Finding communities in large datasets"

In dendroNetwork: Create Networks of Dendrochronological Series using Pairwise Similarity

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(dendroNetwork)

Community detection in very large datasets

When using larger datasets of tree-ring series, calculating the table with similarities can take a lot of time, but finding communities even more. It is therefore recommended to use of parallel computing for Clique Percolation: clique_community_names_par(network, k=3, n_core = 4). This reduces the amount of time significantly. For most datasets clique_community_names() is sufficiently fast and for smaller datasets clique_community_names_par() can even be slower due to the parallelisation. Therefore, the funtion clique_community_names() should be used initially and if this is very slow, start using clique_community_names_par().

The workflow is similar as described in the vignette("dendroNetwork"), but with minor changes:

1. load network.

2. compute similarities.

3. find the maximum clique size: igraph::clique_num(network) .

4. detect communities for each clique size separately:

   • com_cpm_k3 <- clique_community_names_par(network, k=3, n_core = 6).

   • com_cpm_k4 <- clique_community_names_par(network, k=4, n_core = 6).

   • and so on until the maximum clique size.

5. merge these into a single data frame by com_cpm_all <- rbind(com_cpm_k3,com_cpm_k4, com_cpm_k5,... ) .

6. create table for use in cytoscape with all communities: com_cpm_all <- com_cpm_all |> dplyr::count(node, com_name) |> tidyr::spread(com_name, n) .

7. Continue with the visualisation in Cytoscape, see the relevant section in the vignette("dendroNetwork") .

dendroNetwork documentation built on May 29, 2024, 1:08 a.m.