Mercurial > repos > ecology > pampa_communitymetrics

annotate FunctExeCalcCommIndexesGalaxy.r @ 0:ddd5b2e74b8b draft

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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
author ecology
date Tue, 21 Jul 2020 06:00:10 -0400
parents
children 5bd7ddd7601f
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ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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1 #Rscript
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3 #####################################################################################################################
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4 #####################################################################################################################
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5 ################################# Calculate community indexes from observation data #################################
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6 #####################################################################################################################
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7 #####################################################################################################################
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9 ###################### Packages R
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11 suppressMessages(library(tidyr))
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13 ###################### Load arguments and declaring variables
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15 args = commandArgs(trailingOnly=TRUE)
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16 #options(encoding = "UTF-8")
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18 if (length(args) < 4) {
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19 stop("At least one argument must be supplied, an input dataset file (.tabular).", call.=FALSE) #si pas d'arguments -> affiche erreur et quitte / if no args -> error and exit1
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21 } else {
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22 Importdata<-args[1] ###### Nom du fichier importé avec son extension / file name imported with the file type ".filetype"
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23 index <- args[2] ###### List of selected metrics to calculate
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24 source(args[3]) ###### Import functions
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26 }
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27 #### Data must be a dataframe with at least 3 variables : unitobs representing location and year ("observation.unit"), species code ("species.code") and abundance ("number")
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30 #Import des données / Import data
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31 obs<- read.table(Importdata,sep="\t",dec=".",header=TRUE,encoding="UTF-8") #
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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32 obs[obs == -999] <- NA
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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33 factors <- fact.det.f(Obs=obs)
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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34 ObsType <- def.typeobs.f(Obs=obs)
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35 obs <- create.unitobs(data=obs)
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37 vars_data<-c("observation.unit","species.code","number")
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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38 err_msg_data<-"The input dataset doesn't have the right format. It need to have at least the following 3 variables :\n- observation.unit (or point and year)\n- species.code\n- number\n"
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39 check_file(obs,err_msg_data,vars_data,3)
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43 ####################################################################################################
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44 ################## create community metrics table ## Function : calcBiodiv.f #######################
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45 ####################################################################################################
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46
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47 ########################################################################################################################
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48 calcBiodiv.f <- function(Data, MPA, unitobs="observation.unit", code.especes="species.code", nombres="number",
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49 indices=index)
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50 {
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51 ## Purpose: calcul des indices de biodiversité
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52 ## ----------------------------------------------------------------------
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53 ## Arguments: Data : les données à partir desquelles calculer les
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54 ## indices. Doivent comporter au minimum (colones) :
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55 ## * unités d'observations/sites
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56 ## * espèces présentes
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57 ## * nombre d'individus /espèce/unitobs.
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58 ## refesp : le référentiel espèces.
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59 ## MPA : l'AMP (chaîne de charactères).
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60 ## unitobs : nom de la colone d'unités d'observation.
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61 ## code.especes : nom de la colone d'espèces.
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62 ## nombres : nom de la colone de nombres.
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63 ## indices : liste des indices à calculer
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64 ## (vecteur de caractères)
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65 ## ----------------------------------------------------------------------
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66 ## Author: Yves Reecht, Date: 29 oct. 2010, 08:58
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67
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68 ## Supression de tout ce qui n'a pas d'espèce précisee (peut être du non biotique ou identification >= genre) :
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69
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70 notspline <- grep("(sp\\.)$|([1-9])$|^(Absencemacrofaune)$|^(NoID)$|^(Acrobranc)$|^(Acrodigit)$|^(Acroencr)$|^(Acrosubm)$|^(Acrotabu)$|^(Adredure)$|^(Adremoll)$|^(Algaturf)$|^(Balimona)$|^(Corablan)$|^(CoradurV)$|^(Coraenal)$|^(Coramor1)$|^(Coramor2)$|^(Coramou)$|^( Dallcora)$|^(Debrcora)$|^(Debris)$|^(Hare)$|^(HexaChar)$|^(MuraCong)$|^(Nacrbran)$|^(Nacrcham)$|^(Nacrencr)$|^(Nacrfoli)$|^(Nacrmass)$|^(Nacrsubm)$|^(Recrcora)$|^(Roche)$|^(Sable)$|^(Vase)$",Data[, code.especes], value=FALSE)
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71 if (length(notspline) != 0)
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72 {
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73 Data <- Data[-notspline, ]
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74 }else{}
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75
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76 ## Suppression des niveaux de facteur inutilisés :
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77 Data <- dropLevels.f(df=Data)
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78
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79
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80 ## Si les données ne sont pas encore agrégées /espèce/unitobs on le fait ici :
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81 if (nrow(Data) > nrow(expand.grid(unique(Data[ , unitobs]), unique(Data[ , code.especes]))))
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82 {
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83 Data <- agregations.generic.f(Data=Data, metrics=nombres,
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84 factors=c(unitobs, code.especes),
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85 listFact=NULL)
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86 }else{}
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87
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88 df.biodiv <- as.data.frame(as.table(tapply(Data[ , nombres],
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89 Data[ , unitobs],
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
90 sum, na.rm=TRUE)))
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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91
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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92 colnames(df.biodiv) <- c(unitobs, nombres)
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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93
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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parents:
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94 ## ##################################################
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
95 ## Richesse spécifique :
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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96 Data$pres.abs <- presAbs.f(nombres=Data[ , nombres], logical = FALSE)
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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parents:
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97
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
98 df.biodiv$species.richness <- as.vector(tapply(Data$pres.abs,
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
99 Data[ , unitobs], sum, na.rm=TRUE),
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
100 "integer")
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
101 ## ... as.vector to avoid the class "array".
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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102
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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parents:
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103 ## ##################################################
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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104 ## Indices de Simpson et Shannon et dérivés :
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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105
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
106 matNombres <- tapply(Data[ , nombres], # Matrice de nombres d'individus /espèce/unitobs.
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
107 list(Data[ , unitobs], Data[ , code.especes]),
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
108 sum, na.rm=TRUE)
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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109
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
110 matNombres[is.na(matNombres)] <- 0 # Vrais zéros
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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111
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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112 ## Proportion d'individus de chaque espèce dans l'unitobs :
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
113 propIndiv <- sweep(matNombres, 1,
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
114 apply(matNombres, 1, sum, na.rm = TRUE), # Nombre d'individus / unitobs ; équiv df.biodiv$nombre.
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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115 FUN="/")
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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116
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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117 ## Indices de Simpson :
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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118 df.biodiv$simpson <- apply(propIndiv^2, 1, sum, na.rm=TRUE)
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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119
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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120 if (any(is.element(c("all", "simpson.l"), indices)))
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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121 {
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
122 df.biodiv$simpson.l <- 1 - df.biodiv$simpson
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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123 }
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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124
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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parents:
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125 ## calcul de l'indice de Shannon :
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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126 df.biodiv$shannon <- -1 * apply(propIndiv * log(propIndiv), 1, sum, na.rm=TRUE)
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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127
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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parents:
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128 ## calcul de l'indice de Pielou :
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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129 if (any(is.element(c("all", "pielou"), indices)))
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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130 {
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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131 df.biodiv$pielou <- df.biodiv$shannon / log(df.biodiv$species.richness)
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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132 }
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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parents:
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133
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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parents:
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134 ## calcul de l'indice de Hill :
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
135 if (any(is.element(c("all", "hill"), indices)))
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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136 {
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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137 df.biodiv$hill <- (1 - df.biodiv$simpson) / exp(df.biodiv$shannon)
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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138 # équiv df.biodiv$l.simpson / exp(df.biodiv$shannon)
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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139 }
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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140
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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141
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
142 return(df.biodiv)
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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143 }
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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144
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
145 ################# Analysis
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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146
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
147 res <- calc.numbers.f(obs, ObsType=ObsType , factors=factors, nbName="number")
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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parents:
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148
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
149 tableCommunityIndexes <- calcBiodiv.f(res, MPA, unitobs="observation.unit", code.especes="species.code", nombres="number",
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
150 indices=index)
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
151 tableCommunityIndexes <- create.year.point(tableCommunityIndexes)
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
152 #Save dataframe in a tabular format
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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parents:
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153
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
154 filenameComm <- "TabCommunityIndexes.tabular"
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
155 write.table(tableCommunityIndexes, filenameComm, row.names=FALSE, sep="\t", dec=".",fileEncoding="UTF-8")
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
156 cat(paste("\nWrite table with Community indexes. \n--> \"",filenameComm,"\"\n",sep=""))
ddd5b2e74b8b "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
157