_targets.R

# Source packages and functions
source("02Scripts/R/packages.R")
source("02Scripts/R/functions.R")

##  Parallel control ----
# plan(multiprocess)
# future(packages = c("data.table", "here", "magrittr","readxl", "RSQLite","DBI",
#                     "openxlsx", "autoapsimx", "DEoptim"))


# plan(callr)
tar_option_set(
  packages = c("data.table", "here", "magrittr","readxl", "RSQLite","DBI",
               "openxlsx", "autoapsimx", "DEoptim"), 
  # imports = c("package1", "package2")
)

# If use job scheduler ----
REMOTE = FALSE

if(REMOTE){
  # Set cluster 
  plan(batchtools_lsf,template='./openlava_batchtools.tmpl')
  
  # So we can Access LSF 
  RLinuxModules::module('load openlava') 
  
  tar_option_set(deployment="main") # default to host
}


# Construct the instruction
values <-  data.table::data.table(Site = rep(c("AshleyDene", "Iversen12"),each = 10),
                                  SowingDate = rep(paste0("SD", 1:10), 2))


# Raw data path ----
targets0 <- list(
  tar_target(path_richard,here::here("01Data/APSIM_Sim.xlsx")),
  # Constants raw data
  tar_target(rawobs, read_excel(path_richard, 
                     guess_max = 10300, sheet = 2,
                     skip = 9, .name_repair = "universal") %>% 
  as.data.table()),
  tar_target(params, read_excel(here("01Data/SlurpParamList.xlsx")) %>% 
               as.data.table(), cue = tar_cue(mode = "always")),
  # Get SWC data and filter down to the required sown dates
  tar_target(data_SW, as.data.table(read_Sims(path = path_richard))),
  
  # Constant variables
  tar_target(id_vars, c("Experiment", "SowingDate", "Clock.Today", "DAS")),
  tar_target(value_vars, grep("SWmm\\.\\d.", colnames(data_SW), value = TRUE)),
  # Date for reset soil water content
  tar_target(magicDate, as.Date("2011-06-25")),
  # Get the actual dates of sowing
  tar_target(sowingDates, read_Sims(path_richard, source =  "sowingDate")),
  # Modify SD1:5 to magic dates for reset initial swc in the second season
  tar_target(resetDates, reset_SD(sowingDates, magicDate)),
  # Get the LAI for daily value interpolation 
  tar_target(LAI_Height,  read_Sims(path = path_richard, source = "biomass")),
  
  # APSIMX constants
  tar_target(path_apsimx, apsimx_path(debug = FALSE)),
  tar_target(template,
             readLines(here::here("01Data/ApsimxFiles/SlurpTemplate.txt")),
             cue = tar_cue(mode = "always")),
  tar_target(apsimx_Basefile,
             here::here("01Data/ApsimxFiles/SingleSlurp.apsimx")),
  # tar_target(obs_para, "SWCmm"),
  tar_target(parameters, prepare_params(params = params)),
  tar_target(par, parameters$initials),
  tar_target(apsimx_sims_dir, here::here("01Data/ProcessedData/apsimxFiles"))
)


## map through -----
targets1 <- tar_map(
  values = values, 
  names = c("Site", "SowingDate"),
  # Constants
  tar_target(SD, SowingDate),
  tar_target(Sites, Site),
  
  # Site depended targets
  tar_target(path_met, ifelse(Sites == "AshleyDene", 
                              here::here("01Data/ClimateAndObserved/AshleyDene.met"),
                              here::here("01Data/ClimateAndObserved/Iversen12.met"))),
  tar_target(lucerne_height, ifelse(Sites == "AshleyDene", 390L, 595L)),
  tar_target(met, read_met(path_met)),
  
  tar_target(BD, filter_BD(path = here("01Data/BulkDensity.xlsx"), Sites)),
  # Site and Sowing dates depended targets 
  tar_target(SimName, paste0(Sites, "SowingDate", SD)),
  ## Observations
  tar_target(obs, prepare_obs(rawobs, trts = c(Sites, SD))),
  tar_target(cumTT, subset_met(met)),
  tar_target(actualSD, filter_SD(sowingDates, trts = c(Sites, SD))),
  tar_target(resetSD, filter_SD(resetDates, trts = c(Sites, SD))),
  tar_target(CoverData, interp_LAI(biomass = LAI_Height,
                                   sowingDate = actualSD, 
                                   accumTT =  met[,.(Experiment, Clock.Today, AccumTT)], 
                                   trts = c(Sites, SD))),
  # Subset the raw sw into treatment level
  tar_target(SW, filter_SW(data_SW, trts = c(Sites, SD))), 
  tar_target(SW_sub, colwise_meanSW(DT = SW,
                                     id.vars = id_vars,
                                     col.vars = value_vars)),
  tar_target(SW_initials, initialSWC(SW_sub, sowingDate = actualSD, id_vars)),
  tar_target(SW_initials_reset, initialSWC(SW_sub, sowingDate = resetSD, id_vars)),
  tar_target(DUL_LL_range, doDUL_LL_range(SW = SW_sub,
                                          id.vars = id_vars)),
  # Manually adjust the DUL levels to 0.95
  tar_target(DUL_LL_range_arbitrary, DUL_LL_range[,':='(SAT = SW.DUL* 1.05,
                                                        SW.DUL = SW.DUL * 0.95,
                                                        SW.LL = SW.LL * 0.95)]),
  # Combine all into one list
  tar_target(input_list, combine_input( SimName,
                                        obs, 
                                        actualSD,
                                        path_met, #climate met path 
                                        CoverData, 
                                        lucerne_height, # sowing dates
                                        BD,
                                        SW_initials,
                                        DUL_LL_range_arbitrary,
                                        resetSD,
                                        SW_initials_reset
                                        ))
  # Construct the configuration file
  # tar_target(opt.res,
  #            wrapper_deoptim(parameters = parameters,
  #                            par = parameters$initials,
  #                            # obspara =  "SWCmm",
  #                            maxIt = 500,
  #                            np = length(par)*10,
  # 
  #                            Sites, SD,
  #                            template,
  #                            path_apsimx,
  #                            magicDate,
  #                            apsimx_Basefile,
  #                            # obspara,
  #                            apsimx_sims_dir,
  #                            # APSIMEditFun,
  #                            # APSIMRun,
  #                            input_list)
  # )
)

targets_factorial <- list(
  # tar_target(factorialDB, here("01Data/ApsimxFiles/LucerneValidationOptimised.db")),
  # tar_target(report, read_dbtab( factorialDB,
  #                                table = "Report"), 
  #            format = "fst_dt"),
  # tar_target(observed, read_dbtab( factorialDB,
  #                                table = "ObsAllData"), format = "fst_dt")
  )
# Combine plans ----
list(targets0, targets1,targets_factorial)