Description Usage Arguments Value References Examples

View source: R/calcFunctionalIndices.r

The proportion of matrices that are locally stable, these matrices are created by sampling the values of the community matrix
(the Jacobian) from a uniform distribution, preserving the sign structure 1. If the 'ig' parameter is
an `mgraph`

network it needs to have been built with the order `c("Competitive", "Mutualistic", "Trophic")`

It also calculates the mean of the real part of the maximum eingenvalue, which is also a measure of stability 2.
It uses a uniform distribution between 0 and maximum values given by the parameters `negative`

, `positive`

and `selfDamping`

,
corresponding to the sign of interactions and self-limitation effect 3,4.
If the edges of the networks have a weigth attribute and `istrength`

parameter is true, weigth will be used as interaction strength, then the limits of the uniform distribution
will be `negative*-x`

, `positive*x`

where x is the value of the weigth for the edge.
If the values of these parameters are 0 then there is no interaction of that kind.

1 2 3 4 5 6 7 8 9 |

`ig` |
igraph or a list of igraph networks or mgraph network |

`nsim` |
number of simulations to calculate QSS |

`ncores` |
number of cores to use in parallel comutation if 0 it uses sequential processing |

`negative` |
the maximum magnitude of the negative interaction (the effect of the predator on the prey) must be <= 0 |

`positive` |
the maximum magnitude of the positive interaction (the effect of the prey on the predator) must be >= 0 |

`selfDamping` |
the maximum magnitude of the self-limitation (the effect of the species on itself) must be <= 0 |

`istrength` |
If TRUE takes the weigth attribute of the network as interaction strength. |

a data.frame with the QSS, and MEing, the mean of the real part of the maximum eingenvalue

Allesina, S. & Pascual, M. (2008). Network structure, predator - Prey modules, and stability in large food webs. Theor. Ecol., 1, 55–64.

Grilli, J., Rogers, T. & Allesina, S. (2016). Modularity and stability in ecological communities. Nat. Commun., 7, 12031

Monteiro, A.B. & Del Bianco Faria, L. (2017). Causal relationships between population stability and food-web topology. Functional Ecology, 31, 1294–1300.

Borrelli, J. J. 2015. Selection against instability: stable subgraphs are most frequent in empirical food webs. - Oikos 124: 1583–1588.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ```
## Not run:
g <- netData[[2]]
tp <- calc_QSS(g)
# Read Multiplex network and calculate QSS
fileName <- c(system.file("extdata", package = "multiweb"))
dn <- list.files(fileName,pattern = "^Kefi2015.*\\.txt$")
gt <- readMultiplex(dn,types,"inst/extdata", skipColumn = 2)
calc_QSS(gt)
## End(Not run)
``` |

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