R/dhtify.R

In dill/ltdesigntester: Test Performance of Line Transect Designs

#' Make DSsim data usable by dht
#'
#' Get the simulated data and put it into a format that \code{dht} can use. The consists of creating the three tables used by \code{\link{dht}}.
#'
#' @param dsm_data the survey results in \code{dsm}-compatible format (result of calling \code{\link{dsmify}})
#' @param transect_id which transects do the segments belong to? Vector with the same length as the segment table in \code{dsm_data}
#' @param survey a simulated survey
#' @return a \code{list} with three \code{data.frame}s: \code{obs} the observation table, \code{segs} the segment table and \code{dist} the distance data.
#' @export
#' @author David L Miller
#' @importFrom plyr ddply summarize "."
dhtify <- function(dsm_data, survey, transect_id){

  # assemble the sample table
  segs <- survey@transects@sampler.info
  segs$Region.Label <- segs$region
  segs$region <- NULL
  sh_segs <- segs
  if(is.null(transect_id)){
    segs$Sample.Label <- segs$ID
    segs$Effort <- segs$length
  }else{
    segs$Sample.Label <- transect_id
    # ugly hack to get around global var problem
    Region.Label <- Sample.Label <- end.X <- start.X <- NULL
    segs <- ddply(segs, .(Sample.Label), summarize,
                  Effort=sum(length), Region.Label=unique(Region.Label),
                  x_start=min(c(start.X, end.X), na.rm=TRUE),
                  x_end=max(c(start.X, end.X), na.rm=TRUE))
  }

  # assemble observation table
  obs <- dsm_data$obs
  sh_segs$tr <- transect_id
  sh_segs$Sample.Label <- sh_segs$ID
  sh_segs <- sh_segs[,c("Sample.Label", "tr", "Region.Label")]
  obs <- merge(obs, sh_segs, by="Sample.Label")
  obs$Sample.Label <- obs$tr
  obs$tr <- NULL

  if(!("Region.Label" %in% names(obs))){
    obs$Region.Label <- obs$Region.Label.x
    obs$Region.Label.y <- obs$Region.Label.x <- NULL
  }

  obs$size <- 1

  return(list(region=survey@region.table@region.table, sample=segs, obs=obs))
}