docs_old/flows.md

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

Flow models

Data set

Weighted directed networks of pollen transfer from Tur C, Sáez A, Traveset A, Aizen MA. Evaluating the effects of pollinator-mediated interactions using pollen transfer networks: evidence of widespread facilitation in south Andean plant communities. Ecol Lett. 2016;19: 576–586.

Input

A link-list.

R Code

# Import data
data(tur2016)
tur2016_altitude2000 <- tur2016 %>% 
  filter(altitude==2000) %>% 
  select("donor", "receptor", "total") %>% 
  group_by(donor, receptor) %>% 
  summarise(n=mean(total)) %>% 
  rename(from = donor, to = receptor, weight = n) %>% 
  ungroup() %>%
  slice(c(-10,-13,-28)) %>%  # Remove singletons
  filter(from!=to) # Remove self loops

network_object <- create_monolayer_network(tur2016_altitude2000, 
directed = T, bipartite = F)
res_dir <- run_infomap_monolayer(network_object, infomap_executable='Infomap',
                                 flow_model = 'directed',
                                 silent=T,trials=100, two_level=T, seed=200952)
res_rawdir <- run_infomap_monolayer(network_object, infomap_executable='Infomap',
flow_model = 'rawdir',
silent=T,trials=100, two_level=T, seed=200952)

res_dir_modules <- res_dir$modules %>% drop_na()
res_rawdir_modules <- res_rawdir$modules %>% drop_na()


# Compare the results using normalised mutual information
N <- res_dir_modules %>% # Create confusion matrix
  select(-module_level2) %>%
  inner_join(res_rawdir_modules %>% select(node_id,module_level1), by='node_id') %>%
  arrange(module_level1.x,module_level1.y) %>%
  group_by(module_level1.y) %>% select(module_level1.x) %>% table()

# These two different modes of flow can result in different partitions.
NMI(N)

Infomap

Under the hood, the function run_infomap_monolayer runs:

For real measured flows:

./Infomap infomap.txt . -i link-list --tree --seed 200952 -N 100 -f rawdir --two-level

For constraints on flows:

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

Explanation of key arguments: -f directed indicates flow on a directed network. The visitation rates of nodes is obtained with a PageRank algorithm based on the direction and weight of edges. -f rawdir or -f directed: In a rawdir flow model the visitation rates of nodes is determined without a PageRank algorithm but rather by the given direction and weight of edges. In a directed flow model edge weights are assumed to be constraints on flow, and a PageRank algorithm is run first to determine flow.

Output

A tree file is produced by Infomap, but is parsed by run_infomap_monolayer from infomapecology (in R: ?run_infomap_monolayer).

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