R/classes.R

In joergsteinkamp/DGVM3D: 3D Forest Simulation Visualization Tool

#' a Information to draw a triangular object
#'
#' @slot vertices the vertices of the object
#' @slot id the column indices of the vertex matrix to draw the triangular body
#' @slot supp supplementary information
#' @exportClass TriangBody
setClass("TriangBody",
         slots=c(vertices = "matrix",
                 id       = "numeric",
                 supp     = "list")
)

#' One model patch
#'
#' This defines the basic class
#'
#' @slot id unique ID
#' @slot pid the patch id in the vegetation data.frame
#' @slot soil vector of soil layer depth
#' @slot vegetation the vegetation data.frame
#' @slot color.table lookup table for coloring
#' @exportClass Patch
setClass("Patch",
         slots = c(id          = "numeric",
                   pid         = "numeric",
                   soil        = "numeric",
                   vegetation  = "data.frame",
                   color.table = "list")
)

#' One model stand consisting of several patches
#'
#' @slot patches list of patches in one stand
#' @slot area the area of each patch
#' @slot year the year of the current patch vegetation
#' @slot hexagon a \code{\link{TriangBody-class}} Hexagon definition used for all patches
#' @slot layout either 'linear' or 'square'
#' @slot composition either 'spatial' or 'temporal'. Has no effect yet.
#' @slot patch.pos the position of the hexagon centers of each patch
#' @exportClass Stand
setClass("Stand",
         slots=c(patches     = "list",
                 area        = "numeric",
                 year        = "numeric",
                 hexagon     = "TriangBody",
                 layout      = "numeric",
                 composition = "character",
                 patch.pos   = "matrix")
)

#' set some variables used in cascading functions
#'
#' @param x query character 'x' for its value.
#' @param patch.area the patch area in m^2.
#' @param samples 2 element vector. 1. number of samples to determine the next trees position. 2. max. number to repeat the sampling
#' @param overlap fraction of crownradius allowed to overlap.
#' @param sort.column 2 element vector: 1. vegetation data.frame column name to sort by. 2. "descending" (default) or "ascending".
#' @param establish.method where to place the trees: 'random', 'sunflower' or 'row'. If there are trees with positions already 'random' is applied.
#' @param color.column name of the vegetation column to create the canopy colors from.
#' @param verbose print some information.
#' @export
dgvm3d.options <- function(x=NULL,
                           patch.area=NULL,
                           samples=NULL,
                           overlap=NULL,
                           sort.column=NULL,
                           establish.method=NULL,
                           color.column=NULL,
                           verbose=NULL) {
  if (!is.null(x)) {
    if (x=="default") {
      options(dgvm3d.patch.area=1000)
      options(dgvm3d.samples=c(10, 10))
      options(dgvm3d.overlap=0.5)
      options(dgvm3d.sort.column=c("Crownarea", "descending"))
      options(dgvm3d.establish.method="random")
      options(dgvm3d.color.column="ShadeType")
      options(dgvm3d.verbose=TRUE)
      return(TRUE)
    } else {
      if (grepl("^dgvm3d", x)) {
        return(options(x)[[1]])
      } else {
        return(options(paste0("dgvm3d.",x))[[1]])
      }
    }
  }
  if (!is.null(patch.area))
    options(dgvm3d.patch.area=patch.area)
  if (!is.null(samples))
    options(dgvm3d.samples=samples)
  if (!is.null(overlap))
    options(dgvm3d.overlap=overlap)
  if (!is.null(sort.column))
    options(dgvm3d.sort.column=sort.column)
  if (!is.null(establish.method))
    options(dgvm3d.establish.method=establish.method)
  if (!is.null(color.column))
    options(dgvm3d.color.column=color.column)
  if (!is.null(verbose))
    options(dgvm3d.verbose=verbose)
}

## initializing the global options
.onAttach <- function(libname, pkgname) {
  dgvm3d.options("default")
}


#' Vegetation timeseries data from 1860-2005
#'
#' A list of 3 data.frames with simulation results of a LPJ-GUESS model run without random patch disturbance at 3 locations.
#' All patches at all locations were disturbed in 1859.
#'
#'  @name dgvm3d.succession
#'  @docType data
#'  @keywords data
"dgvm3d.succession"