refit.occ: Refit occupancy raster layers function

In dsouthwell/TestPackagev2: Spatially explicit power analysis in dynamic landscapes

Description

This function is only called if stochastic disturbances are modelled at sites. It re-maps occupancy for disturbance-sensitive species given the simulated disturbance events and the relationship between distrubances and occupancy It returns a new raster stack with the updated occupancy raster layers for each species

Usage

refit.occ(occ.new, layers, time.fire, fire.freq, jj, dist.occ.time,
  dist.occ.freq, n.species)

Arguments

occ.new	A raster stack of occupancy maps. Raster layers for fire sensitive species are updated depending on the simulated fire history at time jj
layers	An array of covararite values at each site. These are used to update the occ.new raster stack
time.fire	A vector specifying the time since fire at each site in year jj given the simulated fire history
fire.freq	A vector specifying the number of fires at sites during a 15 year moving window
jj	The year of the monitoring program
dist.occ.time	An integer indentifying which layer in the covariate raster stack is the time since the last disturbance layer
dist.occ.freq	An integer indentifying which layer in the covariate raster stack is the disturbance frequency layer
n.species	Number of species included in power simulations

dsouthwell/TestPackagev2 documentation built on May 28, 2019, 9:38 a.m.