Prepare a steady state model for projections with degradation

This function stores degradation parameters in the refuge_params slot of the params object, and algae adjustment parameters in other_params$algae.

Usage

setDegradation(
  params,
  trajectory = NULL,
  deg_scale,
  bleach_time = 2,
  degrade = FALSE,
  algae_boost = FALSE,
  algae_growth_boost = c(1.11, 1.11, 1.11, 1.11),
  algae_capacity_boost = c(2),
  ...
)

Arguments

params

a mizer object

trajectory

Optional character string naming the degradation scenario. Used for documentation and identification. No functional effect on the simulation.

deg_scale

A matrix (refuge bins x time) giving scaling factors for refuge density. Column 1 represents the bleaching year (initial impact), and subsequent columns represent years 1, 2, 3... post-bleaching. Values are multiplied by the previous timestep's refuge density. Default scaling matrices for 15 years with "rubble", "algae", and "recovery" trajectories are included as data objects in the package.

bleach_time

The year of the simulation to implement bleaching. Defaults to year 2.

degrade

Logical. Whether to enable habitat degradation during projections, i.e. whether reefDegrade() applies the deg_scale trajectory once t reaches bleach_time. Default FALSE.

algae_boost

Logical. Should algae growth and/or carrying capacity be adjusted in response to bleaching? Default is FALSE.

algae_growth_boost

Numeric vector. Multipliers for algae growth rate at bleaching (element 1) and during post-bleaching years (subsequent elements). Only used if algae_boost = TRUE. Vector length determines duration: length 4 means bleaching year plus 3 post-bleaching years. Default is c(1.11, 1.11, 1.11, 1.11) for 4 years of boosting.

algae_capacity_boost

Numeric vector. Multipliers for algae carrying capacity at bleaching (element 1) and during post-bleaching years (subsequent elements). Only used if algae_boost = TRUE. If shorter than algae_growth_boost, will be padded with 1s (no change). Default is c(2.0) (only boosts at bleaching year).

...

Unused

Value

A mizer object with updated degradation parameters stored in refuge_params and algae adjustment parameters in other_params$algae.

See also

algae_dynamics_cc(),detritus_dynamics_cc(), tuneUR_cc(), reefDegrade()