make.stability: making network stability
In fluxweb: Estimate Energy Fluxes in Food Webs

Description Usage Arguments Details Value See Also Examples

Find the smallest scalar multiplying a variable from losses insuring system stability

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make.stability(val.mat, biomasses, losses, efficiencies, growth.rate,
  losses.scale = NULL, bioms.prefs = TRUE, bioms.losses = TRUE,
  ef.level = "prey", interval = c(1e-12, 1), ...)

`val.mat`	A matrix describing fluxes between species (usually a result of `fluxing` function).
`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.
`losses.scale`	Defines a Column from `losses` on which scalar multiplication will be tested. (default `NULL` if the value is independent of losses).
`bioms.prefs`	Logical, if `TRUE` (default) preferences are scaled accordingly to species biomasses.
`bioms.losses`	Logical, if `TRUE` (default) losses are scaled with biomass.
`ef.level`	Set to `"prey"` if efficiencies are defined by prey, `"pred"` if they are a property of the predator.
`interval`	Search interval for returned value.
`...`	Optional parameters for function `uniroot`

The function assumes a monotonous increase of stability with multiplication by a scalar value. Solution is estimated from the uniroot function, and stability using the fluxing function Thus, accordingly to uniroot solving criteria, if stability values at the two extremum parts of the interval are of same sign, an error is raised.

Behavior of the multiplicative term depends on the type of losses:

losses.scale = NULL and is.vector(losses): multiplication will be applied to the losses vector.
losses.scale = NULL and is.matrix(losses): multiplication will be independent of any columns from losses.
losses.scale = FALSE : value used for multiplication always independent of losses.
other values: should refer to an element of losses.

A list from uniroot function.

uniroot for root estimate and stability.value for assessing system stability.

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$efficiencies, 
                  bioms.pref = TRUE, 
                  ef.level = "pred")
make.stability(val.mat, 
               groups.level$biomasses, 
               losses, 
               groups.level$efficiencies, 
               growth.rates, 
               ef.level = "pred")