Monolayer directed network with hierarchical structure

Data set

A binary directed food web from Mouritsen KN, Poulin R, McLaughlin JP, Thieltges DW. Food web including metazoan parasites for an intertidal ecosystem in New Zealand: Ecological Archives E092-173. Ecology. 2011;92: 2006–2006.

In infomapecology:

data(otago_nodes)
data(otago_links)

Input

A link-list.

R Code

data(otago_nodes)
data(otago_links)
otago_nodes_2 <- otago_nodes %>%
  filter(StageID==1) %>%
  select(node_name=WorkingName, node_id_original=NodeID, WorkingName,StageID, everything())
anyDuplicated(otago_nodes_2$node_name)
otago_links_2 <- otago_links %>%
  filter(LinkType=='Predation') %>% # Only include predation links
  filter(ConsumerSpecies.StageID==1) %>%
  filter(ResourceSpecies.StageID==1) %>%
  select(from=ResourceNodeID, to=ConsumerNodeID) %>%
  left_join(otago_nodes_2, by=c('from'='node_id_original')) %>%
  select(from, node_name, to) %>%
  left_join(otago_nodes_2, by=c('to'='node_id_original')) %>%
  select(from=node_name.x, to=node_name.y) %>%
  mutate(weight=1)

# Prepare network objects and run infomap
# Some species will have only incoming or outgoing links, so the next line will result in a warning
network_object <- create_monolayer_object(x=otago_links_2, directed = T, bipartite = F, node_metadata = otago_nodes_2)
infomap_object <- run_infomap_monolayer(network_object, infomap_executable='Infomap',
                                        flow_model = 'directed',
                                        silent=T,trials=100, two_level=F, seed=200952)

Infomap

Under the hood, the function run_infomap_monolayer runs:

./Infomap infomap.txt . -i link-list --tree --seed 200952 -N 100 -f directed --silent

• Here, the most important feature is the lack of the argument -2 (or --two-level), which allows for hierarchical modules (the default in Infomap).
• -f directed indicates flow on a directed network.

Output

A tree file is produced by Infomap, but is parsed by run_infomap_monolayer from infomapecology (in R: ?run_infomap_monolayer). In addition, this data has node attributes, which are added to the final output. In this example: OrganismalGroup and NodeType. In this output excerpt, there are four nodes that belong to the 3rd submodule within top module 1. For these, module_level3 is the leaf id. Modules 2 and 3 do not have sub-modules. Therefore, for these modules the the second level (module_level2) is the leaf id and module_level3 shows an NA value.

node_id	node_name	module_level1	module_level2	module_level3	OrganismalGroup	NodeType
57	Nemertine 1	1	3	1	Nemertean	Taxon
58	Nemertine 2	1	3	2	Nemertean	Taxon
59	Nemertine 3	1	3	3	Nemertean	Taxon
72	Geminosyllis sp.	1	3	4	Annelid	Taxon
98	Green-lipped mussel	2	1	NA	Bivalve	Taxon
140	Pea crab	2	2	NA	Crab	Taxon
39	Ghost Shrimp	3	1	NA	Burrowing Shrimp	Taxon
101	Yellow-eye mullet	3	2	NA	Fish	Taxon
102	New Zealand spotty	3	3	NA	Fish	Taxon