data-raw/DATASET_PNE_1/PNE_RESULTS.R

In MayaGueguen/RFate: Vegetation modelling with the FATE model

###############################################################################
##
## FATE EXAMPLE on Parc National des Ecrins (PNE)
##
###############################################################################

path.save = "data-raw/DATASET_PNE/"
setwd(path.save)

library(RFate)
library(data.table)
library(raster)
library(foreach)
library(xlsx)


###############################################################################
### PNE.RESULTS
###############################################################################

tab.6 = read.xlsx("PNE_PFG_description_delphine_VALIDATION.xls", sheetIndex = 1, stringsAsFactors = FALSE)
for(i in 2:ncol(tab.6)) tab.6[, i] = as.numeric(tab.6[, i])

CC_BAU = stack(list.files("b_RESULTS/", pattern = "CC_BAU", full.names = TRUE))
CC_BAU.names = names(CC_BAU)
CC_BAU = readAll(CC_BAU)
CC_BAU = round(CC_BAU, 3)
names(CC_BAU) = CC_BAU.names

CC_Abandon = stack(list.files("b_RESULTS/", pattern = "CC_Abandon", full.names = TRUE))
CC_Abandon.names = names(CC_Abandon)
CC_Abandon = readAll(CC_Abandon)
CC_Abandon = round(CC_Abandon, 3)
names(CC_Abandon) = CC_Abandon.names

INIT = CC_BAU[[paste0("PNE_CC_BAU_year_", seq(50, 800, 50))]]
names(INIT) = paste0("PNE_INIT_year_", seq(50, 800, 50))

CC_BAU = CC_BAU[[paste0("PNE_CC_BAU_year_", seq(850, 1500, 50))]]

CC_Abandon = CC_Abandon[[paste0("PNE_CC_Abandon_year_", seq(850, 1500, 50))]]

INIT_800 = stack(list.files("b_RESULTS/", pattern = "_str", full.names = TRUE))
INIT_800 = readAll(INIT_800)
toKeep = vector()
for(i in 1:nlayers(INIT_800))
{
  maxi = max(INIT_800[[i]][])
  if (maxi > 0) toKeep = c(toKeep, i)
}
INIT_800 = INIT_800[[toKeep]]

PNE_RESULTS = list(evaluation = as.data.frame(tab.6)
                   , abund_str.equilibrium = INIT_800
                   , forest_cover.init = INIT
                   , forest_cover.CC_BAU = CC_BAU
                   , forest_cover.CC_Abandon = CC_Abandon
)
save(PNE_RESULTS, file = "PNE_RESULTS.RData")

# setwd("../..")
# usethis::use_data(PNE_RESULTS, overwrite = TRUE)