generateA: Generate an interaction matrix

In hallucigenia-sparsa/seqtime: Time Series Analysis of Sequencing Data

Generate an interaction matrix

Description

Generate an interaction matrix, either randomly from a uniform distribution or using Klemm-Eguiluz algorithm to generate a modular and scale-free interaction matrix.

Usage

generateA(N = 100, type = "random", pep = 50, d = -0.5,
  min.strength = -0.5, max.strength = 0.5, c = 0.02,
  ignore.c = FALSE, negedge.symm = FALSE, clique.size = 5,
  groups = c(), intra.group.strength = 0.5,
  inter.group.strength = NA)

Arguments

N	number of species
type	random (sample a uniform distribution), klemm (generate a Klemm-Eguiluz matrix) or empty (zero everywhere, except for diagonal which is set to d)
pep	desired positive edge percentage (only for klemm)
d	diagonal values (should be negative)
min.strength	random: minimal off-diagonal interaction strength (only for random)
max.strength	random: maximal off-diagonal interaction strength, klemm: maximal absolute off-diagonal interaction strength
c	desired connectance (interaction probability)
ignore.c	do not adjust connectance
negedge.symm	set symmetric negative interactions (only for klemm)
clique.size	modularity parameter (only for klemm)
groups	vector of group memberships for each species, assign NA if species does not belong to any group (only for random)
intra.group.strength	interaction strength between members of the same group
inter.group.strength	interaction strength between members of different groups (if not defined, will be assigned randomly)

Value

the interaction matrix

References

Klemm & Eguiluz, Growing Scale-Free Networks with Small World Behavior http://arxiv.org/pdf/cond-mat/0107607v1.pdf

Examples

klemm=generateA(N=10,type="klemm",c=0.5)
groups=c(rep(NA,5),rep(1,10),rep(2,5),rep(3,10),rep(4,10))
Agroup=generateA(N=40,groups=groups,c=0.5,intra.group.strength=0.1,inter.group.strength=-0.5, d=-1)

hallucigenia-sparsa/seqtime documentation built on Jan. 9, 2023, 11:53 p.m.