In the igraph ?modularity部分有示例代码，如下所示
g <- graph.full(5) %du% graph.full(5) %du% graph.full(5)
g <- add.edges(g, c(1,6, 1,11, 6, 11))
wtc <- walktrap.community(g)
modularity(wtc)
#[1] 0.5757575
modularity(g, membership(wtc))
#[1] 0.5757576
的输出wtc shows:
wtc
#Graph community structure calculated with the walktrap algorithm
#Number of communities (best split): 3
#Modularity (best split): 0.5757575
#Membership vector:
# [1] 3 3 3 3 3 1 1 1 1 1 2 2 2 2 2
我对不同部分感到困惑：
modularity(wtc)
# and
modularity(g, membership(wtc))
wtc其本身已经具有最佳的分割及其相关的模块化。为什么打电话modularity on wtc? modularity(g, membership(wtc))我看到的是找到特定预先选择的分割的模块化，这对我来说更有意义（在这种情况下是最佳分割）。
在什么情况下，您期望这些结果会有所不同以及为什么会有所不同，例如
g2 <- structure(list(from = structure(c(2L, 3L, 4L, 1L, 3L, 4L, 1L,
2L, 4L, 1L, 2L, 3L), .Label = c("A", "B", "C", "D"), class = "factor"),
to = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 4L,
4L, 4L), .Label = c("A", "B", "C", "D"), class = "factor"),
weight = c(2L, 0L, 0L, 2L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L
)), .Names = c("from", "to", "weight"), row.names = c(2L,
3L, 4L, 5L, 7L, 8L, 9L, 10L, 12L, 13L, 14L, 15L), class = "data.frame")
g2 <- graph.data.frame(g2, vertices = unique(g2[1]))
set.seed(444)
wtc2 <- walktrap.community(g2)
modularity(wtc2)
# [1] 0.4444444
wtc2
# Graph community structure calculated with the walktrap algorithm
# Number of communities (best split): 2
# Modularity (best split): 0.4444444
# Membership vector:
# B C D A
# 2 1 1 2
modularity(g2, membership(wtc2))
# [1] -0.1666667
sessionInfo()
# R version 3.0.2 (2013-09-25)
# Platform: x86_64-apple-darwin10.8.0 (64-bit)
#
# locale:
# [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] Matrix_1.0-14 lattice_0.20-23 igraph_0.6.6 reshape2_1.2.2 ggplot2_0.9.3.1
#
# loaded via a namespace (and not attached):
# [1] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.3 grid_3.0.2 gtable_0.1.2 labeling_0.2
# [7] MASS_7.3-29 munsell_0.4.2 plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 scales_0.2.3
# [13] stringr_0.6.2 tools_3.0.2
