metanet_build_pipe {metanetwork}

Build and execute 'metanetwork' pipeline

Description

Method executing the whole metanetwork pipeline, including building 'metanetwork' object (build_metanet,append_agg_nets, compute_TL, attach_layout)

Usage

metanet_build_pipe(
  metaweb,
  abTable = NULL,
  trophicTable = NULL,
  compute_local_nets = TRUE,
  verbose = TRUE,
  beta = 0.1
)

Arguments

metaweb

metaweb of the metanetwork, object of class 'graph', 'matrix', 'data.frame' or 'dgCMatrix'. Metaweb needs to be directed and connected. This parameter must be non-null.

abTable

abundances of nodes in local networks, matrix of class 'matrix', columns must have names corresponding to node labels of the metaweb, rows are node abundances in local networks. Default is null, in that case, uniform abundances are assigned

trophicTable

a 'matrix' or 'data.frame' indicating hierarchy of the nodes. Names of the columns correspond to the different resolutions. It indicates the membership of each node of the metaweb. Default is null.

compute_local_nets

a boolean, indicates whether local networks must be computed or not. Default is TRUE

verbose

a boolean indicating whether message along the pipeline should be printed

beta

the diffusion parameter of the diffusion kernel, a positive scalar controlling the squeezing of the network

Value

object of class 'metanetwork', with computed layout stored as node attribute

Examples

library(metanetwork)
library(igraph)

g = make_lattice(dimvector = c(4,4),2,3,directed = TRUE)
meta0 = metanet_build_pipe(g)
ggmetanet(meta0)