R/get.crawl.path.R

In ctmcmove: Modeling Animal Movement with Continuous-Time Discrete-Space Markov Chains

get.crawl.path <-
function(sim.obj,raster,mintime,maxtime,...){
    ## function to simulate a crawl path that does not leave the
    ## borders of a raster object
    ##
    ## Inputs:
    ##
    ## sim.obj - a CRAWL sim.obj
    ## raster - a raster or raster stack object
    ## mintime - time to begin simulation
    ## maxtime - time to end simulation
    ##
    ##
  if(class(raster)=="RasterStack"){
        examplerast=raster[[1]]
  }
  if(class(raster)=="RasterLayer"){
    examplerast=raster
  }

  t=sim.obj$datetime
  t.idx=which(t>=mintime & t<=maxtime)
  t=t[t.idx]

  keep.idx=0
  while(keep.idx==0){
    samp.new <- crwPostIS(sim.obj, fullPost=FALSE)
    path.list=cbind(samp.new$alpha.sim.x[t.idx,'mu'], samp.new$alpha.sim.y[t.idx,'mu'])
    path.loc.idx=cellFromXY(examplerast,path.list)
    if(length(which(is.na(path.loc.idx)))==0){
      keep.idx=1
    }
  }
  list(t=t,xy=path.list,cells.path=path.loc.idx)
}