R/gen_step_out.R

In MadoShi64/rstep: rstep: a workflow for STEP-GENDEC-CN model under R

#' STEP Out files to Excel and CSV
#'
#' @param file.name the name of the file. Usually the name of the site
#' @param workspace the directory, where there are the files you want to format.
#' And where you to store the new files
#' @param state.date the two last digits of the first year. e.g. for 2012 it is "12"
#' @param end.date the two last digits of the last year of simulation.. e.g. for 2020 it is "20"
#'
#' @param format the desired format for the file e.g. xlsx or csv
#'
#' @description gen_step_out writes readable output files in the formats xlsx and csv
#'
#' @return a csv or excel file
#' @export
#'
#' @importFrom utils write.table
#' @importFrom utils write.csv
#' @importFrom utils read.table
#' @importFrom openxlsx write.xlsx
#'
#' @examples
#' \dontrun{
#' gen_step_out("Dahra",workspace,12,20,"csv")
#' }
#'
#'
gen_step_out = function(file.name,
                          workspace,
                          state.date,
                          end.date,
                          format="csv"){

  Output = NULL
  for (i in state.date:end.date){
    df =  read.table(paste0(workspace,"/S01001",i,".out"), header = FALSE, dec=".")
    #assign(paste0("data",i),df)
    Output <- rbind(Output, df) # bind the row of all iterations
  }
  #Combine data frames by rows
  #Output <- rbind(data12, data13, data14, data15, data16, data17, data18, data19, data20)

  #create a sequence of strings for the Titles
  title0 <- c("Jour","Mois","Rain", "Etp","Rayglo","Shum_0","Shum_1","Shum_2","Shum_3","Etot","Trtot","PST","BMs","BMv","Bmlita",
              "Psife","Rstoe","REspCv","REspEv","Psi(1)","Psi(2)","Psi(3)","BMr","RespCr","RespEr","a","BMrs","Epsiloni","Photoresp",
              "Bmlits","Bmburn","Bmfec","Bming","Bmsts","Bmsss","BSOM","Temp","Vent","Vapeur","BurntF","chaTotJ","TqCs",
              "Cs(1)",	"Cs(2)",	"Cs(3)",	"Cs(4)",	"Cs(5)",	"Cs(6)",	"Total_N",	"Amonia",	"End_N_(Norga)",	"Sub_N",	"Bn",	"Co2S","Ih(1)",
              "Ih(2)",	"Ih(3)",	"HCr(1)",	"Hlim",	"HFle",	"HCr(2)",	"Hlim",	"HFle",	"HCr(3)",	"Hlim",	"HFle",	"EP",	"TrP",	"PSTP",	"REspCPv",
              "REspEPv",	"BMPv",	"BPMs",	"(BMPlita)",	"PsifP",	"RstoP",	"BMPr",	"RespCPr",	"RespEPr",	"BMPrs",	"EpsiloniP",	"PhotorespP",
              "(BPburn)", "(BPing)",	"BPsts",	"BPsss",	"BLmv",	"BFlita",	"LAILv",	"hca",	"hcp",	"LAIv",	"LAIPv","G","rss","Snvege","SnSolnu","Sn",
              "Ln",	"Rn",	"H",	"LAIs","LAIPs","LAIlita","vcfv","vcfs","vcfl","vcft","NOFLUX_(kgN/ha/an)","Bc","NOFlux_Process",
              "N2OFlux_Process","NO3","NO2","N2O","En20","wfps","En2o_NOE")#from 52Output put "Vcfs" between Vcfv and Vcfl

  #add the column titles to the new data frame
  colnames(Output) <- title0

  #create date column
  Date <- seq.Date(as.Date(paste0("20",state.date,"-01-01")), length.out = nrow(Output), by = "day", drop=FALSE)# 2012-01-01:the 1st date of the simulation | nrow(Output)= number of row output
  df <- data.frame(Date)
  #add date column to Output data frame
  Output1 <- cbind(df,Output)

  Output1$Shum_0_per <- try((100*Output1$Shum_0) / 20)   #Shum0: 20 mm depth
  Output1$Shum_1_per <- try((100*Output1$Shum_1) / 280)   #Shum1: 280 mm depth
  Output1$Shum_2_per <- try((100*Output1$Shum_2) / 700)   #Shum2: 700 mm depth
  Output1$Shum_3_per <- try((100*Output1$Shum_3) / 2000)  #Shum3: 2000 mm depth
  Output1$Etr <- try(Output1$Trtot + Output1$Etot)               #actual evapotranspiration (etr)
  Output1$vcft <- try(Output1$vcfv+Output1$vcfs+Output1$vcfl)  # total ground cover
  Output1$BMv_s <- try(Output1$BMs+Output1$BMv)
  Output1$BMt <- try(Output1$BMs+Output1$BMv+Output1$Bmlita)
  Output1$BMt_t_ha <- try((Output1$BMs+Output1$BMv+Output1$Bmlita)*0.01)
  Output1$SoilResp <- try((Output1$Co2S*0.5)+ (Output1$RespCr*0.5) + (Output1$RespEr*0.5)+(Output1$RespCPr*0.5)+(Output1$RespEPr*0.5))
  Output1$CO2Soil <- try(Output1$Co2S*0.5)
  Output1$Reco <-  try((Output1$Co2S*0.5) + (Output1$RespCr*0.5) + (Output1$RespEr*0.5)+ (Output1$REspCv*0.5) + (Output1$REspEv*0.5)+(Output1$REspCPv*0.5)+(Output1$REspEPv*0.5)+(Output1$RespCPr*0.5)+(Output1$RespEPr*0.5))
  Output1$Reco_t_ha  <- try(((Output1$Co2S*0.5) + (Output1$RespCr*0.5) + (Output1$RespEr*0.5)+ (Output1$REspCv*0.5) + (Output1$REspEv*0.5)+(Output1$REspCPv*0.5)+(Output1$REspEPv*0.5)+(Output1$RespCPr*0.5)+(Output1$RespEPr*0.5))*0.01)
  Output1$N2Odenit_kg_ha  <- try(Output1$En2o_NOE/1160)-(Output1$N2OFlux_Process/365)
  Output1$N2Onit_kg_ha  <- try(Output1$N2OFlux_Process/365)
  Output1$N2O_total_kg_ha  <- try(Output1$En2o_NOE/1160)
  Output1$N2O_total_t_ha  <- try((Output1$En2o_NOE/1160)*0.001)
  # 1 kg N2O-N = (44/28)*1 kg N2O = 1.57 kg N2O and 1 kg N2O = 265 kg CO2 equivalents !(IPCC, 2014) 5th Assessment
  Output1$N2O_total_kg_CO2_equiv_ha  <- try((Output1$En2o_NOE/1160)*1.57*265)
  # 1kg/ha = 0.001 t/ha
  Output1$N2O_total_t_CO2_equiv_ha  <- try((Output1$En2o_NOE/1160)*1.57*265*0.001)
  #1 kg CO2-C = (44/12)*1 kg CO2 =3.67 kg CO2 ! (IPCC, 2013)
  Output1$Reco_t_CO2_ha  <- try(((Output1$Co2S*0.5) + (Output1$RespCr*0.5) + (Output1$RespEr*0.5)+ (Output1$REspCv*0.5) + (Output1$REspEv*0.5)+(Output1$REspCPv*0.5)+(Output1$REspEPv*0.5)+(Output1$RespCPr*0.5)+(Output1$RespEPr*0.5))*0.01*3.67)
  # Total budget
  Output1$GHG_t_CO2_equiv_ha <- try(((Output1$En2o_NOE/1160)*1.57*265*0.001) + (((Output1$Co2S*0.5) + (Output1$RespCr*0.5) + (Output1$RespEr*0.5)+ (Output1$REspCv*0.5) + (Output1$REspEv*0.5)+(Output1$REspCPv*0.5)+(Output1$REspEPv*0.5)+(Output1$RespCPr*0.5)+(Output1$RespEPr*0.5))*0.01*3.67))
  # GPP
  Output1$GPP  <- try(Output1$PST*0.5)

  if(format == "csv"){
    write.csv(Output1, paste0(workspace,"/",file.name,'.csv'))
  }
  if(format == "xlsx"){
    write.xlsx(Output1,paste0(workspace,"/",file.name,'.xlsx'))
  }
}