R/input.R

In DGVM3D: 3D Forest Simulation Visualization Tool

#' Prepare the output table from LPJ-GUESS for visualization
#'
#' Stand ID and Patch ID start counting at 0 in the standard output. Here the value of 1 is added, to be consistent with R.
#'
#' @param file the filename to be read
#' @param stand.id the stand ID default to 0.
#' @param patch.id if a single patch should be used (default all)
#' @param year if a single year should be used (default all)
#' @param lon if a single longitude should be used (default all). Should be defined, if more than one gridpoint is in the output.
#' @param lat as above
#' @param grass should grasses be included (so far they are not yet further processed).
#' @return individual vegetation data.frame with equal indivuduals from each cohort.
#' @importFrom utils read.table
#' @export
#' @examples
#' \dontrun{
#' dgvm3d.locations = read.table("gridlist.txt",
#'                               col.names=c("Lon", "Lat", "Name"), sep="\t",
#'                               stringsAsFactors=FALSE)
#' dgvm3d.succession=list()
#' for (i in 1:nrow(dgvm3d.locations)) {
#'   dgvm3d.succession[[dgvm3d.locations$Name[i]]] =
#'    read.LPJ("vegstruct.out",
#'             lon=dgvm3d.locations$Lon[i],
#'             lat=dgvm3d.locations$Lat[i])
#'    dgvm3d.succession[[i]] = dgvm3d.succession[[i]][!(dgvm3d.succession[[i]]$Year %% 5) &
#'                                                    dgvm3d.succession[[i]]$Year > 1859, ]
#' }
#' }
read.LPJ <- function(file="vegstruct.out", stand.id=1, patch.id=NULL, year=NULL, lon=NULL, lat=NULL, grass=TRUE) {
  SID=PID=Year=Lon=Lat=Lifeform=NULL
  vegstruct <- read.table(file, header=TRUE, stringsAsFactors = FALSE)
  vegstruct$SID =   vegstruct$SID + 1
  vegstruct$PID =   vegstruct$PID + 1
  ## apply the filters
  vegstruct <- subset(vegstruct, SID == stand.id)
  if (!is.null(patch.id))
    vegstruct <- subset(vegstruct, PID == patch.id)
  if (!is.null(year))
    vegstruct <- subset(vegstruct, Year == year)
  if (!is.null(lon))
    vegstruct <- subset(vegstruct, Lon == lon)
  if (!is.null(lat))
    vegstruct <- subset(vegstruct, Lat == lat)
  if (!grass)
    vegstruct <- subset(vegstruct, Lifeform != 2)

  if (length(unique(vegstruct$Lon)) > 1 || length(unique(vegstruct$Lat)) > 1)
    warning("Several locations are defined. Sure that's what you want?")

  ## vegstruct$Lifeform[vegstruct$Lifeform==1] = "tree"
  ## vegstruct$Lifeform[vegstruct$Lifeform==2] = "grass"
  ##
  ## vegstruct$LeafType[vegstruct$LeafType==1] = "needle"
  ## vegstruct$LeafType[vegstruct$LeafType==2] = "broadleaved"
  ##
  ## vegstruct$PhenType[vegstruct$PhenType==1] = "evergreen"
  ## vegstruct$PhenType[vegstruct$PhenType==1] = "raingreen"
  ## vegstruct$PhenType[vegstruct$PhenType==1] = "summergreen"
  ## vegstruct$PhenType[vegstruct$PhenType==1] = "any"
  ##
  ## vegstruct$Pathway[vegstruct$Pathway==1] = "C3"
  ## vegstruct$Pathway[vegstruct$Pathway==2] = "C4"
  ##
  vegstruct$ShadeType = gapless.rank(vegstruct$ShadeType)
  if (any(2 %in% unique(vegstruct$Lifeform)))
    vegstruct$ShadeType = vegstruct$ShadeType - 1
  ## if (max(vegstruct$ShadeType)==2) {
  ##   vegstruct$ShadeType[vegstruct$ShadeType==1] = "tolerant"
  ##   vegstruct$ShadeType[vegstruct$ShadeType==2] = "intolerant"
  ## } else if (max(vegstruct$ShadeType==3)) {
  ##   vegstruct$ShadeType[vegstruct$ShadeType==1] = "tolerant"
  ##   vegstruct$ShadeType[vegstruct$ShadeType==2] = "intermediate"
  ##   vegstruct$ShadeType[vegstruct$ShadeType==3] = "intolerant"
  ## }

  ## from cohort to individual trees
  veg = vegstruct[rep(seq_len(nrow(vegstruct)), times=vegstruct$N), ]
  veg$N = 1

  return(veg)
}