_targets.R

library(targets)
library(data.table)
library(tarchetypes)

# 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)
  )
)