Mercurial > repos > siwaa > redelac_stics_t

annotate redelacSticsTool.R @ 0:7f8f474a7bd7 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
author siwaa
date Tue, 06 Feb 2024 09:21:00 +0000
parents
children ed9c49c6c6e1
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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"),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
97 # param_df = usms_param)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
98
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
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
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
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"
siwaa
parents:
diff changeset
105 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
106 gen_usms_xml(file = file.path(workspace, paste0("usms__", i, ".xml")),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
107 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
108 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
109
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
110 afterGenXmlTime <- Sys.time()
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
111 durGenX <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
112 lubridate::as.duration(lubridate::interval(beforeGenXmlTime,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
113 afterGenXmlTime))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
114
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
115 beforeGenTxtTime <- Sys.time()
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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116
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
117 foreach (i = ids,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
118 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
119 gen_usms_xml2txt(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
120 javastics = javastics_path,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
121 workspace = workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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122 out_dir = txt_path,
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siwaa
parents:
diff changeset
123 usms_file = paste0("usms__", i, ".xml"),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
124 redelac = redelac,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
125 parallel = parallel,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
126 verbose = FALSE
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parents:
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127 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
128 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
129
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
130 afterGenTxtTime <- Sys.time()
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
131 durGenT <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
132 lubridate::as.duration(lubridate::interval(beforeGenTxtTime, afterGenTxtTime))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
133
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
134 afterGenTxtTime <- Sys.time()
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
135 durGenT <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
136 lubridate::as.duration(lubridate::interval(beforeGenTxtTime, afterGenTxtTime))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
137
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
138 endTime <- Sys.time()
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
139
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
140 dur <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
141 lubridate::as.period(lubridate::as.duration(lubridate::interval(startTime, endTime)))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
142 durGenXP <- lubridate::as.period(durGenX)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
143 durGenTP <- lubridate::as.period(durGenT)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
144
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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145 print("REDELACSticsInputGenerator Report")
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parents:
diff changeset
146 print("=================================")
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
147 print(paste("number of usms: ", nrow(usms_param)))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
148 print(paste("redelac optimization:", redelac))
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siwaa
parents:
diff changeset
149 print(paste("process in parallel:", parallel))
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siwaa
parents:
diff changeset
150 print(paste("nbslots:", nbSlots))
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siwaa
parents:
diff changeset
151
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
152 sprintf(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
153 '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"
siwaa
parents:
diff changeset
154 lubridate::day(dur),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
155 lubridate::hour(dur),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
156 lubridate::minute(dur),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
157 lubridate::second(dur)
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siwaa
parents:
diff changeset
158 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
159
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
160 sprintf(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
161 '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"
siwaa
parents:
diff changeset
162 lubridate::day(durGenXP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
163 lubridate::hour(durGenXP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
164 lubridate::minute(durGenXP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
165 lubridate::second(durGenXP)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
166 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
167
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
168 sprintf(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
169 '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"
siwaa
parents:
diff changeset
170 lubridate::day(durGenTP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
171 lubridate::hour(durGenTP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
172 lubridate::minute(durGenTP),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
173 lubridate::second(durGenTP)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
174 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
175 print(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
176 "==================================================================================="
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
177 )
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"
siwaa
parents:
diff changeset
179
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
180 #
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
181 # Simulation part
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"
siwaa
parents:
diff changeset
183
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
184 # List of successive USMs
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
185 successive_usms_file <- ("successionPlan.csv")
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
186 successive_usms_tab <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
187 read.csv(file = file.path(workspace, successive_usms_file),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
188 sep = ";")
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
189
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
190 # from succesions to simulate retrieving upcSol Cases
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
191
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
192 successRef <- successive_usms_tab["Treatment"]
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siwaa
parents:
diff changeset
193
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siwaa
parents:
diff changeset
194 successRef <- successRef %>%
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siwaa
parents:
diff changeset
195 separate(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
196 col = Treatment,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
197 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
198 sep = "-",
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siwaa
parents:
diff changeset
199 remove = FALSE
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siwaa
parents:
diff changeset
200 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
201
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
202 successRef$upcSol <- paste0(successRef$upc, "-", successRef$sol)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
203
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siwaa
parents:
diff changeset
204 casesUpcSol <- unique(successRef$upcSol)
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 systeme <- successRef$systeme[1]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
207 rotation <- successRef$rotation[1]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
208
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siwaa
parents:
diff changeset
209 successive_usms_tab_split <- list()
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siwaa
parents:
diff changeset
210
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siwaa
parents:
diff changeset
211 for (j in 1:length(casesUpcSol)) {
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siwaa
parents:
diff changeset
212 splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
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siwaa
parents:
diff changeset
213
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siwaa
parents:
diff changeset
214 upc <- splited[1]
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siwaa
parents:
diff changeset
215
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siwaa
parents:
diff changeset
216 sol <- splited[2]
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siwaa
parents:
diff changeset
217
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
218 successive_usms_tab_split[[j]] <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
219 successive_usms_tab[successRef$upcSol == casesUpcSol[j],]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
220 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
221
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
222 result <- foreach(j = 1:length(casesUpcSol)) %:%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
223 foreach(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
224 i = 1:nrow(successive_usms_tab_split[[j]]),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
225 .options.future = list(packages =c("foreach", "SticsRFiles", "SticsOnR"))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
226
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
227 ) %dordopar% {
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 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
230
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
231 vec <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
232 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
233
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
234 list_successive_usms <- list(vec)
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 sim_options <- stics_wrapper_options(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
237 javastics = javastics_path,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
238 stics_exe = paste0(javastics_path, "/bin/stics_modulo"),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
239 workspace = txt_path,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
240 verbose = TRUE,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
241 successive = list_successive_usms
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
242 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
243
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
244 list_usms <- vec
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 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
247
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
248 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
249
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
250 }
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 for (j in 1:length(casesUpcSol)) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
253 splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
254
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
255 upc <- splited[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 sol <- splited[2]
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 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
260 #i=1
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
261 if (i == 1) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
262 simPCP <- result[[j]][[i]]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
263 } else {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
264 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
265 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
266
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 #agregation des sorties dans un dataframe
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
270 sim_df <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
271 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
272
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
273 #ajout des colonnes explicatives + de l'horizon temporel
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
274 sim_df <- sim_df %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
275 separate(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
276 col = usm,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
277 into = c(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
278 "upc",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
279 "sol",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
280 "systeme",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
281 "rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
282 "tete_rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
283 "horizon",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
284 "annee",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
285 "culture"
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
286 ),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
287 sep = "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
288 remove = FALSE
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
289 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
290
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
291 #sauvegarde sous la forme d'un fichier rds
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 if (dir.exists(paste0(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
294 workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
295 "/analyse_simulations_STICS/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
296 systeme,
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 rotation
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
299 )) == FALSE) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
300 dir.create(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
301 paste0(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
302 workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
303 "/analyse_simulations_STICS/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
304 systeme,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
305 "/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
306 rotation
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 recursive = TRUE
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 }
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 saveRDS(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
313 sim_df,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
314 paste0(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
315 workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
316 "/analyse_simulations_STICS/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
317 systeme,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
318 "/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
319 rotation,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
320 "/outputs-",
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 "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
323 upc,
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 sol,
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 scenario,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
328 ".rds"
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
329 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
330 )
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 successive_usms_tab_split[[j]]$Treatment <- NULL
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
333 successive_usms_tab_split[[j]]$Number_USM <- NULL
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
334
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
335 list_usms <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
336 unlist(unname(as.list(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
337 transpose(successive_usms_tab_split[[j]])
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
338 )))
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
339 list_usms <- list_usms[!is.na(list_usms)]
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
340 list_usms <- list_usms[list_usms != '']
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
341
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
342 list_usms_yr1 <- successive_usms_tab_split[[j]]$USM_1
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
343
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
344 for (i in 1:length(list_usms)) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
345 if (i == 1) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
346 #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
347 #en attendant que toutes les simulations tournent correctement
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
348 #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
349 rap_1 <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
350 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
351 col_names = TRUE)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
352 names_col <- colnames(rap_1)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
353
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
354 rap_string <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
355 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
356 skip = 1)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
357
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
358 rap <- as_tibble(rap_string) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
359 separate(col = value,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
360 sep = ";",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
361 into = names_col) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
362 mutate(USM = list_usms[i])
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
363 # }
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 } else {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
366 #if (list_usms[i] %in% list_usms_yr1) {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
367 #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
368 #en attendant que toutes les simulations tournent correctement
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
369 #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
370 rap_string <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
371 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
372 skip = 1,)#}
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
373
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
374 # } else {
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
375 #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
376 #en attendant que toutes les simulations tournent correctement
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
377 #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
378 # rap_string <-
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
379 # 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
380 # }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
381 rap_i <- as_tibble(rap_string) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
382 separate(col = value,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
383 sep = ";",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
384 into = names_col) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
385 mutate(USM = list_usms[i])
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
386
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
387 rap <- bind_rows(rap, rap_i)
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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388
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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389 }
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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390
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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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 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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393
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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394 rap <- rap %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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395 select(USM, everything()) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
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396 mutate(P_usm = str_replace_all(P_usm, " ", "")) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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397 mutate(wlieu = str_replace_all(wlieu, " ", "")) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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398 mutate(stade = str_replace_all(stade, " ", "")) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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399 mutate(nomversion = str_replace_all(nomversion, " ", "")) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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400 mutate(across(3:9, as.numeric)) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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401 mutate(across(13:ncol(rap), as.numeric)) %>%
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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402 #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
403 separate(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
404 col = USM,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
405 into = c(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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406 "upc",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
407 "sol",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
408 "systeme",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
409 "rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
410 "tete_rotation",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
411 "horizon",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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412 "annee",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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413 "culture"
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:
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415 sep = "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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416 remove = FALSE
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
417 )
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
418
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
419 write_delim(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
420 x = rap,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
421 file = paste0(
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
422 workspace,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
423 "/analyse_simulations_STICS/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
424 systeme,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
425 "/",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
426 rotation,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
427 "/report-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
428 rotation,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
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429 "-",
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
430 upc,
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 sol,
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 scenario,
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
435 ".csv"
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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parents:
diff changeset
436 ),
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
437 delim = ";"
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
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
siwaa
parents:
diff changeset
440 }