Mercurial > repos > siwaa > redelac_stics_g

annotate redelacSticsInputGenerator.R @ 3:e344100f3354 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit ff64e62033c2485113100d60c38be73e59ef119c"
author siwaa
date Thu, 29 Jun 2023 10:50:58 +0000
parents c7d424481b03
children 4f8d87b9c246
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c7d424481b03 "planemo upload for repository https://forgemia.inra.fr/redelac"
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1 library(SticsRFiles)
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2 library(dplyr)
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4 workspace <- paste0(getwd(), "/WS")
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5 javastics_path <- getwd()
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7 txt_path <- paste0(getwd(), "/WS/txt_files")
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8 dir.create(txt_path,recursive = T)
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9
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10 USMsFile <- "USMs.csv"
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11 TecFile <- "Tec.csv"
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12 IniFile <- "Ini.csv"
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13 StationFile <- "Station.csv"
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15 # Generate STICS xml files------------------------------------------------------------------------------
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17 # USMs file
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18 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
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19 select(usm_name,datedebut,datefin,finit,nomsol,fstation,fclim1,fclim2,culturean,nbplantes,codesimul,fplt_1,ftec_1,flai_1,fplt_2,ftec_2,flai_2)
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20 gen_usms_xml(file = file.path(workspace, "usms.xml"), param_df = usms_param)
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22 # Tec files
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23 tec_param <- read_params_table(file.path(workspace, TecFile)) %>%
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24 select(!c(annee, date_min, date_max, Date_res_1, Date_res_2, Type_res_1, Type_res_2, Date_trav_1, Date_trav_2, Date_trav_3, Type_trav_1, Type_trav_2 ,Type_trav_3, plante_sem, date_sem, starts_with("nom_vari"), date_ferti_1, date_ferti_2, date_ferti_3, type_eng_1, type_eng_2, type_eng_3, date_rec, date_des, juleclair, nbinfloecl))
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25 gen_tec_xml(param_df = tec_param, out_dir = workspace)
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26 # select(!c(annee, date_min, date_max, Date_res_1, Date_res_2, Type_res_1, Type_res_2, Date_trav_1, Date_trav_2, Date_trav_3, Type_trav_1, Type_trav_2 ,Type_trav_3, plante_sem, date_sem)
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28 # Ini files
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29 ini_param <- read_params_table(file.path(workspace, IniFile))
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30 gen_ini_xml(param_df = ini_param, out_dir = workspace)
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32 # Sta files
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33 sta_param <- read_params_table(file.path(workspace, StationFile))
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34 gen_sta_xml(param_df = sta_param, out_dir = workspace)
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36 # Generate STICS txt files------------------------------------------------------------------------------
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37 # List of USMs
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38 list_usms <- SticsRFiles::get_usms_list(file = file.path(workspace,"usms.xml"))
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40 ### Generate txt files into individual folders
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42 # generate text files
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43 gen_usms_xml2txt(javastics = javastics_path,
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44 workspace = workspace,
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45 out_dir = txt_path,
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46 verbose = TRUE,
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47 usm = list_usms)
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