In MayaGueguen/RFate: Vegetation modelling with the FATE model

Plant Functional Groups

Simulation parameter files

New

# params$name.simul
# params$create.skeleton
# params$create.skeleton[1]
# # if (params$create.skeleton[1] == 1)
# # {
# print(params$required.no_PFG)
# params$required.no_STRATA
# params$required.simul_duration
# params$opt.no_CPU
# params$required.seeding_duration
# params$required.seeding_timestep
# params$required.seeding_input
# params$required.max_abund_low
# params$required.max_abund_medium
# params$required.max_abund_high
# params$doDispersal
# params$doHabSuitability
# params$doDisturbances
# params$doLight
# params$doSoil
# # }

Creation of directory :

if (params$create.skeleton > 0)
{
  PRE_FATE.skeletonDirectory(name.simulation = params$name.simul)
}

Creation of parameter simulation file :

if (params$create.skeleton > 0)
{
  mask.file = list.files(path = paste0(params$name.simul, "/DATA/MASK")
                         , pattern = "^MASK_")
  if (params$upload.mask > 0 && length(mask.file) > 0)
  {
      PRE_FATE.params_simulParameters(name.simulation = params$name.simul
                                      , name.mask = mask.file
      )
  }
}

if (params$create.skeleton > 0)
{
  PRE_FATE.params_globalParameters(name.simulation = params$name.simul
                                   , opt.no_CPU = params$opt.no_CPU
                                   , required.no_PFG = params$required.no_PFG
                                   , required.no_STRATA = params$required.no_STRATA
                                   , required.simul_duration = params$required.simul_duration
                                   , required.seeding_duration = params$required.seeding_duration
                                   , required.seeding_timestep = params$required.seeding_timestep
                                   , required.seeding_input = params$required.seeding_input
                                   , required.max_abund_low = params$required.max_abund_low
                                   , required.max_abund_medium = params$required.max_abund_medium
                                   , required.max_abund_high = params$required.max_abund_high
                                   , doDispersal = params$doDispersal
                                   , DISPERSAL.mode = as.vector(c("(1) uniform kernel" = 1
                                                                  , "(2) exponential kernel" = 2
                                                                  , "(3) exponential kernel with probability" = 3)[params$DISPERSAL.mode])
                                   , doHabSuitability = params$doHabSuitability
                                   , HABSUIT.mode = ifelse(params$HABSUIT.mode == "(1) random", 1, 2)
                                   , doLight = params$doLight
                                   , LIGHT.thresh_medium = params$LIGHT.thresh_medium
                                   , LIGHT.thresh_low = params$LIGHT.thresh_low
                                   , doSoil = params$doSoil
                                   , doDisturbances = params$doDisturbances
                                   , DIST.no = params$DIST.no
                                   , DIST.no_sub = params$DIST.no_sub
                                   , DIST.freq = rep(params$DIST.freq, params$DIST.no)
  )
}

get_tab.global = function() {
  if (!is.null(params$name.simul) && nchar(params$name.simul) > 0)
  {
    path_folder = paste0(params$name.simul, "/DATA/GLOBAL_PARAMETERS/")
    tab = get_files(path_folder)

    if (!is.null(tab) && ncol(tab) > 0)
    {
      params$compt.global.no = ncol(tab)
      params$compt.global.files = colnames(tab)
      return(tab)
    }
  }
}

  tab = get_tab.global()
  tab = as.data.frame(tab)

  if (!is.null(tab) && ncol(tab) > 0)
  {
    tab
  }

Multiple set

Simulation outputs & graphics

# The `params` object is available in the document.
#params$n

A plot of params$n random points.

#plot(rnorm(params$n), rnorm(params$n))

MayaGueguen/RFate documentation built on Oct. 17, 2020, 8:06 a.m.