R/assignStation.r

In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes

#' @export
assignStation <- function(events,maxdist=0.01,res=0.005,expwin=0.05,lines=F,...){
  
  if(lines==T){
    events$X<-with(events,apply(cbind(X1,X2),1,mean))
    events$Y<-with(events,apply(cbind(Y1,Y2),1,mean))
  }
  
  events<-as.EventData(events)
  
  xmax <- max(events$X)+diff(range(events$X))*expwin
  xmin <- min(events$X)-diff(range(events$X))*expwin
  
  ymax <- max(events$Y)+diff(range(events$Y))*expwin
  ymin <- min(events$Y)-diff(range(events$Y))*expwin
  
  W <- owin(c(xmin,xmax),c(ymin,ymax))
  if(lines==F)events.ppp <- as.ppp(subset(events,select=c('X','Y')),W)
  if(lines==T){
    events.ppp <- as.psp(subset(events,select=c('X1','Y1','X2','Y2')),window=W)
    d1<-data.frame(PID=1,SID=1:nrow(events),POS=1,subset(events,select=c("X1","Y1")))
    names(d1)[4:5]<-c("X","Y")
    d2<-data.frame(PID=1,SID=1:nrow(events),POS=2,subset(events,select=c("X2","Y2")))
    names(d2)[4:5]<-c("X","Y")
    towlines<-merge(d1,d2,all=T)
  }
  events.dist<-with(distmap(events.ppp,eps=res),list(xcol,yrow,t(v)))
  names(events.dist)<-c('x','y','z')
  
  CL <- contourLines(events.dist,levels=maxdist)
  CP <- convCP(CL)
  polys <- CP$PolySet
  
  key<-findPolys(events,polys)
  events<-merge(events,key[c('EID','SID')],all=T)
  stations<-calcCentroid(polys)[,-1]
  
  return(list(events=events,stations=stations,polys=polys))
  
  
}