R/MI.indices.R
In jbfagotfede39/aquatools: Tools for freshwater managers
Defines functions
MI.indices
Documented in
MI.indices
#' Calcul d'indices et de listes de MI
#'
#' Calcule d'indices synthétiques à partir de données de captures d'une opération ou plusieurs opérations de suivi MI
#' @name MI.indices
#' @param DataTravail Dataframe contenant les données de captures issues de MI.indices()
#' @param Sortie Forme du dataframe de sortie - \code{indices} (par défault), \code{listefaunistiqueGlobale}, \code{listefaunistiqueMAG20}, \code{listefaunistiqueDCEPrelevement}, \code{listefaunistiqueDCEPhase}, \code{listefaunistiqueDCEequivalentIBGN}, \code{listefaunistiqueIBGN}
#' @keywords donnees
#' @import DBI
#' @import tidyverse
#' @export
#' @examples
#' MI.indices(DataTravail)
#' MI.indices(DataTravail, Sortie = listefaunistiqueMAG20)
##### TODO LIST #####
# Ajout du calcul de la robustesse (avec fct nth (ou top_n) dans summarise <-> fctt à voir pour prendre la deuxième valeur après tri ? Et première pour GIIBGN)
# Ajout du calcul du cb2
#####################
MI.indices <- function(
DataTravail = MI.captures(MI.operations(Sortie = "Complet")),
Sortie = c("indices","listefaunistiqueGlobale","listefaunistiqueMAG20", "listefaunistiqueDCEPrelevement", "listefaunistiqueDCEPhase", "listefaunistiqueDCEequivalentIBGN", "listefaunistiqueIBGN")
)
{
##### Évaluation des choix #####
Sortie <- match.arg(Sortie)
##### Nettoyage ######
DataTravail <- DataTravail %>% mutate(Abondance = as.numeric(Abondance))
##### Systématique et code SANDRE ######
DataTravail <- DataTravail %>% MI.systematique() %>% MI.SANDRE()
##### Évaluation du nombre d'opérations #####
N <- DataTravail %>% distinct(CodeRHJ,Date) %>% n_distinct()
##### Liste indicielle #####
if(Sortie == "indices"){
indices <-
DataTravail %>%
filter(!is.na(Abondance)) %>%
rename(GIIBGNcomplet = 'GI-IBGN.x') %>%
rename(GICB2 = 'GI-CB2.x') %>%
left_join(., DataTravail %>% filter(!is.na(Abondance)) %>% group_by(CodeRHJ, Date, Ordre, FamilleSensIBGN) %>% summarise(TotalIBGN = sum(na.omit(Abondance[IBGN == "Oui"]))) %>% filter(TotalIBGN != 0) %>% mutate(EtatGIIBGN = case_when(
TotalIBGN >= 3 & FamilleSensIBGN == "Perlodidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Chloroperlidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Perlidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Taeniopterygidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Brachycentridae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Capniidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Odontoceridae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Aeshnidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Beraeidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Goeridae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Glossosomatidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Leptophlebiidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Leuctridae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Ephemeridae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Sericostomatidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Nemouridae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Heptageniidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Polymitarcyidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Hydroptilidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Polycentropodidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Rhyacophilidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Psychomyiidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Ephemerellidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Limnephilidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Aphelocheiridae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Hydropsychidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Elmidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Gammaridae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Caenidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Baetidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Chironomidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Asellidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Oligochaeta" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Achètes" ~ "GIIBGNOK",
TotalIBGN >= 3 & Ordre == "Gastéropodes" ~ "GIIBGNOK",
TotalIBGN >= 3 & Ordre == "Bivalves" ~ "GIIBGNOK",
TRUE ~ "GIIBGNpasOK")),
by = c("Ordre", "CodeRHJ", "Date", "FamilleSensIBGN")
) %>%
ungroup() %>%
left_join(., DataTravail %>% filter(!is.na(Abondance)) %>% group_by(CodeRHJ, Date, Ordre, FamilleSensIBGN) %>% summarise(TotalEqIBGN = sum(na.omit(Abondance[PhaseDCE == "A" | PhaseDCE == "B"]))) %>% filter(TotalEqIBGN != 0) %>% mutate(EtatGIEqIBGN = case_when(
TotalEqIBGN >= 3 & FamilleSensIBGN == "Perlodidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Chloroperlidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Perlidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Taeniopterygidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Brachycentridae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Capniidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Odontoceridae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Aeshnidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Beraeidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Goeridae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Glossosomatidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Leptophlebiidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Leuctridae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Ephemeridae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Sericostomatidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Nemouridae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Heptageniidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Polymitarcyidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Hydroptilidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Polycentropodidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Rhyacophilidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Psychomyiidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Ephemerellidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Limnephilidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Aphelocheiridae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Hydropsychidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Elmidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Gammaridae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Caenidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Baetidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Chironomidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Asellidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Oligochaeta" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Achètes" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & Ordre == "Gastéropodes" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & Ordre == "Bivalves" ~ "GIIBGNOK",
TRUE ~ "GIIBGNpasOK")),
by = c("Ordre", "CodeRHJ", "Date", "FamilleSensIBGN")
) %>%
ungroup() %>%
mutate(EtatGIIBGN = ifelse(is.na(EtatGIIBGN), "GIIBGNpasOK", EtatGIIBGN)) %>%
mutate(TotalIBGN = ifelse(is.na(TotalIBGN), 0, TotalIBGN)) %>%
mutate(EtatGIEqIBGN = ifelse(is.na(EtatGIEqIBGN), "GIIBGNpasOK", EtatGIEqIBGN)) %>%
mutate(TotalEqIBGN = ifelse(is.na(TotalEqIBGN), 0, TotalEqIBGN)) %>%
group_by(CodeRHJ, Date) %>%
#View()
summarise(
TotalMAG20 = sum(Abondance[NumEchMAG20 <= 20]),
TotalTEP = sum(Abondance[Ordre == "Plécoptères" | Ordre == "Trichoptères" | Ordre == "Éphéméroptères"]),
TotalCO = sum(Abondance[Taxon == "Chironomidae" | Taxon == "Oligochaeta"]),
TotalDCE = sum(na.omit(Abondance[PhaseDCE == "A" | PhaseDCE == "B" | PhaseDCE == "C"])),
TotalPhaseA = sum(na.omit(Abondance[PhaseDCE == "A"])),
TotalPhaseB = sum(na.omit(Abondance[PhaseDCE == "B"])),
TotalPhaseC = sum(na.omit(Abondance[PhaseDCE == "C"])),
TotalEqIBGN = sum(na.omit(Abondance[PhaseDCE == "A" | PhaseDCE == "B"])),
TotalIBGN = sum(na.omit(Abondance[IBGN == "Oui"])),
GIIBGN = max(na.omit(GIIBGNcomplet[IBGN == "Oui" & EtatGIIBGN == "GIIBGNOK"])),
GIEqIBGN = max(na.omit(GIIBGNcomplet[(PhaseDCE == "A" & EtatGIEqIBGN == "GIIBGNOK") | (PhaseDCE == "B" & EtatGIEqIBGN == "GIIBGNOK")])),
#RobustesseIBGN = nth(GIIBGN[IBGN == "Oui" & EtatGI == "GIIBGNOK"], 1 ,order_by = GIIBGN),
VarieteIBGN = length(unique(FamilleSensIBGN[IBGN == "Oui"])),
VarieteEqIBGN = length(unique(FamilleSensIBGN[PhaseDCE == "A" | PhaseDCE == "B"])),
#GICB2 = max(na.omit(GICB2[IBGN == "Oui"])),
#VarieteCB2 = length(unique(FamilleSensIBGN[IBGN == "Oui"])),
VarieteTotale = length(unique(Taxon)),
VarieteFamiliale = length(unique(FamilleSensIBGN)),
VarietePleco = length(unique(Taxon[Ordre == "Plécoptères"])),
VarieteTricho = length(unique(Taxon[Ordre == "Trichoptères"])),
VarieteEphemero = length(unique(Taxon[Ordre == "Éphéméroptères"])),
VarieteColeo = length(unique(Taxon[Ordre == "Coléoptères"]))
) %>%
mutate_all(funs(replace(., . == 0, NA))) %>%
mutate(NoteIBGN = case_when(VarieteIBGN >= 50 & GIIBGN == 9 ~ 20,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 9 ~ 20,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 9 ~ 20,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 9 ~ 19,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 9 ~ 18,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 9 ~ 17,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 9 ~ 16,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 9 ~ 15,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 9 ~ 14,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 9 ~ 13,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 9 ~ 12,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 9 ~ 11,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 9 ~ 10,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 9 ~ 9,
VarieteIBGN >= 50 & GIIBGN == 8 ~ 20,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 8 ~ 20,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 8 ~ 19,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 8 ~ 18,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 8 ~ 17,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 8 ~ 16,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 8 ~ 15,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 8 ~ 14,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 8 ~ 13,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 8 ~ 12,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 8 ~ 11,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 8 ~ 10,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 8 ~ 9,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 8 ~ 8,
VarieteIBGN >= 50 & GIIBGN == 7 ~ 20,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 7 ~ 19,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 7 ~ 18,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 7 ~ 17,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 7 ~ 16,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 7 ~ 15,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 7 ~ 14,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 7 ~ 13,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 7 ~ 12,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 7 ~ 11,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 7 ~ 10,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 7 ~ 9,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 7 ~ 8,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 7 ~ 7,
VarieteIBGN >= 50 & GIIBGN == 6 ~ 19,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 6 ~ 18,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 6 ~ 17,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 6 ~ 16,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 6 ~ 15,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 6 ~ 14,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 6 ~ 13,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 6 ~ 12,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 6 ~ 11,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 6 ~ 10,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 6 ~ 9,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 6 ~ 8,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 6 ~ 7,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 6 ~ 6,
VarieteIBGN >= 50 & GIIBGN == 5 ~ 18,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 5 ~ 17,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 5 ~ 16,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 5 ~ 15,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 5 ~ 14,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 5 ~ 13,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 5 ~ 12,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 5 ~ 11,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 5 ~ 10,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 5 ~ 9,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 5 ~ 8,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 5 ~ 7,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 5 ~ 6,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 5 ~ 5,
VarieteIBGN >= 50 & GIIBGN == 4 ~ 17,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 4 ~ 16,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 4 ~ 15,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 4 ~ 14,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 4 ~ 13,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 4 ~ 12,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 4 ~ 11,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 4 ~ 10,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 4 ~ 9,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 4 ~ 8,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 4 ~ 7,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 4 ~ 6,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 4 ~ 5,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 4 ~ 4,
VarieteIBGN >= 50 & GIIBGN == 3 ~ 16,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 3 ~ 15,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 3 ~ 14,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 3 ~ 13,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 3 ~ 12,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 3 ~ 11,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 3 ~ 10,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 3 ~ 9,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 3 ~ 8,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 3 ~ 7,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 3 ~ 6,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 3 ~ 5,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 3 ~ 4,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 3 ~ 3,
VarieteIBGN >= 50 & GIIBGN == 2 ~ 15,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 2 ~ 14,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 2 ~ 13,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 2 ~ 12,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 2 ~ 11,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 2 ~ 10,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 2 ~ 9,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 2 ~ 8,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 2 ~ 7,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 2 ~ 6,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 2 ~ 5,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 2 ~ 4,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 2 ~ 3,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 2 ~ 2,
VarieteIBGN >= 50 & GIIBGN == 1 ~ 14,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 1 ~ 13,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 1 ~ 12,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 1 ~ 11,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 1 ~ 10,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 1 ~ 9,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 1 ~ 8,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 1 ~ 7,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 1 ~ 6,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 1 ~ 5,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 1 ~ 4,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 1 ~ 3,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 1 ~ 2,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 1 ~ 1
)
) %>%
mutate(NoteEqIBGN = case_when(VarieteEqIBGN >= 50 & GIEqIBGN == 9 ~ 20,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 9 ~ 20,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 9 ~ 20,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 9 ~ 19,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 9 ~ 18,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 9 ~ 17,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 9 ~ 16,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 9 ~ 15,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 9 ~ 14,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 9 ~ 13,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 9 ~ 12,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 9 ~ 11,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 9 ~ 10,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 9 ~ 9,
VarieteEqIBGN >= 50 & GIEqIBGN == 8 ~ 20,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 8 ~ 20,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 8 ~ 19,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 8 ~ 18,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 8 ~ 17,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 8 ~ 16,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 8 ~ 15,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 8 ~ 14,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 8 ~ 13,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 8 ~ 12,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 8 ~ 11,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 8 ~ 10,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 8 ~ 9,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 8 ~ 8,
VarieteEqIBGN >= 50 & GIEqIBGN == 7 ~ 20,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 7 ~ 19,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 7 ~ 18,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 7 ~ 17,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 7 ~ 16,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 7 ~ 15,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 7 ~ 14,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 7 ~ 13,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 7 ~ 12,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 7 ~ 11,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 7 ~ 10,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 7 ~ 9,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 7 ~ 8,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 7 ~ 7,
VarieteEqIBGN >= 50 & GIEqIBGN == 6 ~ 19,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 6 ~ 18,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 6 ~ 17,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 6 ~ 16,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 6 ~ 15,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 6 ~ 14,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 6 ~ 13,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 6 ~ 12,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 6 ~ 11,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 6 ~ 10,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 6 ~ 9,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 6 ~ 8,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 6 ~ 7,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 6 ~ 6,
VarieteEqIBGN >= 50 & GIEqIBGN == 5 ~ 18,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 5 ~ 17,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 5 ~ 16,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 5 ~ 15,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 5 ~ 14,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 5 ~ 13,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 5 ~ 12,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 5 ~ 11,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 5 ~ 10,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 5 ~ 9,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 5 ~ 8,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 5 ~ 7,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 5 ~ 6,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 5 ~ 5,
VarieteEqIBGN >= 50 & GIEqIBGN == 4 ~ 17,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 4 ~ 16,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 4 ~ 15,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 4 ~ 14,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 4 ~ 13,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 4 ~ 12,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 4 ~ 11,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 4 ~ 10,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 4 ~ 9,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 4 ~ 8,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 4 ~ 7,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 4 ~ 6,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 4 ~ 5,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 4 ~ 4,
VarieteEqIBGN >= 50 & GIEqIBGN == 3 ~ 16,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 3 ~ 15,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 3 ~ 14,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 3 ~ 13,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 3 ~ 12,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 3 ~ 11,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 3 ~ 10,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 3 ~ 9,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 3 ~ 8,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 3 ~ 7,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 3 ~ 6,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 3 ~ 5,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 3 ~ 4,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 3 ~ 3,
VarieteEqIBGN >= 50 & GIEqIBGN == 2 ~ 15,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 2 ~ 14,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 2 ~ 13,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 2 ~ 12,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 2 ~ 11,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 2 ~ 10,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 2 ~ 9,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 2 ~ 8,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 2 ~ 7,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 2 ~ 6,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 2 ~ 5,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 2 ~ 4,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 2 ~ 3,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 2 ~ 2,
VarieteEqIBGN >= 50 & GIEqIBGN == 1 ~ 14,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 1 ~ 13,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 1 ~ 12,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 1 ~ 11,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 1 ~ 10,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 1 ~ 9,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 1 ~ 8,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 1 ~ 7,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 1 ~ 6,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 1 ~ 5,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 1 ~ 4,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 1 ~ 3,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 1 ~ 2,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 1 ~ 1
)
)
return(indices)
}
##### Liste faunistiques #####
#### listefaunistiqueGlobale ####
if(N != 1 & Sortie == "listefaunistiqueGlobale") stop("Établissement des listes faunistiques de plusieurs opérations non encore développé")
if(N == 1 & Sortie == "listefaunistiqueGlobale") stop("Établissement de la listefaunistiqueGlobale d'une seule opération non encore développé")
#### listefaunistiqueMAG20 ####
if(N != 1 & Sortie == "listefaunistiqueMAG20"){
listefaunistiqueMAG20 <-
DataTravail %>%
filter(NumEchMAG20 <= 20) %>%
dcast(Taxon ~ CodeRHJ , value.var = "Abondance", sum) %>%
right_join(DataTravail %>% distinct(Taxon, CodeSANDRE, AffichageSensibilite, Ordre, Famille, Genre, Espece), by = "Taxon") %>%
arrange(AffichageSensibilite, Ordre, Famille, Genre, Espece) %>%
select(Ordre, Famille, Genre, Espece, Taxon, CodeSANDRE, everything(), -AffichageSensibilite) %>%
#rename('Taxon/Prelevement' = Taxon) %>%
mutate_all(funs(replace(., . == 0, NA))) %>%
mutate(Ordre2 = ifelse(lag(Ordre) == Ordre, NA, Ordre)) %>% # Pour clarifier l'affichage
mutate(Ordre2 = ifelse(row_number() == 1, Ordre , Ordre2)) %>%
mutate(Ordre = Ordre2) %>%
select(-Ordre2) %>%
mutate(Famille2 = ifelse(lag(Famille) == Famille, NA, Famille)) %>% # Pour clarifier l'affichage
mutate(Famille2 = ifelse(row_number() == 1, Famille , Famille2)) %>%
mutate(Famille = Famille2) %>%
select(-Famille2)
# mutate(Genre2 = ifelse(lag(Genre) == Genre, NA, Genre)) %>% # Pour clarifier l'affichage
# mutate(Genre2 = ifelse(row_number() == 1, Genre , Genre2)) %>%
# mutate(Genre = Genre2) %>%
#select(-Genre2) %>%
# mutate(Espece2 = ifelse(lag(Espece) == Espece, NA, Espece)) %>% # Pour clarifier l'affichage
# mutate(Espece2 = ifelse(row_number() == 1, Espece , Espece2)) %>%
# mutate(Espece = Espece2) %>%
#select(-Espece2)
return(listefaunistiqueMAG20)
}
if(N == 1 & Sortie == "listefaunistiqueMAG20"){
listefaunistiqueMAG20 <-
DataTravail %>%
filter(NumEchMAG20 <= 20) %>%
dcast(Taxon ~ NumEchMAG20 , value.var = "Abondance", sum) %>%
right_join(DataTravail %>% distinct(Taxon, CodeSANDRE), by = "Taxon") %>%
select(Taxon, CodeSANDRE, everything()) %>%
rename('Taxon/Prelevement' = Taxon) %>%
mutate_all(funs(replace(., . == 0, NA)))
return(listefaunistiqueMAG20)
}
#### listefaunistiqueDCEPrelevement ####
if(N != 1 & Sortie == "listefaunistiqueDCEPrelevement") stop("Établissement des listes faunistiques de plusieurs opérations non encore développé")
if(N == 1 & Sortie == "listefaunistiqueDCEPrelevement"){
listefaunistiqueDCEPrelevement <-
DataTravail %>%
filter(!is.na(NumEchDCE)) %>%
dcast(Taxon ~ NumEchDCE , value.var = "Abondance", sum) %>%
right_join(DataTravail %>% distinct(Taxon, CodeSANDRE), by = "Taxon") %>%
select(Taxon, CodeSANDRE, everything()) %>%
rename('Taxon/Prelevement' = Taxon) %>%
mutate_all(funs(replace(., . == 0, NA)))
return(listefaunistiqueDCEPrelevement)
}
#### listefaunistiqueDCEPhase ####
if(N != 1 & Sortie == "listefaunistiqueDCEPhase") stop("Établissement des listes faunistiques de plusieurs opérations non encore développé")
if(N == 1 & Sortie == "listefaunistiqueDCEPhase"){
listefaunistiqueDCEPhase <-
DataTravail %>%
filter(!is.na(NumEchDCE)) %>%
mutate(Abondance = as.numeric(Abondance)) %>%
dcast(Taxon ~ PhaseDCE , value.var = "Abondance", sum) %>%
right_join(DataTravail %>% distinct(Taxon, CodeSANDRE), by = "Taxon") %>%
select(Taxon, CodeSANDRE, everything()) %>%
rename('Taxon/Phase' = Taxon) %>%
mutate_all(funs(replace(., . == 0, NA)))
return(listefaunistiqueDCEPhase)
}
#### listefaunistiqueDCEequivalentIBGN ####
if(N != 1 & Sortie == "listefaunistiqueDCEequivalentIBGN") stop("Établissement des listes faunistiques de plusieurs opérations non encore développé")
if(N == 1 & Sortie == "listefaunistiqueDCEequivalentIBGN") stop("Établissement de la listefaunistiqueDCEequivalentIBGN d'une seule opération non encore développé")
#### listefaunistiqueIBGN ####
if(N != 1 & Sortie == "listefaunistiqueIBGN") stop("Établissement des listes faunistiques de plusieurs opérations non encore développé")
if(N == 1 & Sortie == "listefaunistiqueIBGN") stop("Établissement de la listefaunistiqueIBGN d'une seule opération non encore développé")
} # Fin de la fonction
jbfagotfede39/aquatools documentation built on Jan. 22, 2025, 1:20 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions MI.indices
Documented in MI.indices
#' Calcul d'indices et de listes de MI
#'
#' Calcule d'indices synthétiques à partir de données de captures d'une opération ou plusieurs opérations de suivi MI
#' @name MI.indices
#' @param DataTravail Dataframe contenant les données de captures issues de MI.indices()
#' @param Sortie Forme du dataframe de sortie - \code{indices} (par défault), \code{listefaunistiqueGlobale}, \code{listefaunistiqueMAG20}, \code{listefaunistiqueDCEPrelevement}, \code{listefaunistiqueDCEPhase}, \code{listefaunistiqueDCEequivalentIBGN}, \code{listefaunistiqueIBGN}
#' @keywords donnees
#' @import DBI
#' @import tidyverse
#' @export
#' @examples
#' MI.indices(DataTravail)
#' MI.indices(DataTravail, Sortie = listefaunistiqueMAG20)
##### TODO LIST #####
# Ajout du calcul de la robustesse (avec fct nth (ou top_n) dans summarise <-> fctt à voir pour prendre la deuxième valeur après tri ? Et première pour GIIBGN)
# Ajout du calcul du cb2
#####################
MI.indices <- function(
DataTravail = MI.captures(MI.operations(Sortie = "Complet")),
Sortie = c("indices","listefaunistiqueGlobale","listefaunistiqueMAG20", "listefaunistiqueDCEPrelevement", "listefaunistiqueDCEPhase", "listefaunistiqueDCEequivalentIBGN", "listefaunistiqueIBGN")
)
{
##### Évaluation des choix #####
Sortie <- match.arg(Sortie)
##### Nettoyage ######
DataTravail <- DataTravail %>% mutate(Abondance = as.numeric(Abondance))
##### Systématique et code SANDRE ######
DataTravail <- DataTravail %>% MI.systematique() %>% MI.SANDRE()
##### Évaluation du nombre d'opérations #####
N <- DataTravail %>% distinct(CodeRHJ,Date) %>% n_distinct()
##### Liste indicielle #####
if(Sortie == "indices"){
indices <-
DataTravail %>%
filter(!is.na(Abondance)) %>%
rename(GIIBGNcomplet = 'GI-IBGN.x') %>%
rename(GICB2 = 'GI-CB2.x') %>%
left_join(., DataTravail %>% filter(!is.na(Abondance)) %>% group_by(CodeRHJ, Date, Ordre, FamilleSensIBGN) %>% summarise(TotalIBGN = sum(na.omit(Abondance[IBGN == "Oui"]))) %>% filter(TotalIBGN != 0) %>% mutate(EtatGIIBGN = case_when(
TotalIBGN >= 3 & FamilleSensIBGN == "Perlodidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Chloroperlidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Perlidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Taeniopterygidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Brachycentridae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Capniidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Odontoceridae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Aeshnidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Beraeidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Goeridae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Glossosomatidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Leptophlebiidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Leuctridae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Ephemeridae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Sericostomatidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Nemouridae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Heptageniidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Polymitarcyidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Hydroptilidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Polycentropodidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Rhyacophilidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Psychomyiidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Ephemerellidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Limnephilidae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Aphelocheiridae" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Hydropsychidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Elmidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Gammaridae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Caenidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Baetidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Chironomidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Asellidae" ~ "GIIBGNOK",
TotalIBGN >= 10 & FamilleSensIBGN == "Oligochaeta" ~ "GIIBGNOK",
TotalIBGN >= 3 & FamilleSensIBGN == "Achètes" ~ "GIIBGNOK",
TotalIBGN >= 3 & Ordre == "Gastéropodes" ~ "GIIBGNOK",
TotalIBGN >= 3 & Ordre == "Bivalves" ~ "GIIBGNOK",
TRUE ~ "GIIBGNpasOK")),
by = c("Ordre", "CodeRHJ", "Date", "FamilleSensIBGN")
) %>%
ungroup() %>%
left_join(., DataTravail %>% filter(!is.na(Abondance)) %>% group_by(CodeRHJ, Date, Ordre, FamilleSensIBGN) %>% summarise(TotalEqIBGN = sum(na.omit(Abondance[PhaseDCE == "A" | PhaseDCE == "B"]))) %>% filter(TotalEqIBGN != 0) %>% mutate(EtatGIEqIBGN = case_when(
TotalEqIBGN >= 3 & FamilleSensIBGN == "Perlodidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Chloroperlidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Perlidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Taeniopterygidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Brachycentridae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Capniidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Odontoceridae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Aeshnidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Beraeidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Goeridae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Glossosomatidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Leptophlebiidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Leuctridae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Ephemeridae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Sericostomatidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Nemouridae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Heptageniidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Polymitarcyidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Hydroptilidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Polycentropodidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Rhyacophilidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Psychomyiidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Ephemerellidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Limnephilidae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Aphelocheiridae" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Hydropsychidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Elmidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Gammaridae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Caenidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Baetidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Chironomidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Asellidae" ~ "GIIBGNOK",
TotalEqIBGN >= 10 & FamilleSensIBGN == "Oligochaeta" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & FamilleSensIBGN == "Achètes" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & Ordre == "Gastéropodes" ~ "GIIBGNOK",
TotalEqIBGN >= 3 & Ordre == "Bivalves" ~ "GIIBGNOK",
TRUE ~ "GIIBGNpasOK")),
by = c("Ordre", "CodeRHJ", "Date", "FamilleSensIBGN")
) %>%
ungroup() %>%
mutate(EtatGIIBGN = ifelse(is.na(EtatGIIBGN), "GIIBGNpasOK", EtatGIIBGN)) %>%
mutate(TotalIBGN = ifelse(is.na(TotalIBGN), 0, TotalIBGN)) %>%
mutate(EtatGIEqIBGN = ifelse(is.na(EtatGIEqIBGN), "GIIBGNpasOK", EtatGIEqIBGN)) %>%
mutate(TotalEqIBGN = ifelse(is.na(TotalEqIBGN), 0, TotalEqIBGN)) %>%
group_by(CodeRHJ, Date) %>%
#View()
summarise(
TotalMAG20 = sum(Abondance[NumEchMAG20 <= 20]),
TotalTEP = sum(Abondance[Ordre == "Plécoptères" | Ordre == "Trichoptères" | Ordre == "Éphéméroptères"]),
TotalCO = sum(Abondance[Taxon == "Chironomidae" | Taxon == "Oligochaeta"]),
TotalDCE = sum(na.omit(Abondance[PhaseDCE == "A" | PhaseDCE == "B" | PhaseDCE == "C"])),
TotalPhaseA = sum(na.omit(Abondance[PhaseDCE == "A"])),
TotalPhaseB = sum(na.omit(Abondance[PhaseDCE == "B"])),
TotalPhaseC = sum(na.omit(Abondance[PhaseDCE == "C"])),
TotalEqIBGN = sum(na.omit(Abondance[PhaseDCE == "A" | PhaseDCE == "B"])),
TotalIBGN = sum(na.omit(Abondance[IBGN == "Oui"])),
GIIBGN = max(na.omit(GIIBGNcomplet[IBGN == "Oui" & EtatGIIBGN == "GIIBGNOK"])),
GIEqIBGN = max(na.omit(GIIBGNcomplet[(PhaseDCE == "A" & EtatGIEqIBGN == "GIIBGNOK") | (PhaseDCE == "B" & EtatGIEqIBGN == "GIIBGNOK")])),
#RobustesseIBGN = nth(GIIBGN[IBGN == "Oui" & EtatGI == "GIIBGNOK"], 1 ,order_by = GIIBGN),
VarieteIBGN = length(unique(FamilleSensIBGN[IBGN == "Oui"])),
VarieteEqIBGN = length(unique(FamilleSensIBGN[PhaseDCE == "A" | PhaseDCE == "B"])),
#GICB2 = max(na.omit(GICB2[IBGN == "Oui"])),
#VarieteCB2 = length(unique(FamilleSensIBGN[IBGN == "Oui"])),
VarieteTotale = length(unique(Taxon)),
VarieteFamiliale = length(unique(FamilleSensIBGN)),
VarietePleco = length(unique(Taxon[Ordre == "Plécoptères"])),
VarieteTricho = length(unique(Taxon[Ordre == "Trichoptères"])),
VarieteEphemero = length(unique(Taxon[Ordre == "Éphéméroptères"])),
VarieteColeo = length(unique(Taxon[Ordre == "Coléoptères"]))
) %>%
mutate_all(funs(replace(., . == 0, NA))) %>%
mutate(NoteIBGN = case_when(VarieteIBGN >= 50 & GIIBGN == 9 ~ 20,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 9 ~ 20,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 9 ~ 20,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 9 ~ 19,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 9 ~ 18,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 9 ~ 17,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 9 ~ 16,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 9 ~ 15,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 9 ~ 14,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 9 ~ 13,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 9 ~ 12,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 9 ~ 11,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 9 ~ 10,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 9 ~ 9,
VarieteIBGN >= 50 & GIIBGN == 8 ~ 20,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 8 ~ 20,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 8 ~ 19,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 8 ~ 18,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 8 ~ 17,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 8 ~ 16,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 8 ~ 15,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 8 ~ 14,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 8 ~ 13,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 8 ~ 12,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 8 ~ 11,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 8 ~ 10,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 8 ~ 9,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 8 ~ 8,
VarieteIBGN >= 50 & GIIBGN == 7 ~ 20,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 7 ~ 19,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 7 ~ 18,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 7 ~ 17,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 7 ~ 16,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 7 ~ 15,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 7 ~ 14,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 7 ~ 13,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 7 ~ 12,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 7 ~ 11,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 7 ~ 10,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 7 ~ 9,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 7 ~ 8,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 7 ~ 7,
VarieteIBGN >= 50 & GIIBGN == 6 ~ 19,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 6 ~ 18,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 6 ~ 17,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 6 ~ 16,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 6 ~ 15,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 6 ~ 14,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 6 ~ 13,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 6 ~ 12,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 6 ~ 11,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 6 ~ 10,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 6 ~ 9,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 6 ~ 8,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 6 ~ 7,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 6 ~ 6,
VarieteIBGN >= 50 & GIIBGN == 5 ~ 18,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 5 ~ 17,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 5 ~ 16,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 5 ~ 15,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 5 ~ 14,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 5 ~ 13,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 5 ~ 12,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 5 ~ 11,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 5 ~ 10,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 5 ~ 9,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 5 ~ 8,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 5 ~ 7,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 5 ~ 6,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 5 ~ 5,
VarieteIBGN >= 50 & GIIBGN == 4 ~ 17,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 4 ~ 16,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 4 ~ 15,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 4 ~ 14,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 4 ~ 13,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 4 ~ 12,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 4 ~ 11,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 4 ~ 10,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 4 ~ 9,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 4 ~ 8,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 4 ~ 7,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 4 ~ 6,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 4 ~ 5,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 4 ~ 4,
VarieteIBGN >= 50 & GIIBGN == 3 ~ 16,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 3 ~ 15,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 3 ~ 14,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 3 ~ 13,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 3 ~ 12,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 3 ~ 11,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 3 ~ 10,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 3 ~ 9,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 3 ~ 8,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 3 ~ 7,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 3 ~ 6,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 3 ~ 5,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 3 ~ 4,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 3 ~ 3,
VarieteIBGN >= 50 & GIIBGN == 2 ~ 15,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 2 ~ 14,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 2 ~ 13,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 2 ~ 12,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 2 ~ 11,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 2 ~ 10,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 2 ~ 9,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 2 ~ 8,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 2 ~ 7,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 2 ~ 6,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 2 ~ 5,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 2 ~ 4,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 2 ~ 3,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 2 ~ 2,
VarieteIBGN >= 50 & GIIBGN == 1 ~ 14,
VarieteIBGN <= 49 & VarieteIBGN >= 45 & GIIBGN == 1 ~ 13,
VarieteIBGN <= 44 & VarieteIBGN >= 41 & GIIBGN == 1 ~ 12,
VarieteIBGN <= 40 & VarieteIBGN >= 37 & GIIBGN == 1 ~ 11,
VarieteIBGN <= 36 & VarieteIBGN >= 33 & GIIBGN == 1 ~ 10,
VarieteIBGN <= 32 & VarieteIBGN >= 29 & GIIBGN == 1 ~ 9,
VarieteIBGN <= 28 & VarieteIBGN >= 25 & GIIBGN == 1 ~ 8,
VarieteIBGN <= 24 & VarieteIBGN >= 21 & GIIBGN == 1 ~ 7,
VarieteIBGN <= 20 & VarieteIBGN >= 17 & GIIBGN == 1 ~ 6,
VarieteIBGN <= 16 & VarieteIBGN >= 13 & GIIBGN == 1 ~ 5,
VarieteIBGN <= 12 & VarieteIBGN >= 10 & GIIBGN == 1 ~ 4,
VarieteIBGN <= 9 & VarieteIBGN >= 7 & GIIBGN == 1 ~ 3,
VarieteIBGN <= 6 & VarieteIBGN >= 4 & GIIBGN == 1 ~ 2,
VarieteIBGN <= 3 & VarieteIBGN >= 1 & GIIBGN == 1 ~ 1
)
) %>%
mutate(NoteEqIBGN = case_when(VarieteEqIBGN >= 50 & GIEqIBGN == 9 ~ 20,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 9 ~ 20,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 9 ~ 20,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 9 ~ 19,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 9 ~ 18,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 9 ~ 17,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 9 ~ 16,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 9 ~ 15,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 9 ~ 14,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 9 ~ 13,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 9 ~ 12,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 9 ~ 11,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 9 ~ 10,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 9 ~ 9,
VarieteEqIBGN >= 50 & GIEqIBGN == 8 ~ 20,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 8 ~ 20,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 8 ~ 19,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 8 ~ 18,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 8 ~ 17,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 8 ~ 16,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 8 ~ 15,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 8 ~ 14,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 8 ~ 13,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 8 ~ 12,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 8 ~ 11,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 8 ~ 10,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 8 ~ 9,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 8 ~ 8,
VarieteEqIBGN >= 50 & GIEqIBGN == 7 ~ 20,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 7 ~ 19,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 7 ~ 18,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 7 ~ 17,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 7 ~ 16,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 7 ~ 15,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 7 ~ 14,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 7 ~ 13,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 7 ~ 12,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 7 ~ 11,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 7 ~ 10,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 7 ~ 9,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 7 ~ 8,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 7 ~ 7,
VarieteEqIBGN >= 50 & GIEqIBGN == 6 ~ 19,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 6 ~ 18,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 6 ~ 17,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 6 ~ 16,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 6 ~ 15,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 6 ~ 14,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 6 ~ 13,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 6 ~ 12,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 6 ~ 11,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 6 ~ 10,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 6 ~ 9,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 6 ~ 8,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 6 ~ 7,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 6 ~ 6,
VarieteEqIBGN >= 50 & GIEqIBGN == 5 ~ 18,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 5 ~ 17,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 5 ~ 16,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 5 ~ 15,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 5 ~ 14,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 5 ~ 13,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 5 ~ 12,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 5 ~ 11,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 5 ~ 10,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 5 ~ 9,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 5 ~ 8,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 5 ~ 7,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 5 ~ 6,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 5 ~ 5,
VarieteEqIBGN >= 50 & GIEqIBGN == 4 ~ 17,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 4 ~ 16,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 4 ~ 15,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 4 ~ 14,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 4 ~ 13,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 4 ~ 12,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 4 ~ 11,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 4 ~ 10,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 4 ~ 9,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 4 ~ 8,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 4 ~ 7,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 4 ~ 6,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 4 ~ 5,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 4 ~ 4,
VarieteEqIBGN >= 50 & GIEqIBGN == 3 ~ 16,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 3 ~ 15,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 3 ~ 14,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 3 ~ 13,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 3 ~ 12,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 3 ~ 11,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 3 ~ 10,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 3 ~ 9,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 3 ~ 8,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 3 ~ 7,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 3 ~ 6,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 3 ~ 5,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 3 ~ 4,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 3 ~ 3,
VarieteEqIBGN >= 50 & GIEqIBGN == 2 ~ 15,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 2 ~ 14,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 2 ~ 13,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 2 ~ 12,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 2 ~ 11,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 2 ~ 10,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 2 ~ 9,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 2 ~ 8,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 2 ~ 7,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 2 ~ 6,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 2 ~ 5,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 2 ~ 4,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 2 ~ 3,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 2 ~ 2,
VarieteEqIBGN >= 50 & GIEqIBGN == 1 ~ 14,
VarieteEqIBGN <= 49 & VarieteEqIBGN >= 45 & GIEqIBGN == 1 ~ 13,
VarieteEqIBGN <= 44 & VarieteEqIBGN >= 41 & GIEqIBGN == 1 ~ 12,
VarieteEqIBGN <= 40 & VarieteEqIBGN >= 37 & GIEqIBGN == 1 ~ 11,
VarieteEqIBGN <= 36 & VarieteEqIBGN >= 33 & GIEqIBGN == 1 ~ 10,
VarieteEqIBGN <= 32 & VarieteEqIBGN >= 29 & GIEqIBGN == 1 ~ 9,
VarieteEqIBGN <= 28 & VarieteEqIBGN >= 25 & GIEqIBGN == 1 ~ 8,
VarieteEqIBGN <= 24 & VarieteEqIBGN >= 21 & GIEqIBGN == 1 ~ 7,
VarieteEqIBGN <= 20 & VarieteEqIBGN >= 17 & GIEqIBGN == 1 ~ 6,
VarieteEqIBGN <= 16 & VarieteEqIBGN >= 13 & GIEqIBGN == 1 ~ 5,
VarieteEqIBGN <= 12 & VarieteEqIBGN >= 10 & GIEqIBGN == 1 ~ 4,
VarieteEqIBGN <= 9 & VarieteEqIBGN >= 7 & GIEqIBGN == 1 ~ 3,
VarieteEqIBGN <= 6 & VarieteEqIBGN >= 4 & GIEqIBGN == 1 ~ 2,
VarieteEqIBGN <= 3 & VarieteEqIBGN >= 1 & GIEqIBGN == 1 ~ 1
)
)
return(indices)
}
##### Liste faunistiques #####
#### listefaunistiqueGlobale ####
if(N != 1 & Sortie == "listefaunistiqueGlobale") stop("Établissement des listes faunistiques de plusieurs opérations non encore développé")
if(N == 1 & Sortie == "listefaunistiqueGlobale") stop("Établissement de la listefaunistiqueGlobale d'une seule opération non encore développé")
#### listefaunistiqueMAG20 ####
if(N != 1 & Sortie == "listefaunistiqueMAG20"){
listefaunistiqueMAG20 <-
DataTravail %>%
filter(NumEchMAG20 <= 20) %>%
dcast(Taxon ~ CodeRHJ , value.var = "Abondance", sum) %>%
right_join(DataTravail %>% distinct(Taxon, CodeSANDRE, AffichageSensibilite, Ordre, Famille, Genre, Espece), by = "Taxon") %>%
arrange(AffichageSensibilite, Ordre, Famille, Genre, Espece) %>%
select(Ordre, Famille, Genre, Espece, Taxon, CodeSANDRE, everything(), -AffichageSensibilite) %>%
#rename('Taxon/Prelevement' = Taxon) %>%
mutate_all(funs(replace(., . == 0, NA))) %>%
mutate(Ordre2 = ifelse(lag(Ordre) == Ordre, NA, Ordre)) %>% # Pour clarifier l'affichage
mutate(Ordre2 = ifelse(row_number() == 1, Ordre , Ordre2)) %>%
mutate(Ordre = Ordre2) %>%
select(-Ordre2) %>%
mutate(Famille2 = ifelse(lag(Famille) == Famille, NA, Famille)) %>% # Pour clarifier l'affichage
mutate(Famille2 = ifelse(row_number() == 1, Famille , Famille2)) %>%
mutate(Famille = Famille2) %>%
select(-Famille2)
# mutate(Genre2 = ifelse(lag(Genre) == Genre, NA, Genre)) %>% # Pour clarifier l'affichage
# mutate(Genre2 = ifelse(row_number() == 1, Genre , Genre2)) %>%
# mutate(Genre = Genre2) %>%
#select(-Genre2) %>%
# mutate(Espece2 = ifelse(lag(Espece) == Espece, NA, Espece)) %>% # Pour clarifier l'affichage
# mutate(Espece2 = ifelse(row_number() == 1, Espece , Espece2)) %>%
# mutate(Espece = Espece2) %>%
#select(-Espece2)
return(listefaunistiqueMAG20)
}
if(N == 1 & Sortie == "listefaunistiqueMAG20"){
listefaunistiqueMAG20 <-
DataTravail %>%
filter(NumEchMAG20 <= 20) %>%
dcast(Taxon ~ NumEchMAG20 , value.var = "Abondance", sum) %>%
right_join(DataTravail %>% distinct(Taxon, CodeSANDRE), by = "Taxon") %>%
select(Taxon, CodeSANDRE, everything()) %>%
rename('Taxon/Prelevement' = Taxon) %>%
mutate_all(funs(replace(., . == 0, NA)))
return(listefaunistiqueMAG20)
}
#### listefaunistiqueDCEPrelevement ####
if(N != 1 & Sortie == "listefaunistiqueDCEPrelevement") stop("Établissement des listes faunistiques de plusieurs opérations non encore développé")
if(N == 1 & Sortie == "listefaunistiqueDCEPrelevement"){
listefaunistiqueDCEPrelevement <-
DataTravail %>%
filter(!is.na(NumEchDCE)) %>%
dcast(Taxon ~ NumEchDCE , value.var = "Abondance", sum) %>%
right_join(DataTravail %>% distinct(Taxon, CodeSANDRE), by = "Taxon") %>%
select(Taxon, CodeSANDRE, everything()) %>%
rename('Taxon/Prelevement' = Taxon) %>%
mutate_all(funs(replace(., . == 0, NA)))
return(listefaunistiqueDCEPrelevement)
}
#### listefaunistiqueDCEPhase ####
if(N != 1 & Sortie == "listefaunistiqueDCEPhase") stop("Établissement des listes faunistiques de plusieurs opérations non encore développé")
if(N == 1 & Sortie == "listefaunistiqueDCEPhase"){
listefaunistiqueDCEPhase <-
DataTravail %>%
filter(!is.na(NumEchDCE)) %>%
mutate(Abondance = as.numeric(Abondance)) %>%
dcast(Taxon ~ PhaseDCE , value.var = "Abondance", sum) %>%
right_join(DataTravail %>% distinct(Taxon, CodeSANDRE), by = "Taxon") %>%
select(Taxon, CodeSANDRE, everything()) %>%
rename('Taxon/Phase' = Taxon) %>%
mutate_all(funs(replace(., . == 0, NA)))
return(listefaunistiqueDCEPhase)
}
#### listefaunistiqueDCEequivalentIBGN ####
if(N != 1 & Sortie == "listefaunistiqueDCEequivalentIBGN") stop("Établissement des listes faunistiques de plusieurs opérations non encore développé")
if(N == 1 & Sortie == "listefaunistiqueDCEequivalentIBGN") stop("Établissement de la listefaunistiqueDCEequivalentIBGN d'une seule opération non encore développé")
#### listefaunistiqueIBGN ####
if(N != 1 & Sortie == "listefaunistiqueIBGN") stop("Établissement des listes faunistiques de plusieurs opérations non encore développé")
if(N == 1 & Sortie == "listefaunistiqueIBGN") stop("Établissement de la listefaunistiqueIBGN d'une seule opération non encore développé")
} # Fin de la fonction
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.