#' FormatNests creates a dataset of class "Nests" to be used with searchR
#' @title Create a dataset of class Nests to be used with searchR
#' @author Marc Girondot \email{marc.girondot@@gmail.com}
#' @return A list with all the nests formated to be used with searchR.
#' @param data Data to be newly formated
#' @param previous Data already formated
#' @param simplify If TRUE, simply the time series by removing identical time series of temperatures
#' @param usemiddletime If TRUE, suppose that recorded temperatures are those at middle segment
#' @param weight Named vector with weight for likelihhod
#' @description Will create a dataset of class Nests to be used with searchR\cr
#' FormatNests(nest, previous=x) with x being a previously formated data.\cr
#' The raw data must be organized being:\cr
#' First column is the time in minutes since the beginning of incubation\cr
#' Each column next is the trace of temperatures, one column for each nest.\cr
#' For example, for two nests:\cr
#' Time   Nest1    Nest2\cr
#' 0       29.8     27.6\cr
#' 90      30.2     28.8\cr
#' 120     30.4     30.7\cr
#' 180     31.2     32.6\cr
#' ...\cr
#' 65800   30.8     32.6\cr
#' 65890            30.2\cr
#' 65950            30.4\cr
#' \cr
#' The Nest1 ends incubation at 65800 minutes whereas Nest2 ends incubation at 65950 (last row\cr
#' with temperature for each).\cr
#' The parameter Weight is a vector: weight=c(Nest1=1, Nest2=1.2)\cr
#' It can be used to format database already formated with old format; in this case, just use data=xxx with xxx being the old format database.\cr
#' @examples 
#' \dontrun{
#' library(embryogrowth)
#' data(nest)
#' formated <- FormatNests(nest, previous=NULL)
#' formated <- FormatNests(nest)
#' }
#' @export


FormatNests <-
  function(data=stop("A dataset must be provided !"), 
           previous=NULL                            , 
           usemiddletime=FALSE                      , 
           simplify=TRUE                            , 
           weight=NULL                              ) {
    
    # Je cree une une fonction qui prepare un fichier pour etre utilise
    # Les differents nids seront des matrices dans une liste
    # Dans chaque matrice on a le temps depuis le debut de l'incubation
    # la temperature en C, la temperature en K, la valeur de r et la masse
    
    # previous=NULL; simplify=TRUE; weight=NULL
    
    if (inherits(data, "Nests")) { #(class(data)=="Nests") {
      
      nidsEC <- data[1:data$IndiceT["NbTS"]]
      for(i in 1:length(nidsEC)) {
        ess <- nidsEC[[i]]
        if (dim(ess)[2]==5) {
          ess <- cbind(ess, IndiceK=NA)
          nidsEC[[i]] <- ess
        }
      }
      
    } else {
      
      nidsEC <- list()
      # meme chose que nids=as.list(NULL)
      
      for (j in 2:dim(data)[2]) {
        
        # je veux le transformer en une liste avec a l'interieur un dataframe par enregistreur
        # je commence par sortir la liste un par un qui n'ont pas de NA
        
        # je stocke les donnees de l'enregistreur dans une matrice
        
        newess2 <- as.numeric(subset(data[,j], !is.na(data[,j])))
        newessT <- as.numeric(subset(data[,1], !is.na(data[,j])))
        
        # 19/10/2012 je calcule les etats intermediaires en terme de temps
        
        ess2 <- newess2[1]
        essT <- newessT[1]
        
        for(i in 1:(length(newess2)-1)) {
          ess2 <- c(ess2, newess2[i+1])
          if (usemiddletime) {
            minutes <- newessT[i]+(newessT[i+1]-newessT[i])/2
          } else {
            minutes <- newessT[i+1]
          }
          essT <- c(essT, minutes)
          
        }
        
        ess2 <- c(ess2, newess2[length(newess2)])
        essT <- c(essT, newessT[length(newess2)])
        
        ess <- matrix(c(essT, ess2, ess2+273.15, rep(NA, 3*length(ess2))), ncol=6)
        
        colnames(ess)<-c("Time", "Temperatures C", "Temperatures K", "r", "Mass", "IndiceK")
        
        
        # ensuite je supprime les temps avec des valeurs de temperatures identiques
        # sauf la derniere qui doit rester - 20/7/2012
        # si que deux lignes, je ne fais rien - 27/7/2012
        if ((dim(ess)[1]>2) & simplify) {
          for (i in 2:(dim(ess)[1]-1)) {
            if (ess[i,2]==ess[i-1,2]) ess[i,1]=NA
          }
          
          if (!is.na(ess[nrow(ess)-1,1]))
            if (ess[nrow(ess), 1] == ess[nrow(ess)-1,1]) {
              ess[nrow(ess),1]=NA
            }
        }
        
        
        
        # nidsEC[[names(data[j])]]<-subset(ess, !is.na(ess[,1]))
        # 23/4/2015
        nidsEC[[colnames(data)[j]]] <- subset(ess, !is.na(ess[,1]))
      }
      
    }
    
    
    if (!is.null(previous)) {
      nidsprevious<-previous[1:previous$IndiceT["NbTS"]]
      nidsEC<-c(nidsEC, nidsprevious)
    }
    
    # J'enregistre les tempmin et max car toujours pareil - Je n'en ai plus besoin; je les garde cependant
    
    # j'enregistre les temp comme des facteurs
    nbts <- length(nidsEC)
    temp<-NULL
    for (j in 1:nbts) {
      temp<- c(temp, nidsEC[[j]][, "Temperatures K"])
    }
    tempmin <- min(temp)
    tempmax <- max(temp)
    
    tempaf<- as.factor(temp)
    templevels <- levels(tempaf)
    
    nidsEC[["IndiceT"]] <- c(Tmin=tempmin,Tmax=tempmax, NbTS=nbts)
    nidsEC[["Temperatures"]] <- templevels
    
    # Je remplis la colonne IndiceK
    
    for (j in 1:nbts) {
      temp<- nidsEC[[j]][, "Temperatures K"]
      nidsEC[[j]][, "IndiceK"] <- match(as.character(temp), nidsEC[["Temperatures"]])
    }
    
    nidsEC[["weight"]] <- weight
    
    nidsEC <- addS3Class(nidsEC, "Nests")
    
    # 27/4/2015
    
    if (any(duplicated(names(nidsEC)[1:(nidsEC[["IndiceT"]]["NbTS"])]))) {
      stop("Nests must have unique names")
    } else {
      return(nidsEC)
    }
    
  }