R/plot.NestsResult.R

In embryogrowth: Tools to Analyze the Thermal Reaction Norm of Embryo Growth

#' plot.NestsResult Plot the embryo growth
#' @title Plot the embryo growth
#' @author Marc Girondot \email{marc.girondot@@gmail.com}
#' @return Nothing
#' @param x A result file generated by searchR
#' @param ... Parameters for plot()
#' @param NestsResult A NestsResult file generated by searchR
#' @param resultmcmc A mcmc result. Will be used rather than SE if provided.
#' @param hessian An Hessian matrix.
#' @param parameters A set of parameters if result is not provided.
#' @param fixed.parameters Another set of parameters if result is not provided.
#' @param SE Standard error for each parameter if result is not provided, or replace the one in NestsResult. Use SE=NA to remove SE from NestResult
#' @param temperatures Timeseries of temperatures formatted using formatNests(). Will replace the one in result.
#' @param integral Function used to fit embryo growth: integral.Gompertz, integral.exponential or integral.linear
#' @param derivate Function used to fit embryo growth: dydt.Gompertz, dydt.exponential or dydt.linear. It will replace the one in NestsResult.
#' @param hatchling.metric Mean and SD of size of hatchlings
#' @param weight Weights of the different nests to estimate likelihood
#' @param stop.at.hatchling.metric TRUE or FALSE. If TRUE, the model stops when proxy of size reached the mean hatchling.metric size.
#' @param M0 Measure of hatchling size proxi at laying date
#' @param series The name or number of the series to be displayed. Only one series can be displayed at a time.
#' @param TSP.borders The limits of TSP in stages. See embryo.stages parameter.
#' @param embryo.stages The embryo stages. At least TSP.borders stages must be provided to estimate TSP borders. See note.
#' @param STRN An object obtained from STRN()
#' @param TSP.begin Where TSP begin during the stage of beginning? In relative proportion of the stage.
#' @param TSP.end Where TSP begin during the stage of ending? In relative proportion of the stage.
#' @param replicate.CI Number of replicates to estimate CI. If 1, no CI is estimated.
#' @param metric.end.incubation The expected metric at the end of incubation. Used to calibrate TSP size. If NULL, take the maximum Mean of the hatchling.metric parameter. If NA, use the actual final size. Can be a vector and is recycled if necessary.
#' @param col.stages The color of the stages
#' @param col.temperatures The color of the temperatures
#' @param col.TSP The color of the TSP
#' @param col.PT The color of the pivotal temperature
#' @param col.S The color of the size or mass. Can be a vector (useful when series="all" option).
#' @param lty.temperatures Type of line for temperatures
#' @param lwd.temperatures Width of line for temperatures
#' @param ylimT Range of temperatures to be displayed
#' @param ylimS Range of size to be displayed
#' @param xlim Range of incubation days to be displayed
#' @param show.metric TRUE or FALSE, does the plot of embryo metric is shown?
#' @param show.stages TRUE or FALSE, does the embryo stages should be displayed?
#' @param show.TSP TRUE or FALSE, does the TSP boders should be displayed?
#' @param show.third TRUE or FALSE, does the first and second third boders should be displayed?
#' @param GTRN.CI How to estimate CI; can be NULL, "SE", "MCMC", or "Hessian"
#' @param show.temperatures TRUE or FALSE, does the temperatures should be displayed?
#' @param show.PT TRUE or FALSE, does the pivotal temperature should be displayed?
#' @param show.fioritures If FALSE, set show.PT, show.temperatures, show.stages, show.TSP, show.third to FALSE, GTRN.CI to NULL
#' @param PT Value for pivotal temperature, mean and SE
#' @param show.hatchling.metric TRUE or FALSE, does the hatchling size should be displayed
#' @param lab.third Label for 2nd third of incubation
#' @param at.lab.third Position of Label for 2nd third of incubation [default=10]; y-lim is scaled by at.lab.third
#' @param at.lab.TSP Position of Label for TSP [default=8]; y-lim is scaled by at.lab.third
#' @param lab.TSP Label for the TSP
#' @param lab.PT Label for Pivotal Temperature
#' @param lab.stages Label for Stages
#' @param xlab Label for axis
#' @param ylabT Label for temperature axis
#' @param ylabS Label for size axis
#' @param mar Parameter mar used for plot
#' @param add If TRUE, all the curves are shown on the same graph 
#' @param progress If FALSE, the progress bar is not shown (useful for use with sweave or knitr)
#' @param parallel Should parallel computing be used ? TRUE or FALSE
#' @description Plot the embryo growth from one or several nests.\cr
#' The embryo.stages is a named vector with relative size as compared to final size at the beginning of the stage. Names are the stages.\cr
#' For example for SCL in Caretta caretta:\cr
#' embryo.stages=structure(c(8.4, 9.4, 13.6, 13.8, 18.9, 23.5, 32.2, 35.2, 35.5, 38.5)/39.33), \cr
#' .Names = c("21", "22", "23", "24", "25", "26", "27", "28", "29", "30", "31"))\cr
#'  indicates that the stages 21 begins at the relative size of 8.4/39.33.\cr
#' Series can be indicated as the name of the series, its number or succesion of TRUE or FALSE. "all" indicates that all series must be printed.\cr
#' show.fioritures parameter does not affect show.hatchling.metric option.\cr
#' Note: Four species have predefined embryo stages. embryo.stages parameter can take the values:\cr
#' \itemize{
#'   \item \code{Caretta caretta.SCL}
#'   \item \code{Chelonia mydas.SCL}
#'   \item \code{Emys orbicularis.SCL}
#'   \item \code{Emys orbicularis.mass}
#'   \item \code{Podocnemis expansa.SCL}
#'   \item \code{Lepidochelys olivacea.SCL}
#'   \item \code{Generic.ProportionDevelopment}
#'   }
#' @examples
#' \dontrun{
#' library(embryogrowth)
#' data(resultNest_4p_SSM)
#' plot(resultNest_4p_SSM, xlim=c(0,70), ylimT=c(22, 32), ylimS=c(0,45), series=1,  
#' 	    SE=c(DHA=1.396525, DHH=4.101217, T12H=0.04330405, Rho25=1.00479), 
#' 	    GTRN.CI = "SE", replicate.CI = 100, 
#' 	    embryo.stages="Caretta caretta.SCL")
#' plot(resultNest_4p_SSM, xlim=c(0,70), ylimT=c(22, 32), ylimS=c(0,45), series=1, 
#' 	    GTRN.CI = "Hessian", replicate.CI = 100, 
#' 	    embryo.stages="Caretta caretta.SCL")
#' plot(resultNest_4p_SSM, xlim=c(0,70), ylimT=c(22, 32), ylimS=c(0,45), series=1,  
#'      resultmcmc = resultNest_mcmc_4p_SSM, 
#' 	    GTRN.CI = "MCMC", replicate.CI = 100, 
#'      embryo.stages="Caretta caretta.SCL")
#' # to plot all the nest at the same time, use
#' plot(resultNest_4p_SSM, xlim=c(0,70), ylimT=c(22, 32), ylimS=c(0,45),  
#' 	    series="all", show.fioritures=FALSE, add=TRUE, 
#' 	    embryo.stages="Caretta caretta.SCL")
#' # to use color different for series
#' plot(resultNest_4p_SSM, xlim=c(0,70), ylimT=c(22, 32), ylimS=c(0,45), add=TRUE, 
#' 	    series="all", show.fioritures=FALSE, col.S=c(rep("black", 5), rep("red", 6)), 
#' 	    embryo.stages="Caretta caretta.SCL")
#' 	    
#' # to plot all the temperature profiles
#' 
#' par(mar=c(4, 4, 1, 1))
#' plot(resultNest_4p_SSM$data[[1]][, 1]/60/24,
#'      resultNest_4p_SSM$data[[1]][, 2], bty="n", 
#'      las=1, xlab="Days of incubation", 
#'      ylab=expression("Temperatures in "*degree*"C"), 
#'      type="l", xlim=c(0,70),ylim=c(20, 35))
#'      
#'      for (i in 2:21) {
#'           par(new=TRUE)
#'           plot(resultNest_4p_SSM$data[[i]][, 1]/60/24,
#'           resultNest_4p_SSM$data[[i]][, 2], bty="n", 
#'           las=1, xlab="", ylab="", type="l", xlim=c(0,70),
#'           ylim=c(20, 35), axes = FALSE)
#'      }
#' }
#' @method plot NestsResult
#' @export


plot.NestsResult <- function(x                                                  , 
                             ...                                                , 
                             parameters=NULL                                    , 
                             fixed.parameters=NULL                              , 
                             resultmcmc = NULL                                  ,
                             hessian = NULL                                     ,
                             SE=NULL                                            , 
                             temperatures=NULL                                  , 
                             integral=NULL                                      , 
                             derivate=NULL                                      , 
                             hatchling.metric=NULL                              , 
                             stop.at.hatchling.metric=FALSE                     , 
                             M0=NULL                                            , 
                             weight=NULL                                        , 
                             series="all"                                       ,
                             TSP.borders=NULL                                   , 
                             embryo.stages=NULL                                 ,
                             STRN=NULL                                          ,
                             TSP.begin=0                                        , 
                             TSP.end=0.5                                        , 
                             replicate.CI=100                                   , 
                             metric.end.incubation="observed"                   ,
                             col.stages="blue"                                  , 
                             col.PT="red"                                       , 
                             col.TSP="gray"                                     , 
                             col.temperatures="green"                           , 
                             col.S="black"                                      , 
                             lty.temperatures=1                                 , 
                             lwd.temperatures=2                                 , 
                             ylimT=NULL                                         , 
                             ylimS=NULL                                         , 
                             xlim=NULL                                          ,
                             show.stages=TRUE                                   , 
                             show.TSP=TRUE                                      , 
                             show.third=TRUE                                    , 
                             GTRN.CI=NULL                                       ,  
                             show.metric=TRUE                                   , 
                             show.fioritures=TRUE                               , 
                             show.temperatures=TRUE                             , 
                             show.PT=TRUE                                       , 
                             PT=c(mean=NA, SE=NA)                               , 
                             show.hatchling.metric=TRUE                         , 
                             add=FALSE                                          , 
                             lab.third="2nd third of incubation"                , 
                             at.lab.third=10                                    , 
                             lab.PT="PT"                                        , 
                             lab.stages="Stages"                                , 
                             at.lab.TSP=8                                       , 
                             lab.TSP="TSP"                                      , 
                             mar = c(4, 5, 4, 5) + 0.3                          , 
                             xlab="Days of incubation"                          , 
                             ylabT=expression("Temperature in " * degree * "C") , 
                             ylabS= "Embryo metric"                             , 
                             progress=TRUE                                      , 
                             parallel=TRUE                                      ) {
  
  #  parameters=NULL; fixed.parameters=NULL; resultmcmc = NULL; SE=NULL; temperatures=NULL; integral=NULL; derivate=NULL; hatchling.metric=NULL; stop.at.hatchling.metric=FALSE; M0=NULL; weight=NULL; series="all"; TSP.borders=NULL; embryo.stages="Caretta caretta.SCL"; TSP.begin=0; TSP.end=0.5; replicate.CI=100; metric.end.incubation="observed"; col.stages="blue"; col.PT="red"; col.TSP="gray"; col.temperatures="green"; col.S="black"; lty.temperatures=1; lwd.temperatures=2; ylimT=NULL; ylimS=NULL; xlim=NULL; show.stages=TRUE; show.TSP=TRUE; show.third=TRUE; CI=NULL;  show.metric=TRUE; show.fioritures=TRUE; show.temperatures=TRUE; show.PT=TRUE; PT=c(mean=NA, SE=NA); show.hatchling.metric=TRUE; add=FALSE; lab.third="2nd third of incubation"; at.lab.third=4; lab.PT="PT"; lab.stages="Stages"; mar = c(4, 5, 4, 5) + 0.3; xlab="Days of incubation"; ylabT=expression("Temperatures in " * degree * "C"); ylabS= "Embryo metric"; progress=TRUE;parallel=TRUE
  # lab.third="2nd third of incubation"; at.lab.third=10; lab.PT="PT"; lab.stages="Stages"; at.lab.TSP=8; lab.TSP="TSP"
  #  x <- resultNest_4p_SSM; xlim=c(0,70); ylimT=c(22, 32); ylimS=c(0,45); series=1; resultmcmc = resultNest_mcmc_4p_SSM; embryo.stages="Caretta caretta.SCL"; replicate.CI = 100
  
  TSP.list <- embryogrowth::TSP.list
  if (!is.null(GTRN.CI)) GTRN.CI <- tolower(GTRN.CI)
  
  if(is.null(embryo.stages) & ((show.stages) | (show.TSP))) {
    warning("You must indicate embryo stages to use show.stages or show.TSP.")
    show.stages <- FALSE
    show.TSP <- FALSE
  }
  
  if (inherits(embryo.stages, "character")) { 
    if (embryo.stages == "fitted") {
      embryo.stages = c("10"=invlogit(logit(0.33)), "11"=invlogit(logit(0.33)), 
                        "12"=invlogit(logit(0.66)), "13"=invlogit(logit(0.66))) 
      TSP.borders = c(10, 12)
      if (!is.null(STRN)) {
        setpar_STRN <- c(STRN$par, STRN$fixedparameter)
        if (is.null(STRN$zero)) {
          zero <- 1E-9
        } else {
          zero <- STRN$zero
        }
        if (!is.na(setpar_STRN["BeginTSP"])) {
          xxbt <- invlogit(setpar_STRN["BeginTSP"])
          if (xxbt == 0) xxbt <- zero
          if (xxbt > 0.95) xxbt <- 0.95
          embryo.stages[as.character(TSP.borders[1])] <- xxbt
          embryo.stages[as.character(TSP.borders[1]+1)] <- xxbt
        }
        if (!is.na(setpar_STRN["EndTSP"])) {
          xxbt <- invlogit(setpar_STRN["EndTSP"]) 
          if (xxbt == 0) xxbt <- zero
          if (xxbt == 1) xxbt <- 1 - zero
          embryo.stages[as.character(TSP.borders[2])] <- xxbt
          embryo.stages[as.character(TSP.borders[2]+1)] <- xxbt
        }
        if (!is.na(setpar_STRN["LengthTSP"])) {
          xxbt <- invlogit(setpar_STRN["BeginTSP"]+abs(setpar_STRN["LengthTSP"]))
          if (xxbt == 0) xxbt <- zero
          if (xxbt == 1) xxbt <- 1 - zero
          embryo.stages[as.character(TSP.borders[2])] <- xxbt 
          embryo.stages[as.character(TSP.borders[2]+1)] <- xxbt
        }
      }
      
    } else {
      
      estages <- TSP.list[[gsub(" ", "_", embryo.stages)]]
      if (is.null(estages)) {
        stop("The TSP for ", embryo.stages, " does not exist")
      } else {
        embryo.stages <- estages[, "metric"]
        names(embryo.stages) <- estages[, "stages"]
        TSP.borders <- c(attributes(estages)$TSP.begin.stages, attributes(estages)$TSP.end.stages)
      }
    }
  }
  
  embryo.stages_ini <- embryo.stages
  
  if (is.null(embryo.stages)) {
    show.TSP <- FALSE
    show.stages <- FALSE
  }
  
  NestsResult <- x
  
  if (is.null(temperatures)) temperatures <- NestsResult$data
  if (is.null(integral)) integral <- NestsResult$integral
  if (is.null(derivate)) derivate <- NestsResult$derivate
  if (is.null(weight)) weight <- NestsResult$weight
  if (is.null(hatchling.metric)) hatchling.metric <- NestsResult$hatchling.metric
  if (is.null(M0)) M0 <- NestsResult$M0
  if (is.null(fixed.parameters)) fixed.parameters <- NestsResult$fixed.parameters
  if (is.null(SE)) SE <- NestsResult$SE
  if (is.null(parameters)) parameters <- NestsResult$par
  if (is.null(hessian)) hessian <- NestsResult$hessian
  
  
  if (!is.null(SE[1])) if (all(is.na(SE[])))  {
    SE <- NULL
  }
  
  if (is.null(replicate.CI)) replicate.CI <- 0
  
  if (!is.null(GTRN.CI)) {
    if (GTRN.CI == "mcmc" & is.null(resultmcmc)) GTRN.CI <- NULL
    if (GTRN.CI == "se" & is.null(SE)) GTRN.CI <- NULL
    if (GTRN.CI == "hessian" & is.null(hessian)) GTRN.CI <- NULL
    if (replicate.CI <= 1) GTRN.CI <- NULL
  }
  
  
  # 27/1/2013
  if (!show.fioritures) {
    show.PT <- FALSE
    show.temperatures <- FALSE
    show.stages <- FALSE
    show.TSP <- FALSE
    GTRN.CI <- NULL
    show.third <- FALSE
  }
  
  if (is.null(GTRN.CI)) {
    GTRN.CI <- "null"
    replicate.CI <- 1
  }
  
  ###############################
  #### je compte le nombre de series  faire
  ###############################
  
  
  NbTS <- temperatures[["IndiceT"]]["NbTS"]
  if (series[[1]]=="all") {
    series<-rep(TRUE, NbTS)
  } else {
    if (any(!is.logical(series))) {
      if (is.numeric(series)) {
        seriesx <- rep(FALSE, NbTS)
        seriesx[series] <- TRUE
      } else {
        seriesx <- (names(temperatures[1:NbTS])==series)
      }
      series <- seriesx
    } else {
      # c'est des valeurs logiques, je verifie si le bon nombre, sinon je complete
      if (length(series)!=NbTS) {
        series <- rep(series, NbTS)
        series <- series[1:NbTS]
      }
    }
  }
  
  nbseries <- sum(series)
  
  if (nbseries==0) {
    stop("No series has been selected")
  }
  
  # fais du recyclage des couleurs des sries si ncessaire
  cptcol.S <- 0
  col.S <- rep(col.S, nbseries)[1:nbseries]
  
  ########################
  #### Je tes_te les series
  ########################
  if (progress) pb <- txtProgressBar(min=0, max=length(which(series)), style=3)
  
  
  for(seriesx in which(series)) {
    
    # seriesx <- 1
    
    
    cptcol.S <- cptcol.S + 1
    if (progress) setTxtProgressBar(pb, cptcol.S)
    
    metric.summary <- info.nests(NestsResult=NULL                                  , 
                                 parameters=parameters                             , 
                                 fixed.parameters=fixed.parameters                 , 
                                 resultmcmc = resultmcmc                           , 
                                 hessian=hessian                                   ,
                                 SE=SE                                             , 
                                 temperatures=temperatures                         , 
                                 integral=integral                                 , 
                                 derivate=derivate                                 , 
                                 hatchling.metric=hatchling.metric                 , 
                                 stop.at.hatchling.metric=stop.at.hatchling.metric , 
                                 M0=M0                                             , 
                                 series=seriesx                                    ,
                                 TSP.borders=TSP.borders                           , 
                                 embryo.stages=embryo.stages                       ,
                                 TSP.begin=TSP.begin                               , 
                                 TSP.end=TSP.end                                   , 
                                 replicate.CI=replicate.CI                         , 
                                 GTRN.CI = GTRN.CI                                 , 
                                 weight=NULL                                       , 
                                 out="dynamic"                                     , 
                                 fill=60                                           , 
                                 SexualisationTRN=NULL                             , 
                                 SexualisationTRN.mcmc=NULL                        , 
                                 SexualisationTRN.CI=NULL                          , 
                                 metric.end.incubation=metric.end.incubation       ,
                                 progressbar=FALSE                                 ,
                                 parallel=parallel                                 ,
                                 probs= c(0.025, 0.5, 0.975)                       , 
                                 metabolic.heating=0                               , 
                                 temperature.heterogeneity=0                       , 
                                 warnings=TRUE                                     , 
                                 tsd=NULL                                          , 
                                 tsd.CI=NULL                                       , 
                                 tsd.mcmc=NULL                                     , 
                                 zero = 1E-9                                       , 
                                 verbose = FALSE                                   )
    par(mar=mar)  
    
    troispoints <- tryCatch(list(...), error=function(e) list())
    # troispoints <- list()
    
    if (add==FALSE | cptcol.S==1) {
      par(new=FALSE)
      L1 <- list(type = "n", axes = TRUE, bty = "n", xlab = xlab, ylab = ylabS, lwd=2, yaxs="r", xaxs="r", ylim=ylimS, xlim=xlim, main="", col=col.S[cptcol.S])
      L2 <- modifyList(list(x=metric.summary$dynamic.metric[[1]][, "Time"]/(60*24), y=metric.summary$dynamic.metric[[1]][, "Metric_50%"]), troispoints)
      do.call(plot, modifyList(L1, L2) )
    }
    
    ylimS <- unname(ScalePreviousPlot()$ylim[1:2])
    xlim <- unname(ScalePreviousPlot()$xlim[1:2])
    
    if (show.TSP) {
      par(new=TRUE)
      plot(1,1, xlim=xlim, ylim=ylimS, axes=FALSE, type="n", xlab="", ylab="")
      x1 <- xlim[1]
      x2 <- xlim[2]
      ty1 <- metric.summary$summary.dynamic.metric[1, "metric.begin.tsp.mean"]
      ty2 <- metric.summary$summary.dynamic.metric[1, "metric.end.tsp.mean"]
      polygon(x=c(x1, x2, x2, x1), y=c(ty1, ty1, ty2, ty2), col=col.TSP, border=NA)
      
      #       text(x=x1+5, y=ty1+(ty2-ty1)/2, labels="TSP")
      x1 <- metric.summary$summary.dynamic.metric[1, "time.begin.tsp.mean"]/(24*60)
      x2 <- metric.summary$summary.dynamic.metric[1, "time.end.tsp.mean"]/(24*60)
      ty1 <- ylimS[1]
      ty2 <- ylimS[2]
      polygon(x=c(x1, x2, x2, x1), y=c(ty1, ty1, ty2, ty2), col=col.TSP, border=NA)
      #       text(x=x1+(x2-x1)/2, y=ty1+5, labels="TSP")
    }
    
    
    if (show.temperatures) {
      # na.omit(metric.summary$metric[[1]][, c("Time", "TempC")])
      x <- metric.summary$dynamic.metric[[1]][, "Time"]/(60*24)
      y <- metric.summary$dynamic.metric[[1]][, "TempC"]
      
      Lx <- modifyList(as.list(troispoints), list(x=x, y=y, axes = FALSE, xlab = "", ylab = "", main="")) 
      L <- modifyList(list(type = "l", bty = "n", xlab = "", ylab = "", xlim=xlim, ylim=ylimT, main="", las=1, col=col.temperatures, lty=lty.temperatures, lwd=lwd.temperatures), Lx) 
      par(new=TRUE)
      do.call(plot, L) 
      
      cex.y2 <- par("cex.axis")
      if (!is.null(troispoints$cex.axis)) cex.y2 <- troispoints$cex.axis
      cex.lab2 <- par("cex.lab")
      if (!is.null(troispoints$cex.lab)) cex.lab2 <- troispoints$cex.lab
      
      axis(side=4, ylim=ylimT, las=1, cex.axis=cex.y2)
      mtext(ylabT, side=4, line=3, cex=cex.lab2*par("cex"))
      
      if (show.PT & !is.na(PT[1])) {
        
        segments(0, PT[1], xlim[2]+xlim[2]*0.05, PT[1], lwd=2, col=col.PT, xpd=TRUE)
        text(xlim[2]+6, PT[1], xpd=TRUE, labels=lab.PT, col=col.PT, cex=0.8)
        if (!is.na(PT[2])) {
          segments(0, PT[1]+PT[2]*2, xlim[2]+xlim[2]*0.05, PT[1]+PT[2]*2, lwd=2, col=col.PT, lty=2, xpd=TRUE)
          segments(0, PT[1]-PT[2]*2, xlim[2]+xlim[2]*0.05, PT[1]-PT[2]*2, lwd=2, col=col.PT, lty=2, xpd=TRUE)
        }
        
      }
    }
    
    if (show.TSP) {
      par(new=TRUE)
      plot(1,1, xlim=xlim, ylim=ylimS, axes=FALSE, type="n", xlab="", ylab="")
      x1 <- xlim[1]
      x2 <- xlim[2]
      ty1 <- metric.summary$summary.dynamic.metric[1, "metric.begin.tsp.mean"]
      ty2 <- metric.summary$summary.dynamic.metric[1, "metric.end.tsp.mean"]
      #       polygon(x=c(x1, x2, x2, x1), y=c(ty1, ty1, ty2, ty2), col=col.TSP, border=NA)
      text(x=x1+5, y=ty1+(ty2-ty1)/2, labels=lab.TSP)
      x1 <- metric.summary$summary.dynamic.metric[1, "time.begin.tsp.mean"]/(24*60)
      x2 <- metric.summary$summary.dynamic.metric[1, "time.end.tsp.mean"]/(24*60)
      ty1 <- ylimS[1]
      ty2 <- ylimS[2]
      #       polygon(x=c(x1, x2, x2, x1), y=c(ty1, ty1, ty2, ty2), col=col.TSP, border=NA)
      text(x=x1+(x2-x1)/2, y=ty1+ty2/at.lab.TSP, labels=lab.TSP, xpd=TRUE)
    }
    
    par(new=TRUE)
    L1 <- list(type = "n", axes = FALSE, bty = "n", xlab = "", ylab = "", yaxs="r", xaxs="r", ylim=ylimS, xlim=xlim, main="")
    L2 <- c(list(x=metric.summary$metric[[1]]$Time/(60*24), y=metric.summary$metric[[1]]$SCL), as.list(troispoints))
    do.call(plot, modifyList(L1, L2) )
    
    if (show.metric) {
      x <- metric.summary$dynamic.metric[[1]][, "Time"]/(60*24)
      y <- metric.summary$dynamic.metric[[1]][, "Metric_50%"]
      L1 <- list(type = "l", lwd=2, col=col.S[cptcol.S])
      L2 <- c(list(x=x, y=y), as.list(troispoints))
      
      do.call(plot_add, modifyList(L1, L2) )
    }
    
    if (GTRN.CI != "null") {
      yp <- metric.summary$dynamic.metric[[1]][, "Metric_2.5%"]
      L2 <- c(list(x=x, y=yp, lty=2), as.list(troispoints))
      do.call(plot_add, modifyList(L1, L2) )
      yp <- metric.summary$dynamic.metric[[1]][, "Metric_97.5%"]
      L2 <- c(list(x=x, y=yp, lty=2), as.list(troispoints))
      do.call(plot_add, modifyList(L1, L2) )
    }
    
    
    
    if (show.hatchling.metric) {
      mean.ts <- metric.summary$summary.dynamic.metric[1, "hatchling.metric.mean.mean"]
      sd.ts <- metric.summary$summary.dynamic.metric[1, "hatchling.metric.sd.mean"]
      segments(0, mean.ts, xlim[2]+0.05*xlim[2], mean.ts, lwd=2, xpd=TRUE)
      if (!is.na(sd.ts)) {
        segments(0, mean.ts-1.96*sd.ts,  xlim[2]+0.05*xlim[2], mean.ts-1.96*sd.ts, lwd=1, lty=2, xpd=TRUE)
        segments(0, mean.ts+1.96*sd.ts,  xlim[2]+0.05*xlim[2], mean.ts+1.96*sd.ts, lwd=1, lty=2, xpd=TRUE)
      }
      if (!is.na(parameters["SD"])) {
        segments(0, mean.ts-1.96*parameters["SD"],  xlim[2]+0.05*xlim[2], mean.ts-1.96*parameters["SD"], lwd=1, lty=2, xpd=TRUE)
        segments(0, mean.ts+1.96*parameters["SD"],  xlim[2]+0.05*xlim[2], mean.ts+1.96*parameters["SD"], lwd=1, lty=2, xpd=TRUE)
      }
    }
    
    if (show.third) {
      x1 <- metric.summary$summary.dynamic.metric[1, "time.begin.middlethird.mean"]/(24*60)
      x2 <- metric.summary$summary.dynamic.metric[1, "time.end.middlethird.mean"]/(24*60)
      ty1 <- ylimS[1]
      ty2 <- ylimS[2]+ylimS[2]/40
      
      segments(x1, ty1, x1, ty2, lwd=1, lty=3, xpd=TRUE)
      segments(x2, ty1, x2, ty2, lwd=1, lty=3, xpd=TRUE)
      par(xpd=TRUE)
      getFromNamespace(".Arrows", ns="HelpersMG")(x1, ylimS[2]+1, x2, ylimS[2]+1, code=3)
      text(x1+(x2-x1)/2, ylimS[2]+ylimS[2]/at.lab.third, labels=lab.third, xpd=TRUE)
    }
    
    
    if (show.stages) {
      ## on affiche les stades
      
      for(i in 1:length(embryo.stages_ini)) {
        y1=embryo.stages_ini[i]*metric.summary$summary.dynamic.metric[1, "metric.end.incubation.mean"]
        segments(0, y1, xlim[2]-4, y1, lwd=1, lty=2, col=col.stages)
        text(xlim[2]-3*(as.numeric(i)%%2), y1, labels=names(embryo.stages_ini[i]), col=col.stages, cex=0.7)
      }
      par(xpd=TRUE)
      text(xlim[2]-2, ylimS[2]+3, labels=lab.stages, col=col.stages, cex=0.7)
    }
    
    
    
    # je rtablis l'axe de la mtrique
    #  par(new=TRUE)
    #  L1 <- list(type = "n", axes = FALSE, bty = "n", xlab = "", ylab = "", yaxs="r", xaxs="r", ylim=ylimS, xlim=xlim, main="")
    #  L2 <- c(list(x=metric.summary$metric[[1]]$Time/(60*24), y=metric.summary$metric[[1]]$SCL), as.list(troispoints))
    #  do.call(plot, modifyList(L1, L2) )
    
    
    # fin des sries
  }
  
  # fin de la fonction
}