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Run_simulatin_generate_data_stratum_local.domain_dat_loop_version_REPLICATES.R
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Run_simulatin_generate_data_stratum_local.domain_dat_loop_version_REPLICATES.R
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#### Load packages ####
library(arrow)
library(NLMR)
library(sf)
library(raster)
library(fasterize)
library(sspm)
library(rgeos)
library(tidyr)
library(readr)
library(dplyr)
library(mgcv)
library(readr)
library(foreach)
library(doParallel)
library(parallelly)
library(ranger)
library(tidyverse)
library(kableExtra)
#### Load the Functions ####
source(file = "Simulation_Depth_Temp_Coordinates_Biomass_function_V2.R")
source(file = "function_patches.R")
source(file = "Make_local.domain_local.arena.R")
source(file = "Resampling_test.R")
source(file = "Run_GAM_predict_replicates.R")
print(paste("Start of Sim generation @",Sys.time()))
reps= as.numeric(Sys.getenv('REPS')) # Number of Replicates
sims= as.numeric(Sys.getenv('SIMS')) # Number of Sims
size= as.numeric(Sys.getenv('SIZE')) # Size of the Landscape
seed= as.numeric(Sys.getenv('SEED')) # Starting seed
var = as.numeric(Sys.getenv('VAR')) # Variation in biomass field --> higher variation = increased biomass variation
percent = as.numeric(Sys.getenv('PERCENT')) # Sets sampling percentage of the sampling of the entire dataset
dir_noww <- paste0("Data")
dir.create(dir_noww)
#### 1. Create and Start Cluster ####
#create the cluster
# n.cores <- parallelly::availableCores()/2
# For windows
n.cores <- as.numeric(Sys.getenv('OMP_NUM_THREADS'))
main.cluster <- parallel::makeCluster(
n.cores,
type = "PSOCK"
)
#check cluster definition (optional)
print(main.cluster)
#register it to be used by %dopar%
doParallel::registerDoParallel(cl = main.cluster)
#check if it is registered (optional)
foreach::getDoParRegistered()
#how many workers are available? (optional)
foreach::getDoParWorkers()
setwd(dir_noww)
print(dir_noww)
foreach(
rep = 1:reps,
.packages = c('mgcv','dplyr','purrr','NLMR','arrow','sspm','raster','foreach','doParallel','parallelly','readr','fasterize')
) %dopar% {
print(paste("Replicate #",rep))
seeds = seed - 1 + rep
set.seed(seeds)
cwd <- getwd() # CURRENT dir
newdir <- paste("Run",rep,"Size",size,"seed",seeds,"nsim",sims,"Percent",percent,Sys.Date(),sep = "_")
dir.create(newdir) # Create new directory
setwd(newdir)
write.table(as.data.frame(newdir),"seed")
#### 1. Run the sim ####
results <- S_land_bio_sim(sims,size,variation = var) # higher variation = increased biomass variation
# Save size of each strata
patches=results$patches_list$patches
patches=st_set_geometry(patches,NULL)
write_parquet(patches,"patches")
#### 2. Write the ogmap files ####
Make_patch_domain_arena_DAT(size,patches=results$patches_list$patches,the_stack=results$the_stack,percent=percent)
# #### 3. Make replicates of each rep (landscape) ####
#Resample_write_PBfall(200)
#
# #### 4. Run the GAM ####
#replicates_gam()
#
# #### 5. Run Comparison + Print graphs ####
# Compare_Graph()
#### 6. Return to Original WD ####
setwd(cwd)
gc()
}
#### Kill the cluster
parallel::stopCluster(cl = main.cluster)
#### Loop to run replicates of simulations in individual folders ####
# for (rep in 1:reps) {
# print(paste("Replicate #",rep))
# seeds = seed - 1 + rep
# set.seed(seeds)
# cwd <- getwd() # CURRENT dir
# setwd("Data/")
# newdir <- paste("Run",rep,"Size",size,"seed",seeds,"nsim",sims,"Percent",percent,Sys.Date(),sep = "_")
# dir.create(newdir) # Create new directory
# setwd(newdir)
# write.table(as.data.frame(newdir),"seed")
# #### 1. Run the sim ####
# results <- S_land_bio_sim(sims,size,variation = var) # higher variation = increased biomass variation
#
# # Save size of each strata
# patches=results$patches_list$patches
# patches=st_set_geometry(patches,NULL)
# write_parquet(patches,"patches")
#
# #### 2. Write the ogmap files ####
# Make_patch_domain_arena_DAT(size,patches=results$patches_list$patches,the_stack=results$the_stack,percent=percent)
#
# # #### 3. Make replicates of each rep (landscape) ####
# Resample_sims_random(200)
# #
# # #### 4. Run the GAM ####
# replicates_gam()
# #
# # #### 5. Run Comparison + Print graphs ####
# # Compare_Graph()
#
# #### 6. Return to Original WD ####
# setwd(cwd)
# gc()
# }
print(paste("End of Sim generation @",Sys.time()))
#################################################