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annotate redelacComputeAclim.R @ 0:80842c5ecb58 draft default tip

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"planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
author siwaa
date Tue, 24 Feb 2026 08:53:06 +0000
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80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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1 library(data.table) #version 1.14.2
80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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2 library(dplyr) #version 1.0.10
80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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3 library(ggplot2)
80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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4 library(rlang)
80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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5 library(stringr)
80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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6 sessionInfo()
80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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7
80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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8 args = commandArgs(trailingOnly = TRUE)
80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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9
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10 climatPath = args[1]
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11 horizons = args[2]
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12 rdsOut = args[3]
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13 csvOut = args[4]
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14 png1Out = args[5]
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15 png2Out = args[6]
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17 liste_mailles_SAFRAN <- list.dirs(climatPath,full.names = F,recursive = F)
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19 #agregation des fichiers climatiques dans un unique fichier
80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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20 fichier_climat_tot<- NULL
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23 for(maille_DRIAS in liste_mailles_SAFRAN){
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80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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25 setwd(paste0(climatPath,"/",maille_DRIAS))
80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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27 filenames <- list.files()
80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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30 fichier_climat_maille_tot <- NULL
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31 f=1
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32 for (filename in filenames)
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33 {
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34 file <- as.data.frame(fread(filename,sep="\t", dec=".", header=FALSE))
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35 if (f==1) {fichier_climat_maille_tot <-file} else {fichier_climat_maille_tot <- bind_rows(fichier_climat_maille_tot,file)}
80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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36 f=f+1
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37 }
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38 fichier_climat_tot<- bind_rows(fichier_climat_tot,fichier_climat_maille_tot)
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39 setwd("../..")
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40 }
80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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41
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42 #rm(file,fichier_climat_maille_tot)
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43
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44 #entete des colonnes
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45 # column 1: name of weather file
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46 # column 2: year
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47 # column 3: month
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48 # column 4: day in month
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49 # column 5: Julian day
80842c5ecb58 "planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/68f4e9db390070700af804f77468145abfc26bc0/tools/REDELACcomputeAclim commit 68f4e9db390070700af804f77468145abfc26bc0-dirty"
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50 # column 6: minimum temperature (degrees C)
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51 # column 7: maximum temperature (degrees C)
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52 # column 8: global radiation (MJ m-2 j-1)
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53 # column 9: Penman PET (mm j-1)
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54 # column 10: rainfall (mm j-1)
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55 # column 11: wind (m s-1)
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56 # column 12: vapour pressure (mbars)
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57 # column 13: CO2 content(ppm)
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58
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59 names(fichier_climat_tot)
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60
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61 names(fichier_climat_tot)<- c("maille_DRIAS","annee","mois","jcal","jjulien","TN","TX","RG","ETP","P","V","PV","CO2")
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62
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63
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64 # sanityzing
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65
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66 trimedHorizon <-str_trim(horizons)
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67 purgedHorizon <-str_sub(trimedHorizon, 1, nchar(trimedHorizon)-1)
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68
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69 listHory <- lapply(unlist(strsplit(purgedHorizon, ",")), function(x) {tmpdata <- str_split(str_trim(x), " ")[[1]]; paste0("(annee<", tmpdata[3], ")&(annee>",tmpdata[2], ")~\"", tmpdata[1], "\"" )})
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70
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71 listHory
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72
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73 paste(listHory, collapse = ",", sep = "")
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74
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75 horizonsFilter <- parse_expr(paste(listHory, collapse = ",", sep = ""))
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76
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77 listHory
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78
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79 fichier_climat_tot <- fichier_climat_tot %>%
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80 mutate(horizon=case_when(!!horizonsFilter))
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81
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82 #fichier_climat_tot <- fichier_climat_tot %>%
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83 # mutate(horizon=case_when((annee>1990)&(annee<2025)~"ref"))
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84
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85 #ecriture du fichier
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86 saveRDS(fichier_climat_tot, rdsOut)
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87
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88 fichier_aclim_an <- fichier_climat_tot %>%
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89 select(maille_DRIAS,horizon,annee,V)%>%
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90 group_by(maille_DRIAS,horizon,annee)%>%
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91 summarise(Vmed = median(V,na.rm=T))%>%
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92 mutate(aclim=-6.2*log(Vmed)+17.5)
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93
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94 fichier_aclim_hor <- fichier_aclim_an %>%
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95 select(maille_DRIAS,horizon,annee,aclim)%>%
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96 group_by(maille_DRIAS,horizon)%>%
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97 summarise(aclim = median(aclim,na.rm=T))%>%
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98 filter(is.na(horizon)==F)
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99
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100
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101 #ecriture des valeurs de aclim par maille SAFRAN et horizon
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102 write.table(fichier_aclim_hor,csvOut,sep=";",dec=",",row.names = F)
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103
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104
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105 #tracage des valeurs calculees de aclim
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106 # ggplot()+geom_boxplot(data=fichier_aclim_an,aes(y=aclim))
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107 # ggplot()+geom_boxplot(data=fichier_aclim_an,aes(y=aclim,x=horizon))
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108 # ggplot()+geom_boxplot(data=fichier_aclim_an,aes(y=aclim,x=as.factor(maille_DRIAS)))
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109
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110 ggplot()+geom_line(data=fichier_aclim_an ,aes(x=annee,y=aclim,group=maille_DRIAS,color=as.factor(maille_DRIAS)))
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111 ggsave(png1Out)
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112 ggplot()+
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113 geom_boxplot(data=fichier_aclim_an %>% filter(is.na(horizon)==F),aes(x=as.factor(maille_DRIAS),y=aclim,fill=horizon))+
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114 xlab("Maille DRIAS")+
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115 theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
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116 ggsave(png2Out)