docs_old/infomapbasics.md

In Ecological-Complexity-Lab/infomap_ecology_package: Community Detection using Infomap, Inspired by Ecological Networks

Infomap arguments

Most of the Infomap arguments we use are common for all the examples and their detailed description can be found here. We explain in each example the most relevant specific arguments. Here is a typical running command:

./Infomap infomap.txt . --tree -i link-list --seed 123 -N 20 -f undirected -2.

• infomap.txt is the name of the input file
• . indicates that the output will be written to the same folder as the input file.
• --tree sets the output format.
• -i link-list indicates that the input is a link list.
• --seed 123 provides a seed to the random number generator such that each run will result in the same output, which is useful for replication.
• -N 20 tells infomap to run 20 trials and select the result of the best one.
• -f undirected indicates flow on an undirected network.
• -2 indicates a two-level solution, with no hierarchical modules (modules within modules).

Infomap output

The output, written into the tree file, is as follows (details here).

# v1.0.6
# ./Infomap infomap.txt . -i link-list --out-name infomap_out --tree --seed 123 -N 20 -f undirected --silent --two-level
# started at 2020-03-11 14:24:12
# completed in 0.0300386 s
# codelength 4.565 bits
# relative codelength savings 2.4337%
# path flow name node_id
1:1 0.00091617 "1" 1
1:2 0.00229043 "7" 7
1:3 0.00114521 "8" 8
1:4 0.00091617 "10" 10
1:5 0.000458085 "11" 11

The first four lines are quite obvious. The 5th line provides the value of the map equations objective function (L) for the optimal partition. After the headings, rows describe module affiliation and flow. The path column is a tree-like format. The last integer after the colon indicates the ID of the leaf in the module, and not the ID of the node. See detailed explanations also in the R function (run_infomap_monolayer) in the package, which automatically reads this output and adds the affiliation of modules to the node table to create an output similar to this:

node_id node_name             module_level1 module_level2 node_type node_group
 1       1 Aglais.urticae                    1             1 c         A         
 2       2 Apis.mellifera                    2             1 c         A         
 3       3 Bombus.lapidarius                 2             2 c         A         
 4       4 Bombus.muscorum                   3             1 c         A         
 5       5 Bombus.pascuorum                  3             2 c         A         
 6       6 Bombus.terrestris                 2             3 c         A 

Here, module_level1 is the module ID and module_level2 is the leaf ID, extracted from the path column. node_type is either c for column or r for row, indicating of the node appears in the column or row of the matrix format.

Ecological-Complexity-Lab/infomap_ecology_package documentation built on June 6, 2024, 5:28 a.m.