analyze_network: Network analysis using k core decomposition

In jgalgarra/kcorebip: Bipartite networks kcore decomposition and visualization

Network analysis using k core decomposition

Description

This function performs the kcore decomposition of a bipartite network. The input is the interaction matrix in a .csv file, with the format of www.web-of-life.es Species of guild a are distributed by colums, and those of guild b by rows. First colum contains the labels of guild b nodes, and first row, the labels of guild a. If the interaction matrix is binary, the cell of species_a_m,species_b_n will be set to 1. If it is weighted, to a real number different of 0.

Usage

analyze_network(
  namenetwork,
  directory = "",
  guild_a = "pl",
  guild_b = "pol",
  plot_graphs = FALSE,
  only_NODF = FALSE,
  weight_direction = "none"
)

Arguments

namenetwork	is the file name that contains the interaction matrix
directory	where the network file is stored
guild_a	prefix for the guild of nodes stored in rows
guild_b	prefix for the guild of nodes stored in columns
plot_graphs	plot kshell histogram and kamada kawai plots
only_NODF	just compute the NODF measurement of nestedness

Value

calc_values a list containing the following objects

• "graph" an igraph::graph object

• "max_core" maximum k shell index

• "nested_values" a list containing all the values provided by the bipartite::nested function, unless only_NODF set TRUE

• "num_guild_a" number of nodes of guild a

• "num_guild_b" number of nodes of guild b

• "links" number of network links

• "meandist" network average kradius

• "meankdegree" network average kdegree

• "spaths_mat" matrix with node to node shortest distance paths

• "matrix" adyacency matrix with nodes of guild a by columns and guild b by rows

• "g_cores" list with the value of kshell for each node

• "modularity_measure" value of igraph::modularity function

Examples

result_analysis <- analyze_network("M_PL_007.csv", directory = "data/", guild_a = "Plant", guild_b = "Pollinator")

jgalgarra/kcorebip documentation built on June 14, 2025, 12:33 a.m.