Mercurial > repos > siwaa > redelac_stics_t

annotate redelacSticsTool.R @ 1:ed9c49c6c6e1 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit c398d524dabc89c0979403d2ff62970fc6c2b404"
author siwaa
date Wed, 07 Feb 2024 11:13:54 +0000
parents 7f8f474a7bd7
children e0d592bb516e
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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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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
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39 # USMs file loading
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41 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
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42 select(
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43 usm_name,
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44 datedebut,
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45 datefin,
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46 finit,
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47 nomsol,
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48 fstation,
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49 fclim1,
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50 fclim2,
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51 culturean,
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52 nbplantes,
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53 codesimul,
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54 fplt_1,
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55 ftec_1,
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56 flai_1,
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57 fplt_2,
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58 ftec_2,
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59 flai_2
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60 )
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61
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62 # Tec files loading and generating xml
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63
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64 tec_param <- read_params_table(file.path(workspace, TecFile))
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65 columnToRemove <-
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66 names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))])
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67 columnToKeep <-
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68 names(tec_param)[names(tec_param) %in% columnToRemove == FALSE]
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69
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70 tec_param <- subset(tec_param, select = columnToKeep)
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71
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72 gen_tec_xml(param_df = tec_param, out_dir = workspace)
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73
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74 # Ini files loading and generating xml
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75
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76 ini_param <- read_params_table(file.path(workspace, IniFile))
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77
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78 gen_ini_xml(param_df = ini_param, out_dir = workspace)
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79
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80 # Station files loading and generating xml
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81
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82 sta_param <- read_params_table(file.path(workspace, StationFile))
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83
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84 gen_sta_xml(param_df = sta_param, out_dir = workspace)
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85
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86 if (parallel) {
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87 doFuture::registerDoFuture()
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88 future::plan(multisession, workers = nbSlots)
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89 `%dordopar%` <- `%dofuture%`
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90 } else {
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91 `%dordopar%` <- `%do%`
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92 }
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93
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94 beforeGenXmlTime <- Sys.time()
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96 #gen_usms_xml(file = file.path(workspace, "usms.xml"),
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parents:
diff changeset
97 # param_df = usms_param)
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parents:
diff changeset
98
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
99 chunckSize <- 1000
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
100 nbUSMs <- nrow(usms_param)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
101
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parents:
diff changeset
102 ids <- seq(1, nbUSMs, chunckSize)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
103
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
104 foreach (i = ids,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
105 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
1
ed9c49c6c6e1 "planemo upload for repository https://forgemia.inra.fr/redelac commit c398d524dabc89c0979403d2ff62970fc6c2b404"
siwaa
parents: 0
diff changeset
106 usmsXfolder = file.path(workspace, paste0("UXF__", i))
ed9c49c6c6e1 "planemo upload for repository https://forgemia.inra.fr/redelac commit c398d524dabc89c0979403d2ff62970fc6c2b404"
siwaa
parents: 0
diff changeset
107 dir.create(usmsXfolder)
ed9c49c6c6e1 "planemo upload for repository https://forgemia.inra.fr/redelac commit c398d524dabc89c0979403d2ff62970fc6c2b404"
siwaa
parents: 0
diff changeset
108 gen_usms_xml(file = file.path(usmsXfolder, paste0("usms__", i, ".xml")),
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
109 param_df = usms_param[i:min(i + chunckSize - 1, nbUSMs),])
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
110 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
111
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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112 afterGenXmlTime <- Sys.time()
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
113 durGenX <-
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siwaa
parents:
diff changeset
114 lubridate::as.duration(lubridate::interval(beforeGenXmlTime,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
115 afterGenXmlTime))
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parents:
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116
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parents:
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117 beforeGenTxtTime <- Sys.time()
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parents:
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118
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parents:
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119 foreach (i = ids,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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120 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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121 gen_usms_xml2txt(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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122 javastics = javastics_path,
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parents:
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123 workspace = workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
124 out_dir = txt_path,
1
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diff changeset
125 usms_file = paste0("UXF__", i, "/usms__", i, ".xml"),
0
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parents:
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126 redelac = redelac,
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127 parallel = parallel,
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128 verbose = FALSE
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129 )
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parents:
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130 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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131
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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132 afterGenTxtTime <- Sys.time()
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
133 durGenT <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
134 lubridate::as.duration(lubridate::interval(beforeGenTxtTime, afterGenTxtTime))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
135
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
136 afterGenTxtTime <- Sys.time()
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
137 durGenT <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
138 lubridate::as.duration(lubridate::interval(beforeGenTxtTime, afterGenTxtTime))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
139
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parents:
diff changeset
140 endTime <- Sys.time()
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parents:
diff changeset
141
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parents:
diff changeset
142 dur <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
143 lubridate::as.period(lubridate::as.duration(lubridate::interval(startTime, endTime)))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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144 durGenXP <- lubridate::as.period(durGenX)
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parents:
diff changeset
145 durGenTP <- lubridate::as.period(durGenT)
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parents:
diff changeset
146
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147 print("REDELACSticsInputGenerator Report")
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parents:
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148 print("=================================")
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parents:
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149 print(paste("number of usms: ", nrow(usms_param)))
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parents:
diff changeset
150 print(paste("redelac optimization:", redelac))
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parents:
diff changeset
151 print(paste("process in parallel:", parallel))
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parents:
diff changeset
152 print(paste("nbslots:", nbSlots))
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siwaa
parents:
diff changeset
153
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
154 sprintf(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
155 'overall duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
156 lubridate::day(dur),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
157 lubridate::hour(dur),
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parents:
diff changeset
158 lubridate::minute(dur),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
159 lubridate::second(dur)
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parents:
diff changeset
160 )
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parents:
diff changeset
161
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
162 sprintf(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
163 'inside gen_usms_xml duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
164 lubridate::day(durGenXP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
165 lubridate::hour(durGenXP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
166 lubridate::minute(durGenXP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
167 lubridate::second(durGenXP)
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parents:
diff changeset
168 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
169
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
170 sprintf(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
171 'inside gen_usms_xml2txt duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
172 lubridate::day(durGenTP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
173 lubridate::hour(durGenTP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
174 lubridate::minute(durGenTP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
175 lubridate::second(durGenTP)
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parents:
diff changeset
176 )
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parents:
diff changeset
177 print(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
178 "==================================================================================="
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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179 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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180
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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181
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
182 #
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
183 # Simulation part
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parents:
diff changeset
184 #
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siwaa
parents:
diff changeset
185
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parents:
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186 # List of successive USMs
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parents:
diff changeset
187 successive_usms_file <- ("successionPlan.csv")
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parents:
diff changeset
188 successive_usms_tab <-
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parents:
diff changeset
189 read.csv(file = file.path(workspace, successive_usms_file),
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parents:
diff changeset
190 sep = ";")
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parents:
diff changeset
191
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
192 # from succesions to simulate retrieving upcSol Cases
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siwaa
parents:
diff changeset
193
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siwaa
parents:
diff changeset
194 successRef <- successive_usms_tab["Treatment"]
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siwaa
parents:
diff changeset
195
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siwaa
parents:
diff changeset
196 successRef <- successRef %>%
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siwaa
parents:
diff changeset
197 separate(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
198 col = Treatment,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
199 into = c("upc", "sol", "systeme", "rotation", "tete_rotation", "horizon"),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
200 sep = "-",
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siwaa
parents:
diff changeset
201 remove = FALSE
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siwaa
parents:
diff changeset
202 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
203
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
204 successRef$upcSol <- paste0(successRef$upc, "-", successRef$sol)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
205
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siwaa
parents:
diff changeset
206 casesUpcSol <- unique(successRef$upcSol)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
207
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siwaa
parents:
diff changeset
208 systeme <- successRef$systeme[1]
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siwaa
parents:
diff changeset
209 rotation <- successRef$rotation[1]
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siwaa
parents:
diff changeset
210
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siwaa
parents:
diff changeset
211 successive_usms_tab_split <- list()
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siwaa
parents:
diff changeset
212
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siwaa
parents:
diff changeset
213 for (j in 1:length(casesUpcSol)) {
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siwaa
parents:
diff changeset
214 splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
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siwaa
parents:
diff changeset
215
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siwaa
parents:
diff changeset
216 upc <- splited[1]
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siwaa
parents:
diff changeset
217
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siwaa
parents:
diff changeset
218 sol <- splited[2]
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siwaa
parents:
diff changeset
219
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
220 successive_usms_tab_split[[j]] <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
221 successive_usms_tab[successRef$upcSol == casesUpcSol[j],]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
222 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
223
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
224 result <- foreach(j = 1:length(casesUpcSol)) %:%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
225 foreach(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
226 i = 1:nrow(successive_usms_tab_split[[j]]),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
227 .options.future = list(packages =c("foreach", "SticsRFiles", "SticsOnR"))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
228
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
229 ) %dordopar% {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
230
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
231 nusms <- as.numeric(successive_usms_tab_split[[j]][i, 2])
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
232
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
233 vec <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
234 as.character(successive_usms_tab_split[[j]][i, c(3:(2 + nusms))])
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
235
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
236 list_successive_usms <- list(vec)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
237
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
238 sim_options <- stics_wrapper_options(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
239 javastics = javastics_path,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
240 stics_exe = paste0(javastics_path, "/bin/stics_modulo"),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
241 workspace = txt_path,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
242 verbose = TRUE,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
243 successive = list_successive_usms
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
244 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
245
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
246 list_usms <- vec
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
247
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
248 cat(paste0("--> succession : ", successive_usms_tab_split[[j]][i, 1], " launched\n"))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
249
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
250 return(stics_wrapper(model_options = sim_options, situation = list_usms))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
251
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
252 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
253
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
254 for (j in 1:length(casesUpcSol)) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
255 splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
256
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
257 upc <- splited[1]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
258
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
259 sol <- splited[2]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
260
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
261 for (i in 1:nrow(successive_usms_tab_split[[j]])) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
262 #i=1
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
263 if (i == 1) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
264 simPCP <- result[[j]][[i]]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
265 } else {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
266 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
267 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
268
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
269 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
270
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
271 #agregation des sorties dans un dataframe
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
272 sim_df <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
273 rbindlist(simPCP$sim_list, use.names = TRUE, idcol = "usm")
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
274
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
275 #ajout des colonnes explicatives + de l'horizon temporel
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
276 sim_df <- sim_df %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
277 separate(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
278 col = usm,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
279 into = c(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
280 "upc",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
281 "sol",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
282 "systeme",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
283 "rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
284 "tete_rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
285 "horizon",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
286 "annee",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
287 "culture"
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
288 ),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
289 sep = "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
290 remove = FALSE
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
291 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
292
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
293 #sauvegarde sous la forme d'un fichier rds
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
294
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
295 if (dir.exists(paste0(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
296 workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
297 "/analyse_simulations_STICS/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
298 systeme,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
299 "/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
300 rotation
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
301 )) == FALSE) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
302 dir.create(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
303 paste0(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
304 workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
305 "/analyse_simulations_STICS/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
306 systeme,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
307 "/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
308 rotation
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
309 ),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
310 recursive = TRUE
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
311 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
312 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
313
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
314 saveRDS(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
315 sim_df,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
316 paste0(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
317 workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
318 "/analyse_simulations_STICS/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
319 systeme,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
320 "/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
321 rotation,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
322 "/outputs-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
323 rotation,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
324 "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
325 upc,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
326 "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
327 sol,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
328 "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
329 scenario,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
330 ".rds"
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
331 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
332 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
333
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
334 successive_usms_tab_split[[j]]$Treatment <- NULL
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
335 successive_usms_tab_split[[j]]$Number_USM <- NULL
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
336
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
337 list_usms <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
338 unlist(unname(as.list(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
339 transpose(successive_usms_tab_split[[j]])
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
340 )))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
341 list_usms <- list_usms[!is.na(list_usms)]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
342 list_usms <- list_usms[list_usms != '']
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
343
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
344 list_usms_yr1 <- successive_usms_tab_split[[j]]$USM_1
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
345
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
346 for (i in 1:length(list_usms)) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
347 if (i == 1) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
348 #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
349 #en attendant que toutes les simulations tournent correctement
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
350 #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
351 rap_1 <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
352 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
353 col_names = TRUE)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
354 names_col <- colnames(rap_1)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
355
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
356 rap_string <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
357 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
358 skip = 1)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
359
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
360 rap <- as_tibble(rap_string) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
361 separate(col = value,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
362 sep = ";",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
363 into = names_col) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
364 mutate(USM = list_usms[i])
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
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
367 } else {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
368 #if (list_usms[i] %in% list_usms_yr1) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
369 #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
370 #en attendant que toutes les simulations tournent correctement
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
371 #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
372 rap_string <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
373 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
374 skip = 1,)#}
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
375
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
376 # } else {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
377 #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
378 #en attendant que toutes les simulations tournent correctement
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
379 #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
380 # rap_string <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
381 # 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
382 # }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
383 rap_i <- as_tibble(rap_string) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
384 separate(col = value,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
385 sep = ";",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
386 into = names_col) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
387 mutate(USM = list_usms[i])
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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388
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
389 rap <- bind_rows(rap, rap_i)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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390
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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391 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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392
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
393 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
394 rm(rap_1, names_col, rap_string, rap_i)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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395
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
396 rap <- rap %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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397 select(USM, everything()) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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398 mutate(P_usm = str_replace_all(P_usm, " ", "")) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
399 mutate(wlieu = str_replace_all(wlieu, " ", "")) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
400 mutate(stade = str_replace_all(stade, " ", "")) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
401 mutate(nomversion = str_replace_all(nomversion, " ", "")) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
402 mutate(across(3:9, as.numeric)) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
403 mutate(across(13:ncol(rap), as.numeric)) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
404 #separate(col=P_usm,into=c("upc","sol","systeme","rotation","tete_rotation","horizon","annee","culture"),sep="-",remove = FALSE)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
405 separate(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
406 col = USM,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
407 into = c(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
408 "upc",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
409 "sol",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
410 "systeme",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
411 "rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
412 "tete_rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
413 "horizon",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
414 "annee",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
415 "culture"
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 sep = "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
418 remove = FALSE
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
419 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
420
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
421 write_delim(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
422 x = rap,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
423 file = paste0(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
424 workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
425 "/analyse_simulations_STICS/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
426 systeme,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
427 "/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
428 rotation,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
429 "/report-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
430 rotation,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
431 "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
432 upc,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
433 "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
434 sol,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
435 "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
436 scenario,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
437 ".csv"
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
438 ),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
439 delim = ";"
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
440 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
441
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
442 }