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

# Use this to add a copy-code buttong
klippy::klippy(position = c('top', 'right'), color = 'darkred')

knitr::opts_chunk$set(echo = TRUE)

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.