| as.SimilarityMatrix | Convert a matrix to a similarity matrix. 'as.SimilarityMatrix' convert an adjacency matrix to a similarity matrix. |
| as.symmetricAdjacencyMatrix | convert to a symmetric adjacency matrix |
| getEigenvalueList | generate eigenvalues for all ensemble matrices 'getEigenvalueList' get eigenvalues from ensemble matrices |
| getEns | generate ensemble matrix 'getEns' get ensemble matrix from given similarity matrix and temperature |
| getEnsList | generating a list of ensemble matrices based on the similarity matrix and temperatures |
| GetSim | 'GetSim' get similarity matrix from a distance matrix |
| monkeyGrooming | Grooming network data |
| plotCLUSTERS | generate tree plots for each ensemble matrix 'plotCLUSTERS' plot all cluster trees |
| plotMultiEigenvalues | plot eigenvalues 'plotMultiEigenvalues' plot eigenvalues to determine number of communities by finding the elbow point |
| plotTheCluster | generate tree plots for selected ensemble matrix 'plotTrees' plot one cluster tree |
| temperatureSample | generate temperatures 'temperatureSample' generate tempatures based on either random or fixed intervals |