View source: R/network-kanalysis.R
analyze_network | R Documentation |
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.
analyze_network(namenetwork, directory = "", guild_a = "pl",
guild_b = "pol", plot_graphs = FALSE, only_NODF = FALSE)
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 |
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
result_analysis <- analyze_network("M_PL_007.csv", directory = "data/", guild_a = "Plant", guild_b = "Pollinator")
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