Mercurial > repos > siwaa > redelac_stics_t

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 4cad1cb9719e5d2ca13cf8a5c8b98b2409303b59"
author siwaa
date Wed, 19 Aug 2026 14:35:50 +0000
parents 15317ef4816b
children
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1 library(SticsRFiles)
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2 library(SticsOnR)
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3 library(dplyr)
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4 library(lubridate)
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5 library(parallel)
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6 library(doParallel)
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7 library(doFuture)
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8 library(stringr)
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9 library(readxl)
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10 library(data.table)
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11 library(readr)
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12 library(tidyr)
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13 library(arrow)
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14 sessionInfo()
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16 args = commandArgs(trailingOnly = TRUE)
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18 startTime <- Sys.time()
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20 workspace <- paste0(getwd(), "/WS")
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21 javastics_path <- getwd()
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22 default_config_path <- paste0(javastics_path, "/config")
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24 txt_path <- paste0(getwd(), "/WS/txt_files")
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25 dir.create(txt_path, recursive = T)
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27 USMsFile <- "USMs.csv"
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28 TecFile <- "Tec.csv"
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29 IniFile <- "Ini.csv"
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30 StationFile <- "Station.csv"
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32 redelac <- (args[1] == "optim")
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33 parallel <- (args[2] == "parallel")
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34 print(paste("parallel:", parallel, args[2]))
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35 nbSlots <- as.integer(args[3])
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36 print(paste("nbslots:", nbSlots))
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37 scenario <- args[4]
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38 resulType <- args[5]
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40 parquetOut <- (resulType == "parquet" || resulType == "both" )
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41 baseOut <- (resulType == "rds+csv" || resulType == "both" )
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43 # USMs file loading
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45 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
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46 select(
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47 usm_name,
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48 datedebut,
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49 datefin,
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50 finit,
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51 nomsol,
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52 fstation,
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53 fclim1,
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54 fclim2,
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55 culturean,
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56 nbplantes,
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57 codesimul,
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58 fplt_1,
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59 ftec_1,
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60 flai_1,
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61 fplt_2,
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62 ftec_2,
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63 flai_2
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64 )
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65
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66 # Tec files loading and generating xml
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67
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68 tec_param <- read_params_table(file.path(workspace, TecFile))
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69
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70 # sanitizing (trying to)
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71
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72 paramDesc = SticsRFiles:::get_param_desc()
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73
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74 paramTecDesc <- paramDesc[paramDesc$kind=="PARTEC",]
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75
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76 expectedTypes <- setNames(as.list(paramTecDesc$type), paramTecDesc$name)
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77
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78 expectedTypes <- lapply(expectedTypes, function(x) {
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79 if (identical(x, "real")) "numeric" else x
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80 })
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81
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82 check <- sapply(names(tec_param), function(col) {
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83 colref <- col
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84 col <- sub("_[0-9]+$", "", col)
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85 if (!col %in% names(expectedTypes)) {
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86 NA
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87 } else {
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88 class(tec_param[[colref]])[1] == expectedTypes[[col]]
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89 }
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90 })
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91
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92 finalCheck <- check[!is.na(check)]
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93
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94 toFix <- finalCheck[sapply(finalCheck, function(x) x == FALSE)]
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95
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96 converters <- list(
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97 integer = as.integer,
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98 numeric = as.numeric,
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99 character = as.character,
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100 logical = as.logical,
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101 factor = as.factor,
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102 Date = as.Date
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103 )
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104
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105 for (col in names(toFix)) {
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106 if (col %in% names(tec_param)) {
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107 type <- expectedTypes[[sub("_[0-9]+$", "", col)]]
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108 if (type %in% names(converters)) {
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109 tec_param[[col]] <- converters[[type]](tec_param[[col]])
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110 } else {
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111 warning(sprintf("Unknown type '%s' for column '%s'", type, col))
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112 }
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113 }
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114 }
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115
0
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116 columnToRemove <-
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117 names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))])
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118 columnToKeep <-
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119 names(tec_param)[names(tec_param) %in% columnToRemove == FALSE]
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120
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121 tec_param <- subset(tec_param, select = columnToKeep)
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122
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123 gen_tec_xml(param_df = tec_param, out_dir = workspace)
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124
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125 # Ini files loading and generating xml
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126
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127 ini_param <- read_params_table(file.path(workspace, IniFile))
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128
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129 gen_ini_xml(param_df = ini_param, out_dir = workspace)
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130
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131 # Station files loading and generating xml
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132
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133 sta_param <- read_params_table(file.path(workspace, StationFile))
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134
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135 gen_sta_xml(param_df = sta_param, out_dir = workspace)
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136
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137 if (parallel) {
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138 doFuture::registerDoFuture()
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139 future::plan(multisession, workers = nbSlots)
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140 `%dordopar%` <- `%dofuture%`
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141 } else {
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142 `%dordopar%` <- `%do%`
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143 }
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144
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145 beforeGenXmlTime <- Sys.time()
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146
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147 #gen_usms_xml(file = file.path(workspace, "usms.xml"),
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148 # param_df = usms_param)
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149
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150 chunckSize <- 1000
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151 nbUSMs <- nrow(usms_param)
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152
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153 ids <- seq(1, nbUSMs, chunckSize)
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154
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155 foreach (i = ids,
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156 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
15
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157 usmsXfolder = file.path(workspace, paste0("UXF__", i))
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158 dir.create(usmsXfolder)
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159 gen_usms_xml(file = file.path(usmsXfolder, paste0("usms__", i, ".xml")),
0
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160 param_df = usms_param[i:min(i + chunckSize - 1, nbUSMs),])
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161 }
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162
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163 afterGenXmlTime <- Sys.time()
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164 durGenX <-
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165 lubridate::as.duration(lubridate::interval(beforeGenXmlTime,
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166 afterGenXmlTime))
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167
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168 beforeGenTxtTime <- Sys.time()
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169
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170 foreach (i = ids,
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171 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
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172 gen_usms_xml2txt(
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173 javastics = javastics_path,
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174 workspace = workspace,
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175 out_dir = txt_path,
1
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176 usms_file = paste0("UXF__", i, "/usms__", i, ".xml"),
0
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177 redelac = redelac,
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178 parallel = parallel,
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179 verbose = FALSE
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180 )
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181 }
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182
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183 afterGenTxtTime <- Sys.time()
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184 durGenT <-
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185 lubridate::as.duration(lubridate::interval(beforeGenTxtTime, afterGenTxtTime))
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186
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187 #
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188 # Simulation part
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189 #
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190
18
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191 beforeSimsTime <- Sys.time()
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192
0
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193 # List of successive USMs
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194 successive_usms_file <- ("successionPlan.csv")
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parents:
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195 successive_usms_tab <-
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parents:
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196 read.csv(file = file.path(workspace, successive_usms_file),
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parents:
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197 sep = ";")
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parents:
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198
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parents:
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199 # from succesions to simulate retrieving upcSol Cases
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parents:
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200
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parents:
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201 successRef <- successive_usms_tab["Treatment"]
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parents:
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202
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parents:
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203 successRef <- successRef %>%
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parents:
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204 separate(
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parents:
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205 col = Treatment,
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parents:
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206 into = c("upc", "sol", "systeme", "rotation", "tete_rotation", "horizon"),
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parents:
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207 sep = "-",
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parents:
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208 remove = FALSE
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parents:
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209 )
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parents:
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210
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parents:
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211 successRef$upcSol <- paste0(successRef$upc, "-", successRef$sol)
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parents:
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212
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siwaa
parents:
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213 casesUpcSol <- unique(successRef$upcSol)
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parents:
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214
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parents:
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215 systeme <- successRef$systeme[1]
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parents:
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216 rotation <- successRef$rotation[1]
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parents:
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217
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parents:
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218 successive_usms_tab_split <- list()
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parents:
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219
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parents:
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220 for (j in 1:length(casesUpcSol)) {
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parents:
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221 splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
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parents:
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222
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parents:
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223 upc <- splited[1]
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parents:
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224
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parents:
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225 sol <- splited[2]
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parents:
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226
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parents:
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227 successive_usms_tab_split[[j]] <-
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parents:
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228 successive_usms_tab[successRef$upcSol == casesUpcSol[j],]
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parents:
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229 }
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parents:
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230
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parents:
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231 result <- foreach(j = 1:length(casesUpcSol)) %:%
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parents:
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232 foreach(
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parents:
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233 i = 1:nrow(successive_usms_tab_split[[j]]),
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parents:
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234 .options.future = list(packages =c("foreach", "SticsRFiles", "SticsOnR"))
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235
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parents:
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236 ) %dordopar% {
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parents:
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237
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parents:
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238 nusms <- as.numeric(successive_usms_tab_split[[j]][i, 2])
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239
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parents:
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240 vec <-
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parents:
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241 as.character(successive_usms_tab_split[[j]][i, c(3:(2 + nusms))])
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parents:
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242
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parents:
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243 list_successive_usms <- list(vec)
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parents:
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244
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parents:
diff changeset
245 sim_options <- stics_wrapper_options(
5
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246 stics_exe = "stics_modulo",
0
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parents:
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247 workspace = txt_path,
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248 verbose = TRUE,
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249 force = TRUE,
0
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parents:
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250 successive = list_successive_usms
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parents:
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251 )
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parents:
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252
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parents:
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253 list_usms <- vec
23
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parents: 22
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254
0
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parents:
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255 cat(paste0("--> succession : ", successive_usms_tab_split[[j]][i, 1], " launched\n"))
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parents:
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256
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parents:
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257 return(stics_wrapper(model_options = sim_options, situation = list_usms))
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258
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parents:
diff changeset
259 }
19
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260
18
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parents: 17
diff changeset
261 afterSimsTime <- Sys.time()
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diff changeset
262 durSimsT <-
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diff changeset
263 lubridate::as.duration(lubridate::interval(beforeSimsTime, afterSimsTime))
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diff changeset
264 durSimsTP <- lubridate::as.period(durSimsT)
0
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265
18
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parents: 17
diff changeset
266 #
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parents: 17
diff changeset
267 # Output part
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parents: 17
diff changeset
268 #
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parents: 17
diff changeset
269
23
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parents: 22
diff changeset
270 for (j in 1:length(casesUpcSol)) {
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diff changeset
271 successive_usms_tab_split[[j]]$Treatment <- NULL
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diff changeset
272 successive_usms_tab_split[[j]]$Number_USM <- NULL
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parents: 22
diff changeset
273 }
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274
18
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diff changeset
275 beforeOutputsTime <- Sys.time()
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276
23
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parents: 22
diff changeset
277 foreach(
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diff changeset
278 j = 1:length(casesUpcSol),
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diff changeset
279 .options.future = list(packages =c("foreach", "tidyr", "arrow"))
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diff changeset
280 ) %dordopar% {
21
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diff changeset
281
0
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parents:
diff changeset
282 splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
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parents:
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283
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parents:
diff changeset
284 upc <- splited[1]
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parents:
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285
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parents:
diff changeset
286 sol <- splited[2]
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parents:
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287
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parents:
diff changeset
288 for (i in 1:nrow(successive_usms_tab_split[[j]])) {
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parents:
diff changeset
289 #i=1
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parents:
diff changeset
290 if (i == 1) {
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siwaa
parents:
diff changeset
291 simPCP <- result[[j]][[i]]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
292 } else {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
293 simPCP$sim_list <- c(simPCP$sim_list, result[[j]][[i]]$sim_list)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
294 }
23
3b44cb0a1e76 "planemo upload for repository https://forgemia.inra.fr/redelac commit 4cad1cb9719e5d2ca13cf8a5c8b98b2409303b59"
siwaa
parents: 22
diff changeset
295
20
475aa4451308 "planemo upload for repository https://forgemia.inra.fr/redelac commit b4077990f5df769fbae45689f5bb12dbc81b2e4e"
siwaa
parents: 19
diff changeset
296 }
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
297
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
298 #agregation des sorties dans un dataframe
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
299 sim_df <-
23
3b44cb0a1e76 "planemo upload for repository https://forgemia.inra.fr/redelac commit 4cad1cb9719e5d2ca13cf8a5c8b98b2409303b59"
siwaa
parents: 22
diff changeset
300 rbindlist(simPCP$sim_list, use.names = TRUE, idcol = "usm")
3b44cb0a1e76 "planemo upload for repository https://forgemia.inra.fr/redelac commit 4cad1cb9719e5d2ca13cf8a5c8b98b2409303b59"
siwaa
parents: 22
diff changeset
301
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
302
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
303 #ajout des colonnes explicatives + de l'horizon temporel
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
304 sim_df <- sim_df %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
305 separate(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
306 col = usm,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
307 into = c(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
308 "upc",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
309 "sol",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
310 "systeme",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
311 "rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
312 "tete_rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
313 "horizon",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
314 "annee",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
315 "culture"
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
316 ),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
317 sep = "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
318 remove = FALSE
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
319 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
320
23
3b44cb0a1e76 "planemo upload for repository https://forgemia.inra.fr/redelac commit 4cad1cb9719e5d2ca13cf8a5c8b98b2409303b59"
siwaa
parents: 22
diff changeset
321 cat(paste0("--> rotation upc sol : ", " ", rotation, " ", upc, " " , sol, " to be gathered\n"))
3b44cb0a1e76 "planemo upload for repository https://forgemia.inra.fr/redelac commit 4cad1cb9719e5d2ca13cf8a5c8b98b2409303b59"
siwaa
parents: 22
diff changeset
322
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
323 #sauvegarde sous la forme d'un fichier rds
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
324
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
325 if (baseOut) {
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
326
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
327 if (dir.exists(paste0(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
328 workspace,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
329 "/analyse_simulations_STICS/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
330 systeme,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
331 "/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
332 rotation
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
333 )) == FALSE) {
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
334 dir.create(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
335 paste0(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
336 workspace,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
337 "/analyse_simulations_STICS/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
338 systeme,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
339 "/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
340 rotation
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
341 ),
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
342 recursive = TRUE
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
343 )
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
344 }
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
345
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
346 saveRDS(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
347 sim_df,
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
348 paste0(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
349 workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
350 "/analyse_simulations_STICS/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
351 systeme,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
352 "/",
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
353 rotation,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
354 "/outputs-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
355 rotation,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
356 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
357 upc,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
358 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
359 sol,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
360 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
361 scenario,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
362 ".rds"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
363 )
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
364 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
365 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
366
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
367 if (parquetOut) {
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
368
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
369 if (dir.exists(paste0(
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
370 workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
371 "/analyse_simulations_STICS/",
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
372 "/donnees_parquet_outputs/"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
373 )) == FALSE) {
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
374 dir.create(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
375 paste0(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
376 workspace,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
377 "/analyse_simulations_STICS/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
378 "/donnees_parquet_outputs/"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
379 ),
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
380 recursive = TRUE
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
381 )
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
382 }
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
383
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
384 write_parquet(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
385 sim_df,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
386 paste0(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
387 workspace,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
388 "/analyse_simulations_STICS/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
389 "/donnees_parquet_outputs/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
390 "outputs-",
17
fa4e7fd1d3f7 "planemo upload for repository https://forgemia.inra.fr/redelac commit d102b73678f095281635bf5f00d86a4a77a1ae9e"
siwaa
parents: 16
diff changeset
391 systeme,
fa4e7fd1d3f7 "planemo upload for repository https://forgemia.inra.fr/redelac commit d102b73678f095281635bf5f00d86a4a77a1ae9e"
siwaa
parents: 16
diff changeset
392 "-",
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
393 rotation,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
394 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
395 upc,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
396 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
397 sol,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
398 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
399 scenario,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
400 ".parquet"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
401
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
402 ))
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
403 }
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
404
19
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
405 #successive_usms_tab_split[[j]]$Treatment <- NULL
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
406 #successive_usms_tab_split[[j]]$Number_USM <- NULL
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
407
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
408 list_usms <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
409 unlist(unname(as.list(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
410 transpose(successive_usms_tab_split[[j]])
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
411 )))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
412 list_usms <- list_usms[!is.na(list_usms)]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
413 list_usms <- list_usms[list_usms != '']
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
414
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
415 list_usms_yr1 <- successive_usms_tab_split[[j]]$USM_1
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
416
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
417 for (i in 1:length(list_usms)) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
418 if (i == 1) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
419 #ajout d'une condition sur l'existence du fichier "mod_rapport.sti" pour la concatenation
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
420 #en attendant que toutes les simulations tournent correctement
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
421 #if(exists(file.path(txt_path, list_usms[i], "mod_rapport.sti"))==TRUE){
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
422 rap_1 <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
423 read_delim(file.path(txt_path, list_usms[i], "mod_rapport.sti"),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
424 col_names = TRUE)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
425 names_col <- colnames(rap_1)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
426
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
427 rap_string <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
428 read_lines(file = file.path(txt_path, list_usms[i], "mod_rapport.sti"),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
429 skip = 1)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
430
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
431 rap <- as_tibble(rap_string) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
432 separate(col = value,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
433 sep = ";",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
434 into = names_col) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
435 mutate(USM = list_usms[i])
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
436 # }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
437
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
438 } else {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
439 #if (list_usms[i] %in% list_usms_yr1) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
440 #ajout d'une condition sur l'existence du fichier "mod_rapport.sti" pour la concatenation
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
441 #en attendant que toutes les simulations tournent correctement
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
442 #if(exists(file.path(txt_path, list_usms[i], "mod_rapport.sti"))==TRUE){
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
443 rap_string <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
444 read_lines(file = file.path(txt_path, list_usms[i], "mod_rapport.sti"),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
445 skip = 1,)#}
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
446
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
447 # } else {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
448 #ajout d'une condition sur l'existence du fichier "mod_rapport.sti" pour la concatenation
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
449 #en attendant que toutes les simulations tournent correctement
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
450 #if(exists(file.path(txt_path, list_usms[i], "mod_rapport.sti"))==TRUE){
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
451 # rap_string <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
452 # read_file(file = file.path(txt_path, list_usms[i], "mod_rapport.sti"))#}
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
453 # }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
454 rap_i <- as_tibble(rap_string) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
455 separate(col = value,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
456 sep = ";",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
457 into = names_col) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
458 mutate(USM = list_usms[i])
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
459
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
460 rap <- bind_rows(rap, rap_i)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
461
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
462 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
463
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
464 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
465 rm(rap_1, names_col, rap_string, rap_i)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
466
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
467 rap <- rap %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
468 select(USM, everything()) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
469 mutate(P_usm = str_replace_all(P_usm, " ", "")) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
470 mutate(wlieu = str_replace_all(wlieu, " ", "")) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
471 mutate(stade = str_replace_all(stade, " ", "")) %>%
5
e0d592bb516e "planemo upload for repository https://forgemia.inra.fr/redelac commit 1b434482800e773a592b5fc6f472e7df465e91ce"
siwaa
parents: 1
diff changeset
472 mutate(nomversion = str_replace_all(P_usm, " ", "")) %>%
e0d592bb516e "planemo upload for repository https://forgemia.inra.fr/redelac commit 1b434482800e773a592b5fc6f472e7df465e91ce"
siwaa
parents: 1
diff changeset
473 mutate(across(4:10, as.numeric)) %>%
e0d592bb516e "planemo upload for repository https://forgemia.inra.fr/redelac commit 1b434482800e773a592b5fc6f472e7df465e91ce"
siwaa
parents: 1
diff changeset
474 mutate(across(14:ncol(rap), as.numeric)) %>%
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
475 separate(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
476 col = USM,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
477 into = c(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
478 "upc",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
479 "sol",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
480 "systeme",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
481 "rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
482 "tete_rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
483 "horizon",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
484 "annee",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
485 "culture"
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
486 ),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
487 sep = "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
488 remove = FALSE
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
489 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
490
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
491 if (baseOut) {
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
492
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
493 write_delim(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
494 x = rap,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
495 file = paste0(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
496 workspace,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
497 "/analyse_simulations_STICS/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
498 systeme,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
499 "/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
500 rotation,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
501 "/report-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
502 rotation,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
503 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
504 upc,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
505 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
506 sol,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
507 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
508 scenario,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
509 ".csv"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
510 ),
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
511 delim = ";"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
512 )
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
513 }
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
514
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
515 if (parquetOut) {
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
516
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
517 if (dir.exists(paste0(
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
518 workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
519 "/analyse_simulations_STICS/",
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
520 "/donnees_parquet_report/"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
521 )) == FALSE) {
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
522 dir.create(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
523 paste0(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
524 workspace,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
525 "/analyse_simulations_STICS/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
526 "/donnees_parquet_report/"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
527 ),
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
528 recursive = TRUE
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
529 )
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
530 }
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
531
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
532 write_parquet(
16
816fbce5cf58 "planemo upload for repository https://forgemia.inra.fr/redelac commit cfb92a37e4cb2054f9d8caa5bd8f46c9f4a7be68"
siwaa
parents: 15
diff changeset
533 rap,
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
534 paste0(
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
535 workspace,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
536 "/analyse_simulations_STICS/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
537 "/donnees_parquet_report/",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
538 "report-",
17
fa4e7fd1d3f7 "planemo upload for repository https://forgemia.inra.fr/redelac commit d102b73678f095281635bf5f00d86a4a77a1ae9e"
siwaa
parents: 16
diff changeset
539 systeme,
fa4e7fd1d3f7 "planemo upload for repository https://forgemia.inra.fr/redelac commit d102b73678f095281635bf5f00d86a4a77a1ae9e"
siwaa
parents: 16
diff changeset
540 "-",
15
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
541 rotation,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
542 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
543 upc,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
544 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
545 sol,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
546 "-",
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
547 scenario,
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
548 ".parquet"
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
549
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
550 ))
af807768332e "planemo upload for repository https://forgemia.inra.fr/redelac commit 179e64aac208ae8af4d7416a7d5ff4b9da572850"
siwaa
parents: 5
diff changeset
551 }
18
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
552 }
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
553
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
554 afterOutputsTime <- Sys.time()
19
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
555
18
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
556 durOutT <-
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
557 lubridate::as.duration(lubridate::interval(beforeOutputsTime, afterOutputsTime))
19
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
558
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
559
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
560 durGenXP <- lubridate::as.period(durGenX)
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
561 durGenTP <- lubridate::as.period(durGenT)
18
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
562 durOutTP <- lubridate::as.period(durOutT)
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
563
19
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
564 endTime <- Sys.time()
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
565
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
566 dur <-
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
567 lubridate::as.period(lubridate::as.duration(lubridate::interval(startTime, endTime)))
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
568
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
569 print("REDELACSticsInputGenerator Report")
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
570 print("=================================")
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
571 print(paste("number of usms: ", nrow(usms_param)))
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
572 print(paste("redelac optimization:", redelac))
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
573 print(paste("process in parallel:", parallel))
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
574 print(paste("nbslots:", nbSlots))
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
575
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
576 sprintf(
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
577 'overall duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
578 lubridate::day(dur),
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
579 lubridate::hour(dur),
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
580 lubridate::minute(dur),
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
581 lubridate::second(dur)
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
582 )
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
583 print(
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
584 "==================================================================================="
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
585 )
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
586
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
587 sprintf(
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
588 'inside gen_usms_xml duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
589 lubridate::day(durGenXP),
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
590 lubridate::hour(durGenXP),
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
591 lubridate::minute(durGenXP),
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
592 lubridate::second(durGenXP)
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
593 )
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
594 print(
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
595 "==================================================================================="
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
596 )
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
597
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
598 sprintf(
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
599 'inside gen_usms_xml2txt duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
600 lubridate::day(durGenTP),
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
601 lubridate::hour(durGenTP),
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
602 lubridate::minute(durGenTP),
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
603 lubridate::second(durGenTP)
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
604 )
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
605 print(
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
606 "==================================================================================="
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
607 )
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
608
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
609 sprintf(
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
610 'Simulations duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
611 lubridate::day(durSimsTP),
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
612 lubridate::hour(durSimsTP),
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
613 lubridate::minute(durSimsTP),
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
614 lubridate::second(durSimsTP)
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
615 )
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
616 print(
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
617 "==================================================================================="
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
618 )
8848db582840 "planemo upload for repository https://forgemia.inra.fr/redelac commit 9f38541b8f84bf16077819d47c96dbc69e3d1675"
siwaa
parents: 18
diff changeset
619
18
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
620 sprintf(
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
621 'outputs generating duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
622 lubridate::day(durOutTP),
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
623 lubridate::hour(durOutTP),
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
624 lubridate::minute(durOutTP),
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
625 lubridate::second(durOutTP)
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
626 )
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
627 print(
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
628 "==================================================================================="
8293d67cd1a9 "planemo upload for repository https://forgemia.inra.fr/redelac commit b972382172a3923486a799d46efe363d21e8ea1d"
siwaa
parents: 17
diff changeset
629 )