robinCompareFast: robinCompareFast

View source: R/ROBINFast.R

robinCompareFastR Documentation

robinCompareFast

Description

This function compares two community detection algorithms. Is the parallelized and faster version of robinCompare

Usage

robinCompareFast(
  graph,
  method1 = c("walktrap", "edgeBetweenness", "fastGreedy", "leadingEigen", "louvain",
    "spinglass", "labelProp", "infomap", "optimal", "leiden", "other"),
  args1 = list(),
  method2 = c("walktrap", "edgeBetweenness", "fastGreedy", "leadingEigen", "louvain",
    "spinglass", "labelProp", "infomap", "optimal", "leiden", "other"),
  args2 = list(),
  measure = c("vi", "nmi", "split.join", "adjusted.rand"),
  FUN1 = NULL,
  FUN2 = NULL,
  verbose = TRUE,
  BPPARAM = BiocParallel::bpparam()
)

Arguments

graph

The output of prepGraph.

method1

The first clustering method, one of "walktrap", "edgeBetweenness", "fastGreedy", "louvain", "spinglass", "leadingEigen", "labelProp", "infomap","optimal".

args1

A list of arguments to be passed to the method1 (see i.e. cluster_leiden for a list of possible method parameters).

method2

The second custering method one of "walktrap", "edgeBetweenness","fastGreedy", "louvain", "spinglass", "leadingEigen", "labelProp", "infomap","optimal".

args2

A list of arguments to be passed to the method2 (see i.e. cluster_leiden for a list of possible method parameters).

measure

The stability measure, one of "vi", "nmi", "split.join", "adjusted.rand" all normalized and used as distances. "nmi" refers to 1- nmi and "adjusted.ran" refers to 1-adjusted.rand.

FUN1

personal designed function when method1 is "others". see methodCommunity.

FUN2

personal designed function when method2 is "others". see methodCommunity.

verbose

flag for verbose output (default as TRUE).

BPPARAM

the BiocParallel object of class bpparamClass that specifies the back-end to be used for computations. See bpparam for details.

Value

A list object with two matrices: - the matrix "Mean1" with the means of the procedure for the first method - the matrix "Mean2" with the means of the procedure for the second method


robin documentation built on June 24, 2024, 5:11 p.m.