Generate an interaction matrix, either randomly from a uniform distribution or using Klemm-Eguiluz algorithm to generate a modular and scale-free interaction matrix.
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)
| 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) |
the interaction matrix
Klemm & Eguiluz, Growing Scale-Free Networks with Small World Behavior http://arxiv.org/pdf/cond-mat/0107607v1.pdf
klemm=generateA(N=10,type="klemm",c=0.5)#> [1] "Adjusting connectance to 0.5" #> [1] "Initial edge number 80" #> [1] "Initial connectance 0.777777777777778" #> [1] "Number of edges removed 25" #> [1] "Final connectance 0.5" #> [1] "Final connectance: 0.5" #> [1] "Initial edge number 55" #> [1] "Initial connectance 0.5" #> [1] "Number of negative edges already present: 10" #> [1] "Converting 18 edges into negative edges" #> [1] "Final connectance: 0.5" #> [1] "Final arc number (excluding self-arcs) 45" #> [1] "Final negative arc number (excluding self-arcs) 18" #> [1] "PEP: 60"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)#> [1] "Adjusting connectance to 0.5" #> [1] "Initial edge number 1600" #> [1] "Initial connectance 1" #> [1] "Number of edges removed 780" #> [1] "Final connectance 0.5" #> [1] "Final connectance: 0.5"