stability.value {fluxweb} | R Documentation |
Estimates network stability
Description
Computes resilience of the system through Jacobian matrix eigenvalues.
Usage
stability.value(val.mat, biomasses, losses, efficiencies, growth.rate,
bioms.prefs = TRUE, bioms.losses = TRUE, ef.level = "prey",
full.output = FALSE)
Arguments
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 |
Details
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 (seeef.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 otherwisebioms.pref
: IfTRUE
, preferencesw_{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]}{\sum_k mat[i,k]* biomasses[k]}
bioms.losses
: IfTRUE
, 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 impliesefficiencies
parameter to be a matrixfull.output
: IfTRUE
, function result is a list of eigenvalues and eigenvectors of the Jacobian matrix.
Value
Maximum eigenvalue of the Jacobian matrix of a Lotka Voltera like system of equations. If full.output, Jacobian eigenvalues and eigenvectors are returned.
Author(s)
Benoit Gauzens, benoit.gauzens@gmail.com
Examples
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")