ARLClustering - Testing Dolphins dataset

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Dataset description

The Dolphins network dataset is provided as a gml file, containing 62 nodes and 159 edges.

Loading network dataset

Graph Label : Dolphins Network
Total Nodes : 62
Total Edges : 159
Average Degree : 5.129032

# Start the timer
t1 <- system.time({
  dataset_path <- system.file("extdata", "dolphins.gml", package = "arlclustering")
  if (dataset_path == "") {
    stop("dolphins.gml file not found")
  }
  
  g <- arlc_get_network_dataset(dataset_path, "Dolphins")
  g$graphLabel
  g$totalEdges
  g$totalNodes
  g$averageDegree
})

# Display the total processing time
message("Graph loading Processing Time: ", t1["elapsed"], " seconds\n")
#> Graph loading Processing Time: 0.0129999999999999 seconds

Generate Transactions

Next, we generate transactions from the graph, with a total rows of 53.

# Start the timer
t2 <- system.time({
  
  transactions <- arlc_gen_transactions(g$graph)
  transactions
})

# Display the total processing time
message("Transaction dataset Processing Time: ", t2["elapsed"], " seconds\n")
#> Transaction dataset Processing Time: 0.0250000000000004 seconds

Get Apriori Thresholds

We obtain the apriori thresholds for the generated transactions. The following are the thresholds for the apriori execution: - The Minimum Support : 0.05 - The Minimum Confidence : 0.5 - The Lift : 13.25 - The Gross Rules length : 201 - The selection Ratio : 4

# Start the timer
t3 <- system.time({
  params <- arlc_get_apriori_thresholds(transactions,
                                      supportRange = seq(0.05, 0.07, by = 0.01),
                                      Conf = 0.5)
  params$minSupp
  params$minConf
  params$bestLift
  params$lenRules
  params$ratio
})

# Display the total processing time
message("Graph loading Processing Time: ", t3["elapsed"], " seconds\n")
#> Graph loading Processing Time: 0.044 seconds

Generate Gross Rules

We use the obtained parameters to generate gross rules, where we obtain 201 rules.

# Start the timer
t4 <- system.time({
  minLenRules <- 1
  maxLenRules <- params$lenRules
  if (!is.finite(maxLenRules) || maxLenRules > 5*length(transactions)) {
    maxLenRules <- 5*length(transactions)
  }
  
  grossRules <- arlc_gen_gross_rules(transactions,
                                     minSupp = params$minSupp,
                                     minConf = params$minConf,
                                     minLenRules = minLenRules+1,
                                     maxLenRules = maxLenRules)
  #grossRules$TotalRulesWithLengthFilter
})
#> Apriori
#> 
#> Parameter specification:
#>  confidence minval smax arem  aval originalSupport maxtime support minlen
#>         0.5    0.1    1 none FALSE            TRUE       5    0.05      2
#>  maxlen target  ext
#>     201  rules TRUE
#> 
#> Algorithmic control:
#>  filter tree heap memopt load sort verbose
#>     0.1 TRUE TRUE  FALSE TRUE    2    TRUE
#> 
#> Absolute minimum support count: 2 
#> 
#> set item appearances ...[0 item(s)] done [0.00s].
#> set transactions ...[62 item(s), 53 transaction(s)] done [0.00s].
#> sorting and recoding items ... [46 item(s)] done [0.00s].
#> creating transaction tree ... done [0.00s].
#> checking subsets of size 1 2 3 4 done [0.00s].
#> writing ... [201 rule(s)] done [0.00s].
#> creating S4 object  ... done [0.00s].

# Display the total number of clusters and the total processing time
message("Gross rules generation Time: ", t4["elapsed"], " seconds\n")
#> Gross rules generation Time: 0.0110000000000001 seconds

Filter Significant and Non-Redundant Rules

We filter out redundant rules from the generated gross rules. Next, we filter out non-significant rules from the non-redundant rules, and we obtain the 172 rule items.

t5 <- system.time({
  NonRedRules <- arlc_get_NonR_rules(grossRules$GrossRules)
  NonRSigRules <- arlc_get_significant_rules(transactions,
                                             NonRedRules$FiltredRules)
  #NonRSigRules$TotFiltredRules
})
# Display the total number of clusters and the total processing time
message("\nClearing rules Processing Time: ", t5["elapsed"], " seconds\n")
#> 
#> Clearing rules Processing Time: 0.179 seconds

Clean and genarate final Rules

We clean the final set of rules to prepare for clustering. Then, we generate clusters based on the cleaned rules. The total identified clusters is 17 clusters.

t6 <- system.time({
  cleanedRules <- arlc_clean_final_rules(NonRSigRules$FiltredRules)
  clusters <- arlc_generate_clusters(cleanedRules)
  #clusters$TotClusters
})
# Display the total number of clusters and the total processing time
message("Cleaning final rules Processing Time: ", t6["elapsed"], " seconds\n")
#> Cleaning final rules Processing Time: 0.0140000000000002 seconds


message("The total comsumed time is:",t1["elapsed"]+ t2["elapsed"]+t3["elapsed"]+t4["elapsed"]+t5["elapsed"]+t6["elapsed"], "seconds\n")
#> The total comsumed time is:0.286000000000001seconds

Plot Clusters

Finally, we visualize the identified clusters.

arlc_clusters_plot(g$graph,
                   g$graphLabel,
                   clusters$Clusters)
#> 
#> Total Identified Clusters: 17
#>  =========================
#>   Community 01:2 8 14 26 58
#>   Community 02:6 7 18 42
#>   Community 03:7 10 14 18 42 58
#>   Community 04:9 37
#>   Community 05:10 14 18 55 58
#>   Community 06:11 43
#>   Community 07:15 17 21 34 38 39 41 44
#>   Community 08:16 30 52
#>   Community 09:17 34 35 39 41 44 51
#>   Community 10:18 27 42 55
#>   Community 11:19 22 25 30 46 52
#>   Community 12:22 25 30 44 46 51 52
#>   Community 13:34 38 39 53
#>   Community 14:38 39 51 60
#>   Community 15:42 55 58
#>   Community 16:43 48
#>   Community 17:44 53
#>  =========================

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