeans clustering for a different combinations of indices and kernel

Usage

clustInd_kkmeans(
  ind_data,
  vars_combinations,
  kernel_list = c("rbfdot", "polydot"),
  n_cluster = 2,
  true_labels = NULL,
  n_cores = 1
)

Arguments

ind_data

Dataframe containing indices applied to the original data and its first and second derivatives. See generate_indices.

vars_combinations

list containing one or more combinations of indices in ind_data. If it is non-named, the names of the variables are set to vars1, ..., varsk, where k is the number of elements in vars_combinations.

kernel_list

List of kernels

n_cluster

Number of clusters to create

true_labels

Vector of true labels for validation (if it is not known true_labels is set to NULL)

n_cores

Number of cores to do parallel computation. 1 by default, which mean no parallel execution.

Value

A list containing kernel-kmeans clustering results for each configuration.

Examples

vars1 <- c("dtaEI", "dtaMEI")
vars2 <- c("dtaHI", "dtaMHI")
data <- ehymet::sim_model_ex1()
data_ind <- generate_indices(data)
clustInd_kkmeans(data_ind, list(vars1, vars2))
#> Using automatic sigma estimation (sigest) for RBF or laplace kernel 
#> Using automatic sigma estimation (sigest) for RBF or laplace kernel 
#>  Setting default kernel parameters  
#>  Setting default kernel parameters  
#> $kkmeans_rbfdot_dtaEIdtaMEI
#> $kkmeans_rbfdot_dtaEIdtaMEI$cluster
#>   [1] 1 2 2 2 2 1 2 1 1 2 2 2 1 2 1 1 2 2 1 2 1 1 1 1 2 2 2 1 1 2 2 2 2 2 2 2 2
#>  [38] 2 2 1 2 1 2 2 2 2 2 1 2 2 1 1 1 1 1 1 1 2 2 1 1 1 2 1 2 2 1 1 2 1 1 1 2 1
#>  [75] 1 2 2 2 1 1 1 1 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 2 2 1
#> 
#> $kkmeans_rbfdot_dtaEIdtaMEI$internal_metrics
#> $kkmeans_rbfdot_dtaEIdtaMEI$internal_metrics$davies_bouldin
#> [1] 1.458379
#> 
#> $kkmeans_rbfdot_dtaEIdtaMEI$internal_metrics$dunn
#> [1] 0.01120901
#> 
#> $kkmeans_rbfdot_dtaEIdtaMEI$internal_metrics$silhouette
#> [1] 0.3107621
#> 
#> $kkmeans_rbfdot_dtaEIdtaMEI$internal_metrics$infomax
#> [1] 0.9988455
#> 
#> 
#> $kkmeans_rbfdot_dtaEIdtaMEI$time
#> [1] 0.01720166
#> 
#> 
#> $kkmeans_rbfdot_dtaHIdtaMHI
#> $kkmeans_rbfdot_dtaHIdtaMHI$cluster
#>   [1] 1 2 1 2 1 1 1 2 2 1 2 2 2 1 2 2 2 2 2 1 1 1 2 1 2 2 2 2 1 2 1 2 1 1 2 2 2
#>  [38] 2 2 1 2 2 2 1 2 1 1 2 2 2 2 1 1 1 1 1 2 1 1 2 1 1 2 1 1 1 1 1 1 1 2 2 1 2
#>  [75] 1 2 2 1 2 1 2 1 2 2 2 1 1 1 2 2 1 2 1 1 1 1 1 1 2 2
#> 
#> $kkmeans_rbfdot_dtaHIdtaMHI$internal_metrics
#> $kkmeans_rbfdot_dtaHIdtaMHI$internal_metrics$davies_bouldin
#> [1] 1.552428
#> 
#> $kkmeans_rbfdot_dtaHIdtaMHI$internal_metrics$dunn
#> [1] 0.0115923
#> 
#> $kkmeans_rbfdot_dtaHIdtaMHI$internal_metrics$silhouette
#> [1] 0.3362841
#> 
#> $kkmeans_rbfdot_dtaHIdtaMHI$internal_metrics$infomax
#> [1] 1
#> 
#> 
#> $kkmeans_rbfdot_dtaHIdtaMHI$time
#> [1] 0.01049328
#> 
#> 
#> $kkmeans_polydot_dtaEIdtaMEI
#> $kkmeans_polydot_dtaEIdtaMEI$cluster
#>   [1] 1 2 1 2 1 1 1 2 2 1 2 2 2 2 2 2 2 2 2 1 1 1 2 1 2 2 2 2 1 2 1 2 1 1 2 2 2
#>  [38] 2 2 1 2 2 2 2 2 1 1 2 2 2 1 1 1 1 1 1 1 1 2 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1
#>  [75] 1 2 2 1 1 1 1 1 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 2 2 2
#> 
#> $kkmeans_polydot_dtaEIdtaMEI$internal_metrics
#> $kkmeans_polydot_dtaEIdtaMEI$internal_metrics$davies_bouldin
#> [1] 0.6690505
#> 
#> $kkmeans_polydot_dtaEIdtaMEI$internal_metrics$dunn
#> [1] 0.01564565
#> 
#> $kkmeans_polydot_dtaEIdtaMEI$internal_metrics$silhouette
#> [1] 0.5272745
#> 
#> $kkmeans_polydot_dtaEIdtaMEI$internal_metrics$infomax
#> [1] 0.985815
#> 
#> 
#> $kkmeans_polydot_dtaEIdtaMEI$time
#> [1] 0.01222348
#> 
#> 
#> $kkmeans_polydot_dtaHIdtaMHI
#> $kkmeans_polydot_dtaHIdtaMHI$cluster
#>   [1] 1 2 2 2 2 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 2 1 2 2 2 2 1 2 1 2 1 1 2 2 2
#>  [38] 2 2 1 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 2 1 1 1 2 1 1 1 1 1 2 1 1 1 2 1
#>  [75] 1 2 2 2 1 1 1 1 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 2 2 2
#> 
#> $kkmeans_polydot_dtaHIdtaMHI$internal_metrics
#> $kkmeans_polydot_dtaHIdtaMHI$internal_metrics$davies_bouldin
#> [1] 0.6134443
#> 
#> $kkmeans_polydot_dtaHIdtaMHI$internal_metrics$dunn
#> [1] 0.02153625
#> 
#> $kkmeans_polydot_dtaHIdtaMHI$internal_metrics$silhouette
#> [1] 0.5476103
#> 
#> $kkmeans_polydot_dtaHIdtaMHI$internal_metrics$infomax
#> [1] 0.9988455
#> 
#> 
#> $kkmeans_polydot_dtaHIdtaMHI$time
#> [1] 0.01191306
#> 
#>