Description Usage Arguments Details Value Author(s) Examples

Computes resilience of the system through Jacobian matrix eigenvalues.

1 2 3 | ```
stability.value(val.mat, biomasses, losses, efficiencies, growth.rate,
bioms.prefs = TRUE, bioms.losses = TRUE, ef.level = "prey",
full.output = FALSE)
``` |

`val.mat` |
A matrix describing fluxes between species (usually a result of |

`biomasses` |
A vector of species biomasses. |

`losses` |
A vector or an array of species energy losses (excluding predation). |

`efficiencies` |
A vector or an array of conversion efficiencies of species in the adjacency matrix. These values describe the proportion of consumed energy that is converted to biomass of the consumer. |

`growth.rate` |
A vector defining growth rate of basal species. |

`bioms.prefs` |
Logical, if |

`bioms.losses` |
Logical, if |

`ef.level` |
Set to |

`full.output` |
Logical, if |

`losses`

: Express species energetic losses not related to consumption. Usually metabolic or death rates. When an array is provided, losses associated to each species correspond to line sums.`efficiencies`

: Determines how efficient species are to convert energy (see`ef.level`

for more details). Providing an array will assume values depending on both prey and predator identity.`growth.rate`

: Growth rates of basal species defined. Length of the vector should be equal to the number of species. expects positive numeric values for index corresponding to basal species, NA otherwise`bioms.pref`

: If`TRUE`

, preferences*w_{ij}*of predator j on prey i are scaled according to species biomass using the following formula:*w_{i,j} = \frac{mat[i,j] * biomasses[i]}{∑_k mat[i,k]* biomasses[k]}*`bioms.losses`

: If`TRUE`

, function will assume that losses are defined per biomass unit. Thus, total losses will be thereafter multiplied by biomass values for each species.`ef.level`

: If`"prey"`

(resp`"pred"`

), the total amount of energy that can be metabolized from a trophic link will be determined by prey (resp pred) identity.`"link.specific"`

assumes that efficiencies are defined for each trophic interaction and implies`efficiencies`

parameter to be a matrix`full.output`

: If`TRUE`

, function result is a list of eigenvalues and eigenvectors of the Jacobian matrix.

Maximum eigenvalue of the Jacobian matrix of a Lotka Voltera like system of equations. If full.output, Jacobian eigenvalues and eigenvectors are returned.

Benoit Gauzens, benoit.gauzens@gmail.com

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ```
losses = 0.15 * groups.level$bodymasses^(-0.25)
# growth rates of basal sppecies
growth.rates = rep(NA, dim(groups.level$mat)[1])
growth.rates[colSums(groups.level$mat) == 0] = 0.5
val.mat = fluxing(groups.level$mat,
groups.level$biomasses,
losses,
groups.level$efficiencies,
bioms.pref = TRUE,
ef.level = "pred")
stability.value(val.mat,
groups.level$biomasses,
losses,
groups.level$efficiencies,
growth.rates,
ef.level = "pred")
``` |

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