Scales the refuge density by a given value at set times

Allows for the gradual degradation of habitat structure following an acute disturbance by decreasing the availability of refuge over time.

Usage

reefDegrade(params, n, n_pp, n_other, t, ...)

Arguments

params

A MizerParams object

n

A matrix of species abundances (species x size).

n_pp

A vector of the resource abundance by size

n_other

A list of abundances for other dynamical components of the ecosystem

t

The time for which to do the calculation (Not used by standard mizer rate functions but useful for extensions with time-dependent parameters.)

...

Unused

Value

A numeric vector of scaled refuge densities for each size bin

Details

The degradation is controlled by a scaling matrix deg_scale where:

• Column 1 represents the bleaching year (initial impact)

• Columns 2+ represent years 1, 2, 3... post-bleaching

At each timestep, the scaling factors are multiplied by the previous timestep's refuge density. setDegradation() can also configure an independent, optional post-bleaching algae growth/capacity boost (see getAlgaeBoost()); that boost is unrelated to refuge density and is not computed by this function.

See also

Other mizer rate functions: reefEncounter(), reefFeedingLevel(), reefMort(), reefPredMort(), reefRates(), reefVulnerable()