cliqueR

R Library used to calculate Maximal Cliques, Maximum Cliques, and Paracliques for graphs

Examples

Load the package.

library(cliqueR)

There are three different function calls, each with their own set of parameters:

• Maximal
• Maximum
• Paraclique

Maximal

To find the maximal clique, you need the file name at a bare minimum. The other parameters are the following:

• least: Lower bound of clique size to include. (a value less than 3 will simply return every edge in the graph).
• most: Upper bound of clique size to include.
• profile: Option to return a clique profile instead of all cliques. By default, these values are 3, -1, and 0 respectively.

Example calls:

cliqueR.maximal("inst/extdata/bio-yeast.el")
cliqueR.maximal("inst/extdata/bio-yeast.el", 5)

Maximum

To find the maximum clique, you need the file name at a bare minimum. It also has an optional second parameter called sizeOnly which defaults to FALSE. This option allows the user to return the size of the maximum clique.

Example calls:

cliqueR.maximum("inst/extdata/bio-yeast.el")
cliqueR.maximum("inst/extdata/bio-yeast.el", TRUE)

Paraclique

Paraclique returns a list of paracliques ordered by size. At a minimum, the file name is required as the first parameter. It also has the following additional parameters:

• igf: Glom Factor, initialized to 1.0.
• min_mc_size: The minimum clique size to include. Initialized to 5.
• min_pc_size: The minimum paraclique size to include. Initialzed to 5.
• max_num_pcs: Max number of paracliques to include. Initialized to -1.