R/archigrow.R

In archiDART: Plant Root System Architecture Analysis Using DART and RSML Files

archigrow<-function(inputlie=NULL, inputtps=NULL, inputrsml=NULL,  res=NULL, unitlength="px", rsml.date="age", rsml.connect=TRUE, plot=TRUE, twod=NULL, export.colors=FALSE, unittime=NULL, unitangle="d", rotation=0, numdate=NULL, finalscale=NULL, coldyn=NULL, GRscale=NULL, main=NULL, xlab=NULL, ylab=NULL, zlab=NULL, xlim=NULL, ylim=NULL, zlim=NULL, ...){
  
  # Errors interception
  
  if (is.null(inputlie)==TRUE & is.null(inputtps)==TRUE & is.null(inputrsml)==TRUE){stop("inputlie/inputps and/or inputrsml must be provided")}
  
  if (is.null(inputlie)==FALSE) {if (mode(inputlie)!="character"){stop("mode(inputlie) must be character")}}
  
  if (is.null(inputtps)==FALSE) {if (mode(inputtps)!="character"){stop("mode(inputtps) must be character")}}
  
  if (is.null(inputlie)==FALSE|is.null(inputtps)==FALSE){if (is.null(unittime)==TRUE){stop("If inputlie/inputtps is not NULL, unittime must be provided")}}
  
  if (is.null(inputlie)==FALSE|is.null(inputtps)==FALSE){
    if (is.null(inputlie)==TRUE|is.null(inputtps)==TRUE){stop("If inputlie/inputtps is not NULL, inputtps/inputlie must be provided")}}
  
  if (is.null(inputrsml)==FALSE) {if (mode(inputrsml)!="character"){stop("mode(inputrsml) must be character")}}
  
  if (is.null(inputlie)==FALSE & is.null(res)==TRUE & unitlength!="px"){stop("If unitlength is not px, res must be specified")}
  if (is.null(res)==FALSE){
    if (mode(res)!="numeric"){stop("mode(res) must be numeric")}
    if (res<=0|length(res)>1){stop("res must be a single positive value")}}
  
  if (mode(unitlength)!="character"){stop("mode(unitlength) must be character")}
  if (unitlength=="px"|unitlength=="mm"|unitlength=="cm") {} else {stop("unitlength must be either px (pixels), mm (millimeters) or cm (centimeters)")}
  
  if (is.null(rsml.date)==FALSE){
    if (is.character(rsml.date)==TRUE|is.numeric(rsml.date)==TRUE){} else {stop("If rsml.date is not NULL, rsml.date must be a character string or a positive numeric value")}
    if (is.numeric(rsml.date)==TRUE){if (rsml.date<=0|length(rsml.date)>1){stop("If mode(rsml.date) is numeric, rsml.date must be a single positive value")}}}
  
  if (mode(rsml.connect)!="logical"){stop("mode(rsml.connect) must be logical")}
  
  if (mode(plot)!="logical"){stop("mode(plot) must be logical")}
  
  if (mode(export.colors)!="logical"){stop("mode(export.colors) must be logical")}
  
  if (plot==FALSE & export.colors==TRUE){stop("If plot=FALSE, colors will not be exported")}
  
  if (plot==TRUE & is.null(coldyn)==TRUE){stop("If plot=TRUE, coldyn must be specified")}
  
  if (is.null(unittime)==FALSE) {if (mode(unittime)!="character"){stop("mode(unittime) must be character")}}
  
  if (mode(unitangle)!="character"){stop("mode(unitangle) must be character")}
  if(unitangle=="d"|unitangle=="r") {} else {stop("unitangle must be either d (degrees) or r (radians)")}
  
  if (mode(rotation)!="numeric"){stop("mode(rotation) must be numeric")}
  if (rotation<0){stop("rotation must be a positive value")}
  
  if (is.null(numdate)==FALSE)
  {if (mode(numdate)!="numeric"){stop("mode(numdate) must be numeric")}
   for (i in 1:length(numdate)){if (numdate[i]<=0){stop("numdate must be either a positive value or a vector of positive values")}}
   numdate.sort<-sort(numdate)
   for (i in 1:length(numdate)) {if (numdate[i]!=numdate.sort[i]){stop("Numeric elements in numdate must be sorted by increasing values")}}}
  
  if (is.null(numdate)==FALSE & is.null(finalscale)==TRUE) {stop("If numdate is not NULL, finascale must be specified")}
  
  if (is.null(finalscale)==FALSE) {if (mode(finalscale)!="logical"){stop("mode(finalscale) must be logical")}}
  
  if (is.null(GRscale)==FALSE){
    if (mode(GRscale)!="numeric") {stop("mode(GRscale) must be numeric")}
    if (length(GRscale)!=2|diff(GRscale)==0){stop("length(GRscale) must be equal to 2: c(min, max)")}
    if (GRscale[1]<0|GRscale[2]<0){stop("GRscale must be a vector of positive values")}}
  
  if (is.null(twod)==FALSE){
    if (mode(twod)!="character"){stop("mode(twod) must be character")}
    if (length(twod)!=2){stop("twod must be a vector of 2 character elements")}
    twod<-sort(twod)
    if (all.equal(twod, c("x", "y"))==TRUE|all.equal(twod, c("x", "z"))==TRUE|all.equal(twod, c("y", "z"))==TRUE) {} else {stop("twod must be c(x,y), c(x,z), or c(y,z)")}}
  
  # Reading of DART and rsml files
  
  if (is.null(inputtps)==FALSE){
    filenames.tps<-mixedsort(list.files(path=inputtps, pattern="\\.tps$"))
    path.tps<-rep(inputtps, length.out=length(filenames.tps))
    filenamestps<-sub(x=filenames.tps, pattern="\\.tps$", replacement="")
    message(paste("Number of DART tps files in inputtps:", length(filenames.tps), sep=" "))}
  
  if (is.null(inputlie)==FALSE){
    filenames.lie<-mixedsort(list.files(path=inputlie, pattern="\\.lie$"))
    path.lie<-rep(inputlie, length.out=length(filenames.lie))
    filenameslie<-sub(x=filenames.lie, pattern="\\.lie$", replacement="")
    message(paste("Number of DART lie files in inputlie:", length(filenames.lie), sep=" "))}
  
  if (is.null(inputrsml)==FALSE) {
    filenames.rsml<-mixedsort(list.files(path=inputrsml, pattern="\\.rsml$"))
    path.rsml<-rep(inputrsml, length.out=length(filenames.rsml))
    filenamesrsml<-sub(x=filenames.rsml, pattern="\\.rsml$", replacement="")
    message(paste("Number of rsml files in inputrsml:", length(filenames.rsml), sep=" "))}
  
  if (is.null(inputrsml)==TRUE){
    if (length(filenames.lie)==0){stop("There is no lie file in inputlie")}
    if (length(filenames.tps)==0){stop("There is no tps file in inputtps")}}
  else {
    if (is.null(inputlie)==TRUE){if (length(filenames.rsml)==0){stop("There is no rsml file in inputrsml")}}
    else{
      if (length(filenames.lie)==0){stop("There is no lie file in inputlie")}
      if (length(filenames.tps)==0){stop("There is no tps file in inputtps")}
      if (length(filenames.rsml)==0){stop("There is no rsml file in inputrsml")}}}
  
  
  if (is.null(inputrsml)==TRUE){ # Only DART files
    
    TIME<-lapply(paste(path.tps, "/", filenames.tps, sep=""), read.table, header=TRUE)
    
    LIE<-lapply(paste(path.lie, "/", filenames.lie, sep=""), read.table, header=TRUE)
    
    #Unit conversion DART files
    if (unitlength=="mm") {cunit<-(10*cm(1)/res)}
    if (unitlength=="cm") {cunit<-(cm(1)/res)}
    if (unitlength=="px") {cunit<-1}
    
   if (length(TIME)==1) {
     age<-list()
      for (i in 1:length(LIE)) {
        age[[i]]<-TIME[[1]]$Date
        if(length(age[[i]])!=max(LIE[[i]]$Date)){message(paste("Note: The number of observation dates in", filenames.tps[[1]], "is not equal to max(Date) in", filenames.lie[[i]], sep=" "))}}}
   else {
      age<-list()
      if (length(TIME)!=length(LIE)) {stop("If there is more than one tps file in inputtps, the number of lie files in inputlie and tps files in inputtps must be equal")}
      for (i in 1:length(LIE)) {
        if(filenameslie[i]!=filenamestps[i]) {stop("Input lie files and their corresponding tps files must have the same name")}
        age[[i]]<-TIME[[i]]$Date
        if (length(age[[i]])!=max(LIE[[i]]$Date)) {message(paste("Note: The number of observation dates in", filenames.tps[[i]], "is not equal to max(Date) in", filenames.lie[[i]], sep=" "))}}
      for (i in 1:length(LIE)){age[[i]]<-TIME[[i]]$Date}}}
  
  else {
    if (is.null(inputlie)==TRUE){ # Only RSML files
      
      LIE<-list()
      TIME<-list()
      age<-list()
      res1<-c()
      unitlength1<-c()
      unittime1<-c()
      filenameslie<-c()
      RSML <- lapply(paste(path.rsml, "/", filenames.rsml, sep=""), rsmlToDART, final.date=rsml.date, connect=rsml.connect) # Read RSML files
      for (i in 1:length(RSML)){
        res1<-append(res1, rep(as.numeric(RSML[[i]]$resolution), length(RSML[[i]]$lie)))
        unitlength1<-append(unitlength1, rep(as.character(RSML[[i]]$length), length(RSML[[i]]$lie)))
        unittime1<-append(unittime1, rep(as.character(RSML[[i]]$time), length(RSML[[i]]$lie)))
        LIE<-append(LIE, RSML[[i]]$lie)
        TIME<-append(TIME, RSML[[i]]$tps)
        length1<-length(RSML[[i]]$lie)
        
        l<-length(age)
        for (j in 1:length1) {
          age[[l+j]]<-RSML[[i]]$tps[[j]]$Date}
        
        if (length1>1){
          num<-c(1:length1)
          filenameslie[(length(filenameslie)+1):(length(filenameslie)+length1)]<-paste(rep(filenamesrsml[i], length.out=length1), num, sep="")}
        if (length1==1){
          filenameslie[(length(filenameslie)+1)]<-filenamesrsml[i]}}
      
      #Unit conversion rsml
      
      cunit1<-vector(length=length(res1))
      
      for (i in 1:length(res1)){
        
        if (unitlength=="cm"){
          
          if (unitlength1[i]=="pixel") {
            cunit1[i]<-1
            message(paste("Unit in ", filenameslie[i], " is pixel. Unitlength not used and results expressed in pixels", sep=""))}
          if (unitlength1[i]=="m") {cunit1[i]<-100/res1[i]}
          if (unitlength1[i]=="cm") {cunit1[i]<-1/res1[i]}
          if (unitlength1[i]=="mm") {cunit1[i]<-1/res1[i]/10}
          if (unitlength1[i]=="um") {cunit1[i]<-1/res1[i]/10000}
          if (unitlength1[i]=="nm") {cunit1[i]<-1/res1[i]/10000000}
          if (unitlength1[i]=="inch") {cunit1[i]<-1/res1[i]*cm(1)}}
        
        if (unitlength=="mm"){
          if (unitlength1[i]=="pixel") {
            cunit1[i]<-1
            message(paste("Unit in ", filenameslie[i], " is pixel. Unitlength not used and results expressed in pixels", sep=""))}
          if (unitlength1[i]=="m") {cunit1[i]<-1/res1[i]*1000}
          if (unitlength1[i]=="cm") {cunit1[i]<-1/res1[i]*10}
          if (unitlength1[i]=="mm") {cunit1[i]<-1/res1[i]}
          if (unitlength1[i]=="um") {cunit1[i]<-1/res1[i]/1000}
          if (unitlength1[i]=="nm") {cunit1[i]<-1/res1[i]/1000000}
          if (unitlength1[i]=="inch") {cunit1[i]<-1/res1[i]*cm(1)*10}}
        
        if (unitlength=="px"){cunit1[i]<-1}}}
    
    else { # DART and RSML files
      
      TIME<-lapply(paste(path.tps, "/", filenames.tps, sep=""), read.table, header=TRUE) # Read TPS files
      
      LIE<-lapply(paste(path.lie, "/", filenames.lie, sep=""), read.table, header=TRUE) # read LIE files
      
      res1<-rep(res, length(filenames.lie))
      unitlength1<-rep(unitlength, length(filenames.lie))
      unittime1<-rep(unittime, length(filenames.lie))
      
      if (length(TIME)==1) {
        age<-list()
        for (i in 1:length(LIE)) {
          age[[i]]<-TIME[[1]]$Date
          if(length(age[[i]])!=max(LIE[[i]]$Date)){message(paste("Note: The number of observation dates in", filenames.tps[[1]], "is not equal to max(Date) in", filenames.lie[[i]], sep=" "))}}}
      else {
        age<-list()
        if (length(TIME)!=length(LIE)) {stop("If there is more than one tps file in inputtps, the number of lie files in inputlie and tps files in inputtps must be equal")}
        for (i in 1:length(LIE)) {
          if(filenameslie[i]!=filenamestps[i]) {stop("Input lie files and their corresponding tps files must have the same name")}
          age[[i]]<-TIME[[i]]$Date
          if (length(age[[i]])!=max(LIE[[i]]$Date)) {message(paste("Note: The number of observation dates in", filenames.tps[[i]], "is not equal to max(Date) in", filenames.lie[[i]], sep=" "))}}
        for (i in 1:length(LIE)){age[[i]]<-TIME[[i]]$Date}}
      
      RSML <- lapply(paste(path.rsml, "/", filenames.rsml, sep=""), rsmlToDART, final.date=rsml.date, connect=rsml.connect) # Read RSML files
      
      for (i in 1:length(RSML)){
        res1<-append(res1, rep(as.numeric(RSML[[i]]$resolution), length(RSML[[i]]$lie)))
        unitlength1<-append(unitlength1, rep(as.character(RSML[[i]]$length), length(RSML[[i]]$lie)))
        unittime1<-append(unittime1, rep(as.character(RSML[[i]]$time), length(RSML[[i]]$lie)))
        LIE<-append(LIE, RSML[[i]]$lie)
        length1<-length(RSML[[i]]$lie)
        
        l<-length(age)
        for (j in 1:length1) {
          age[[l+j]]<-RSML[[i]]$tps[[j]]$Date}
        
        if (length1>1){
          num<-c(1:length1)
          filenameslie[(length(filenameslie)+1):(length(filenameslie)+length1)]<-paste(rep(filenamesrsml[i], length.out=length1), num, sep="")}
        if (length1==1){
          filenameslie[(length(filenameslie)+1)]<-filenamesrsml[i]}}
      
      #Unit conversion DART and RSML
      cunit1<-vector(length=length(res1))
      
      if (unitlength=="mm") {cunit1[1:length(filenames.lie)]<-(10*cm(1)/res)}
      if (unitlength=="cm") {cunit1[1:length(filenames.lie)]<-cm(1)/res}
      if (unitlength=="px") {cunit1[1:length(filenames.lie)]<-1}
      
      for (i in (length(filenames.lie)+1):length(res1)){
        
        if (unitlength=="cm"){
          
          if (unitlength1[i]=="pixel") {
            cunit[i]<-1
            message(paste("Unit in ", filenameslie[i], " is pixel. Unitlength not used and results expressed in pixels", sep=""))}
          if (unitlength1[i]=="m") {cunit1[i]<-100/res1[i]}
          if (unitlength1[i]=="cm") {cunit1[i]<-1/res1[i]}
          if (unitlength1[i]=="mm") {cunit1[i]<-1/res1[i]/10}
          if (unitlength1[i]=="um") {cunit1[i]<-1/res1[i]/10000}
          if (unitlength1[i]=="nm") {cunit1[i]<-1/res1[i]/10000000}
          if (unitlength1[i]=="inch") {cunit1[i]<-1/res1[i]*cm(1)}}
        
        if (unitlength=="mm"){
          if (unitlength1[i]=="pixel") {
            cunit[i]<-1
            message(paste("Unit in ", filenameslie[i], " is pixel. Unitlength not used and results expressed in pixels", sep=""))}
          if (unitlength1[i]=="m") {cunit1[i]<-1/res1[i]*1000}
          if (unitlength1[i]=="cm") {cunit1[i]<-1/res1[i]*10}
          if (unitlength1[i]=="mm") {cunit1[i]<-1/res1[i]}
          if (unitlength1[i]=="um") {cunit1[i]<-1/res1[i]/1000}
          if (unitlength1[i]=="nm") {cunit1[i]<-1/res1[i]/1000000}
          if (unitlength1[i]=="inch") {cunit1[i]<-1/res1[i]*cm(1)*10}}
        
        if (unitlength=="px"){cunit1[i]<-1}}}}
  
  # Unit conversion and rotation
  
  if (unitangle=="r") {
    cunitangle<-1
    rotation<-rotation}
  if (unitangle=="d") {
    cunitangle<-180/pi
    rotation<-rotation*(1/cunitangle)}
  
  rot.matrix<-matrix(c(cos(rotation), sin(rotation), -sin(rotation), cos(rotation)), nrow=2, ncol=2)
  
  for (i in 1:length(LIE)){
    
    if (is.null(inputrsml)==FALSE){cunit<-cunit1[i]}
    
    if (!("Z" %in% colnames(LIE[[i]]))){
      LIE[[i]]$X<-LIE[[i]]$X*cunit
      LIE[[i]]$Y<-LIE[[i]]$Y*cunit
      newcoord<-rot.matrix%*%t(as.matrix(data.frame(LIE[[i]]$X, LIE[[i]]$Y)))
      LIE[[i]]$X<-newcoord[1,]
      LIE[[i]]$Y<-newcoord[2,]}
    else {
      LIE[[i]]$X<-LIE[[i]]$X*cunit
      LIE[[i]]$Y<-LIE[[i]]$Y*cunit
      LIE[[i]]$Z<-LIE[[i]]$Z*cunit}}
  
  # Calculation of a standardized growth rate matrix and a corresponding color matrix
  
  GRlist<-list()
  
  for (i in 1:length(LIE)){
    
    a<-length(age[[i]])
    message(paste("Number of observation dates for ", filenameslie[i], ": ", a, sep=""))
    
    if (is.null(inputrsml)==FALSE){unittime<-unittime1[i]}

    growthrate<-matrix(nrow=sum(LIE[[i]]$Bran=="true"), ncol=length(age[[i]]))
    r<-0
    nodeorder<-rep(0, nrow(LIE[[i]]))
    rootorder<-c()
    
    for (l in 1:nrow(LIE[[i]])){
      
      if (LIE[[i]]$Bran[l]=="true"){
        
        if (LIE[[i]]$Prec[l]==0) {
          r<-r+1
          ord<-1
          nodeorder[l]<-ord
          rootorder[r]<-ord}
        if (LIE[[i]]$Prec[l]!=0) {
          r<-r+1
          c<-LIE[[i]]$Date[l]
          prec<-LIE[[i]]$Prec[l]
          ord<-nodeorder[prec]+1
          nodeorder[l]<-ord
          rootorder[r]<-nodeorder[l]
          if (c==1) {
            if (!("Z" %in% colnames(LIE[[i]]))){
            distGR<-distance2D(x1=LIE[[i]]$X[l], y1=LIE[[i]]$Y[l], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec])
            growthrate[r,c]<-distGR/age[[i]][c]}
            else {
              distGR<-distance3D(x1=LIE[[i]]$X[l], y1=LIE[[i]]$Y[l], z1=LIE[[i]]$Z[l], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec], z2=LIE[[i]]$Z[prec])
              growthrate[r,c]<-distGR/age[[i]][c]}}
          
          if (c>1) {
            if (!("Z" %in% colnames(LIE[[i]]))){
              distGR<-distance2D(x1=LIE[[i]]$X[l], y1=LIE[[i]]$Y[l], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec])
              growthrate[r,c]<-distGR/(age[[i]][c]-age[[i]][c-1])}
            else {
              distGR<-distance3D(x1=LIE[[i]]$X[l], y1=LIE[[i]]$Y[l], z1=LIE[[i]]$Z[l], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec], z2=LIE[[i]]$Z[prec])
              growthrate[r,c]<-distGR/(age[[i]][c]-age[[i]][c-1])}}}
      
        m<-LIE[[i]]$Suiv[l]
        
        if (m!=0){
        
        while (LIE[[i]]$Apic[m]=="false") {
          
          nodeorder[m]<-ord
          
          if (LIE[[i]]$Date[m]==LIE[[i]]$Date[LIE[[i]]$Prec[m]]){
          
              c<-LIE[[i]]$Date[m]
              prec<-LIE[[i]]$Prec[m]
              
              if (c==1) {
                if (!("Z" %in% colnames(LIE[[i]]))){
                  distGR<-distance2D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec])
                  growthrate[r,c]<-growthrate[r,c] + distGR/age[[i]][c]}
                else {
                  distGR<-distance3D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], z1=LIE[[i]]$Z[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec], z2=LIE[[i]]$Z[prec])
                  growthrate[r,c]<-growthrate[r,c] + distGR/age[[i]][c]}}
              
              if (c>1) {
                if (!("Z" %in% colnames(LIE[[i]]))){
                  distGR<-distance2D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec])
                  growthrate[r,c]<-growthrate[r,c] + distGR/(age[[i]][c]-age[[i]][c-1])}
                else {
                  distGR<-distance3D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], z1=LIE[[i]]$Z[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec], z2=LIE[[i]]$Z[prec])
                  growthrate[r,c]<-growthrate[r,c] + distGR/(age[[i]][c]-age[[i]][c-1])}}}
          
          if (LIE[[i]]$Date[m]!=LIE[[i]]$Date[LIE[[i]]$Prec[m]]){
            
            c<-LIE[[i]]$Date[m]
            prec<-LIE[[i]]$Prec[m]
            
            if (c==1) {
              if (!("Z" %in% colnames(LIE[[i]]))){
                distGR<-distance2D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec])
                growthrate[r,c]<-distGR/age[[i]][c]}
              else {
                distGR<-distance3D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], z1=LIE[[i]]$Z[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec], z2=LIE[[i]]$Z[prec])
                growthrate[r,c]<-distGR/age[[i]][c]}}
            
            if (c>1) {
              if (!("Z" %in% colnames(LIE[[i]]))){
                distGR<-distance2D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec])
                growthrate[r,c]<-distGR/(age[[i]][c]-age[[i]][c-1])}
              else {
                distGR<-distance3D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], z1=LIE[[i]]$Z[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec], z2=LIE[[i]]$Z[prec])
                growthrate[r,c]<-distGR/(age[[i]][c]-age[[i]][c-1])}}}
        
          m<-LIE[[i]]$Suiv[m]}
      
          if (LIE[[i]]$Apic[m]=="true"){
            
            nodeorder[m]<-ord
            
            if (LIE[[i]]$Date[m]==LIE[[i]]$Date[LIE[[i]]$Prec[m]]){
              
              c<-LIE[[i]]$Date[m]
              prec<-LIE[[i]]$Prec[m]
              
              if (c==1) {
                if (!("Z" %in% colnames(LIE[[i]]))){
                  distGR<-distance2D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec])
                  growthrate[r,c]<-growthrate[r,c] + distGR/age[[i]][c]}
                else {
                  distGR<-distance3D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], z1=LIE[[i]]$Z[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec], z2=LIE[[i]]$Z[prec])
                  growthrate[r,c]<-growthrate[r,c] + distGR/age[[i]][c]}}
              
              if (c>1) {
                if (!("Z" %in% colnames(LIE[[i]]))){
                  distGR<-distance2D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec])
                  growthrate[r,c]<-growthrate[r,c] + distGR/(age[[i]][c]-age[[i]][c-1])}
                else {
                  distGR<-distance3D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], z1=LIE[[i]]$Z[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec], z2=LIE[[i]]$Z[prec])
                  growthrate[r,c]<-growthrate[r,c] + distGR/(age[[i]][c]-age[[i]][c-1])}}}
            
            if (LIE[[i]]$Date[m]!=LIE[[i]]$Date[LIE[[i]]$Prec[m]]){
              
              c<-LIE[[i]]$Date[m]
              prec<-LIE[[i]]$Prec[m]
              
              if (c==1) {
                if (!("Z" %in% colnames(LIE[[i]]))){
                  distGR<-distance2D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec])
                  growthrate[r,c]<-distGR/age[[i]][c]}
                else {
                  distGR<-distance3D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], z1=LIE[[i]]$Z[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec], z2=LIE[[i]]$Z[prec])
                  growthrate[r,c]<-distGR/age[[i]][c]}}
              
              if (c>1) {
                if (!("Z" %in% colnames(LIE[[i]]))){
                  distGR<-distance2D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec])
                  growthrate[r,c]<-distGR/(age[[i]][c]-age[[i]][c-1])}
                else {
                  distGR<-distance3D(x1=LIE[[i]]$X[m], y1=LIE[[i]]$Y[m], z1=LIE[[i]]$Z[m], x2=LIE[[i]]$X[prec], y2=LIE[[i]]$Y[prec], z2=LIE[[i]]$Z[prec])
                  growthrate[r,c]<-distGR/(age[[i]][c]-age[[i]][c-1])}}}}}}}
    
    growthrate[is.na(growthrate)]<-0

    if (plot==TRUE){
      
      if (is.null(GRscale)==TRUE) {
        maxi<-matrix(max(growthrate), nrow=nrow(growthrate), ncol=ncol(growthrate))
        mini<-matrix(min(growthrate), nrow=nrow(growthrate), ncol=ncol(growthrate))}
      else {
        maxi<-max(GRscale)
        mini<-min(GRscale)
        if (maxi<max(growthrate)){stop(paste("max(GRscale) must be positive and superior or equal to", max(growthrate), sep=" "))}
        if (mini>min(growthrate)){stop(paste("min(GRscale) must belong to [0,", min(growthrate), "]", sep=""))}}
      growthratesd<-(growthrate-mini)/(maxi-mini)
      pal<-colorRamp(coldyn)
      colors<-matrix(nrow=nrow(growthratesd), ncol=ncol(growthratesd))
      for (c in 1:ncol(growthratesd)){
        colors[,c]<-rgb(pal(growthratesd[,c]), maxColorValue=255)}}
    
    # Creating an output list for the growth rate matrices
      
      Num<-c(1:nrow(growthrate))
      num<-c(1:length(age[[i]]))
      
      if (is.null(inputrsml)==FALSE) {
        if (rsml.connect==TRUE){
          GR<-data.frame(Num, rootorder, growthrate)
          colnames(GR)<-c("Root", "Ord", paste("Date", t(num), sep=""))}
        if (rsml.connect==FALSE){
          GR<-data.frame(Num, growthrate)
          colnames(GR)<-c("Root", paste("Date", t(num), sep=""))}}
      
      if (is.null(inputrsml)==TRUE) {
        GR<-data.frame(Num, rootorder, growthrate)
        colnames(GR)<-c("Root", "Ord", paste("Date", t(num), sep=""))}
      
      if (plot==TRUE & export.colors==TRUE) {
        colors1<-data.frame(Num, colors)
        colnames(colors1)<-c("Root", paste("Date", t(num), sep=""))}
      
      dateandage<-data.frame(Date=num, Age=age[[i]])
      
      if (export.colors==FALSE) {outputresults<-list(unit=paste(unitlength, "/", unittime, sep=""), time=dateandage, GR=GR)} else {outputresults<-list(unit=paste(unitlength, "/", unittime, sep=""), time=dateandage, GR=GR, colors=colors1)}
      GRlist[[i]]<-outputresults
      names(GRlist)[i]<-filenameslie[i]

    # Plotting of vectorized root systems
    
    if (plot==TRUE){
    
    if (is.null(numdate)==TRUE){
      
      LIE[[i]]$X<-LIE[[i]]$X-min(LIE[[i]]$X)
      LIE[[i]]$Y<-LIE[[i]]$Y-min(LIE[[i]]$Y)
      if ("Z" %in% colnames(LIE[[i]])) {LIE[[i]]$Z<-LIE[[i]]$Z-min(LIE[[i]]$Z)}
      minx<-min(LIE[[i]]$X)
      maxx<-max(LIE[[i]]$X)
      miny<-min(LIE[[i]]$Y)
      maxy<-max(LIE[[i]]$Y)
      if ("Z" %in% colnames(LIE[[i]])){
        minz<-min(LIE[[i]]$Z)
        maxz<-max(LIE[[i]]$Z)}
      if (is.null(main)==TRUE){main1<-filenameslie[i]} else {main1<-main}
      if (is.null(xlim)==TRUE){xlim1<-c(minx,maxx)} else {xlim1<-xlim}
      if (is.null(ylim)==TRUE){ylim1<-c(maxy,miny)} else {ylim1<-ylim}
      if ("Z" %in% colnames(LIE[[i]]) & is.null(zlim)==TRUE){zlim1<-c(minz,maxz)} else {zlim1<-zlim}
      if (is.null(xlab)==TRUE){xlab1<-paste("X (", unitlength, ")", sep="")} else {xlab1<-xlab}
      if (is.null(ylab)==TRUE){ylab1<-paste("Y (", unitlength, ")", sep="")} else {ylab1<-ylab}
      if ("Z" %in% colnames(LIE[[i]]) & is.null(zlab)==TRUE){zlab1<-paste("Z (", unitlength, ")", sep="")} else {zlab1<-zlab}

      if (!("Z" %in% colnames(LIE[[i]]))){
      
      plot(LIE[[i]]$X[1], LIE[[i]]$Y[1], type="n", xlim=xlim1, ylim=ylim1, main=main1, ylab=ylab1, xlab=xlab1,...)
      r<-0
      for (k in 1:nrow(LIE[[i]])){
        if(LIE[[i]]$Bran[k]=="true"){
          r<-r+1
          a<-LIE[[i]]$Prec[k]
          b<-LIE[[i]]$Date[k]
          if (a!=0) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[k],y1=LIE[[i]]$Y[k], col=colors[r,b],...)}
          m<-LIE[[i]]$Suiv[k]
          if (m!=0){
          while (LIE[[i]]$Apic[m]=="false"){
            a<-LIE[[i]]$Prec[m]
            b<-LIE[[i]]$Date[m]
            segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)
            m<-LIE[[i]]$Suiv[m]}
          if (LIE[[i]]$Apic[m]=="true"){
            a<-LIE[[i]]$Prec[m]
            b<-LIE[[i]]$Date[m]
            segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)}}}}}
      
      else {
        
        if (is.null(twod)==TRUE){
        
        LIE[[i]]$col<-colors[as.matrix(LIE[[i]][,c("root", "Date")])]
        root<-sum(LIE[[i]]$Suiv==0)
        end<-which(LIE[[i]]$Suiv==0)
        
        if (!requireNamespace("rgl", quietly = TRUE)) {
          stop("3D plotting with archigrow() requires package `rgl`. Please install it and try again.")}
        
        rgl::open3d()
        rgl::plot3d(x=LIE[[i]]$X[1], y=LIE[[i]]$Y[1], z=LIE[[i]]$Z[1], type="n", xlim=xlim1, ylim=ylim1, zlim=zlim1, main=main1, ylab=ylab1, xlab=xlab1, zlab=zlab1,...)
        for (k in 1:root){
          if (k==1) {
            dataroot<-as.matrix(LIE[[i]][k:end[k],c(7:9, ncol(LIE[[i]]))])} 
          else {
            if (LIE[[i]]$Prec[end[k-1]+1]!=0){
              dataroot<-as.matrix(LIE[[i]][(end[k-1]+1):end[k],c(7:9, ncol(LIE[[i]]))])
              dataroot<-rbind(LIE[[i]][LIE[[i]]$Num==LIE[[i]]$Prec[end[k-1]+1],c(7:9, ncol(LIE[[i]]))], dataroot)}
            else{
              dataroot<-as.matrix(LIE[[i]][(end[k-1]+1):end[k],c(7:9, ncol(LIE[[i]]))])}}
          
          rgl::lines3d(dataroot[,1:3], col=dataroot[,4], smooth=FALSE, ...)}}
        
        else {
          
          if (all.equal(twod, c("x", "y"))==TRUE) {
            
            plot(LIE[[i]]$X[1], LIE[[i]]$Y[1], type="n", xlim=xlim1, ylim=ylim1, main=main1, ylab=ylab1, xlab=xlab1,...)
            r<-0
            for (k in 1:nrow(LIE[[i]])){
              if(LIE[[i]]$Bran[k]=="true"){
                r<-r+1
                a<-LIE[[i]]$Prec[k]
                b<-LIE[[i]]$Date[k]
                if (a!=0) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[k],y1=LIE[[i]]$Y[k], col=colors[r,b],...)}
                m<-LIE[[i]]$Suiv[k]
                if (m!=0){
                  while (LIE[[i]]$Apic[m]=="false"){
                    a<-LIE[[i]]$Prec[m]
                    b<-LIE[[i]]$Date[m]
                    segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)
                    m<-LIE[[i]]$Suiv[m]}
                  if (LIE[[i]]$Apic[m]=="true"){
                    a<-LIE[[i]]$Prec[m]
                    b<-LIE[[i]]$Date[m]
                    segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)}}}}}
          
          if (all.equal(twod, c("x", "z"))==TRUE){
            
            plot(LIE[[i]]$X[1], LIE[[i]]$Z[1], type="n", xlim=xlim1, ylim=zlim1, main=main1, ylab=zlab1, xlab=xlab1,...)
            r<-0
            for (k in 1:nrow(LIE[[i]])){
              if(LIE[[i]]$Bran[k]=="true"){
                r<-r+1
                a<-LIE[[i]]$Prec[k]
                b<-LIE[[i]]$Date[k]
                if (a!=0) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Z[a],x1=LIE[[i]]$X[k],y1=LIE[[i]]$Z[k], col=colors[r,b],...)}
                m<-LIE[[i]]$Suiv[k]
                if (m!=0){
                  while (LIE[[i]]$Apic[m]=="false"){
                    a<-LIE[[i]]$Prec[m]
                    b<-LIE[[i]]$Date[m]
                    segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Z[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Z[m], col=colors[r,b],...)
                    m<-LIE[[i]]$Suiv[m]}
                  if (LIE[[i]]$Apic[m]=="true"){
                    a<-LIE[[i]]$Prec[m]
                    b<-LIE[[i]]$Date[m]
                    segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Z[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Z[m], col=colors[r,b],...)}}}}}
          
          if (all.equal(twod, c("y", "z"))==TRUE){
            
            plot(LIE[[i]]$Z[1], LIE[[i]]$Y[1], type="n", xlim=zlim1, ylim=ylim1, main=main1, ylab=ylab1, xlab=zlab1,...)
            r<-0
            for (k in 1:nrow(LIE[[i]])){
              if(LIE[[i]]$Bran[k]=="true"){
                r<-r+1
                a<-LIE[[i]]$Prec[k]
                b<-LIE[[i]]$Date[k]
                if (a!=0) {segments(x0=LIE[[i]]$Z[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$Z[k],y1=LIE[[i]]$Y[k], col=colors[r,b],...)}
                m<-LIE[[i]]$Suiv[k]
                if (m!=0){
                  while (LIE[[i]]$Apic[m]=="false"){
                    a<-LIE[[i]]$Prec[m]
                    b<-LIE[[i]]$Date[m]
                    segments(x0=LIE[[i]]$Z[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$Z[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)
                    m<-LIE[[i]]$Suiv[m]}
                  if (LIE[[i]]$Apic[m]=="true"){
                    a<-LIE[[i]]$Prec[m]
                    b<-LIE[[i]]$Date[m]
                    segments(x0=LIE[[i]]$Z[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$Z[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)}}}}}}}}
    
    if (is.null(numdate)==FALSE) {
      
      for (l in 1:length(numdate)){if (numdate[l]>max(LIE[[i]]$Date)){message(paste("Warning: numdate contains a numerical value greater than max(Date) in", filenames.lie[[i]], sep=" "))}}
      
      if (finalscale==TRUE){
        
        LIE[[i]]$X<-LIE[[i]]$X-min(LIE[[i]]$X)
        LIE[[i]]$Y<-LIE[[i]]$Y-min(LIE[[i]]$Y)
        if ("Z" %in% colnames(LIE[[i]])) {LIE[[i]]$Z<-LIE[[i]]$Z-min(LIE[[i]]$Z)}
        minx<-min(LIE[[i]]$X)
        maxx<-max(LIE[[i]]$X)
        miny<-min(LIE[[i]]$Y)
        maxy<-max(LIE[[i]]$Y)
        if ("Z" %in% colnames(LIE[[i]])) {
          minz<-min(LIE[[i]]$Z)
          maxz<-max(LIE[[i]]$Z)}
        for (j in 1:length(numdate)){
          if (is.null(main)==TRUE){main1<-paste(filenameslie[i], "-numdate=", numdate[j], sep="")} else {main1<-main}
          if (is.null(xlim)==TRUE){xlim1<-c(minx,maxx)} else {xlim1<-xlim}
          if (is.null(ylim)==TRUE){ylim1<-c(maxy,miny)} else {ylim1<-ylim}
          if ("Z" %in% colnames(LIE[[i]]) & is.null(zlim)==TRUE){zlim1<-c(minz,maxz)} else {zlim1<-zlim}
          if (is.null(xlab)==TRUE){xlab1<-paste("X (", unitlength, ")", sep="")} else {xlab1<-xlab}
          if (is.null(ylab)==TRUE){ylab1<-paste("Y (", unitlength, ")", sep="")} else {ylab1<-ylab}
          if ("Z" %in% colnames(LIE[[i]]) & is.null(zlab)==TRUE){zlab1<-paste("Z (", unitlength, ")", sep="")} else {zlab1<-zlab}
          
          if (!("Z" %in% colnames(LIE[[i]]))){
          
          plot(LIE[[i]]$X[1], LIE[[i]]$Y[1], type="n", xlim=xlim1, ylim=ylim1, main=main1, xlab=xlab1, ylab=ylab1,...)
          r<-0
          for (k in 1:nrow(LIE[[i]])){
            if(LIE[[i]]$Bran[k]=="true"){
              r<-r+1
              a<-LIE[[i]]$Prec[k]
              b<-LIE[[i]]$Date[k]
              if (a!=0 & b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[k],y1=LIE[[i]]$Y[k], col=colors[r,b],...)}
              m<-LIE[[i]]$Suiv[k]
              if (m!=0){
              while (LIE[[i]]$Apic[m]=="false"){
                a<-LIE[[i]]$Prec[m]
                b<-LIE[[i]]$Date[m]
                if (b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)}
                m<-LIE[[i]]$Suiv[m]}
              if (LIE[[i]]$Apic[m]=="true"){
                a<-LIE[[i]]$Prec[m]
                b<-LIE[[i]]$Date[m]
                if (b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)}}}}}}
          
          else{
            
            if (is.null(twod)==TRUE){
            
            LIE[[i]]$col<-colors[as.matrix(LIE[[i]][,c("root", "Date")])]
            dataroot1<-LIE[[i]][LIE[[i]]$Date<=numdate[j],]
            root<-sum(dataroot1$Bran=="true")
            if (root>1) {
              end<-which(dataroot1$Bran=="true")-1
              end<-end[-1]
              end[length(end)+1]<-nrow(dataroot1)}
            else {end<-nrow(dataroot1)}
            
            if (!requireNamespace("rgl", quietly = TRUE)) {
              stop("3D plotting with archigrow() requires package `rgl`. Please install it and try again.")}
            
            rgl::open3d()
            rgl::plot3d(x=LIE[[i]]$X[1], y=LIE[[i]]$Y[1], z=LIE[[i]]$Z[1], type="n", xlim=xlim1, ylim=ylim1, zlim=zlim1, main=main1, ylab=ylab1, xlab=xlab1, zlab=zlab1,...)
            for (k in 1:root){
              if (k==1) {
                dataroot<-as.matrix(dataroot1[k:end[k],c(7:9, ncol(LIE[[i]]))])} 
              else {
                if (dataroot1$Prec[end[k-1]+1]!=0){
                  dataroot<-as.matrix(dataroot1[(end[k-1]+1):end[k],c(7:9, ncol(LIE[[i]]))])
                  dataroot<-rbind(dataroot1[dataroot1$Num==dataroot1$Prec[end[k-1]+1],c(7:9, ncol(LIE[[i]]))], dataroot)}
                else{
                  dataroot<-as.matrix(dataroot1[(end[k-1]+1):end[k],c(7:9, ncol(LIE[[i]]))])}}
      
              rgl::lines3d(dataroot[,1:3], col=dataroot[,4], smooth=FALSE, ...)}}
            
            else {
              
              if (all.equal(twod, c("x", "y"))==TRUE) {
                
                plot(LIE[[i]]$X[1], LIE[[i]]$Y[1], type="n", xlim=xlim1, ylim=ylim1, main=main1, ylab=ylab1, xlab=xlab1,...)
                r<-0
                for (k in 1:nrow(LIE[[i]])){
                  if(LIE[[i]]$Bran[k]=="true"){
                    r<-r+1
                    a<-LIE[[i]]$Prec[k]
                    b<-LIE[[i]]$Date[k]
                    if (a!=0 & b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[k],y1=LIE[[i]]$Y[k], col=colors[r,b],...)}
                    m<-LIE[[i]]$Suiv[k]
                    if (m!=0){
                      while (LIE[[i]]$Apic[m]=="false"){
                        a<-LIE[[i]]$Prec[m]
                        b<-LIE[[i]]$Date[m]
                        if (b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)}
                        m<-LIE[[i]]$Suiv[m]}
                      if (LIE[[i]]$Apic[m]=="true"){
                        a<-LIE[[i]]$Prec[m]
                        b<-LIE[[i]]$Date[m]
                        if (b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)}}}}}}
              
              if (all.equal(twod, c("x", "z"))==TRUE){
                
                plot(LIE[[i]]$X[1], LIE[[i]]$Z[1], type="n", xlim=xlim1, ylim=zlim1, main=main1, ylab=zlab1, xlab=xlab1,...)
                r<-0
                for (k in 1:nrow(LIE[[i]])){
                  if(LIE[[i]]$Bran[k]=="true"){
                    r<-r+1
                    a<-LIE[[i]]$Prec[k]
                    b<-LIE[[i]]$Date[k]
                    if (a!=0 & b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Z[a],x1=LIE[[i]]$X[k],y1=LIE[[i]]$Z[k], col=colors[r,b],...)}
                    m<-LIE[[i]]$Suiv[k]
                    if (m!=0){
                      while (LIE[[i]]$Apic[m]=="false"){
                        a<-LIE[[i]]$Prec[m]
                        b<-LIE[[i]]$Date[m]
                        if (b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Z[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Z[m], col=colors[r,b],...)}
                        m<-LIE[[i]]$Suiv[m]}
                      if (LIE[[i]]$Apic[m]=="true"){
                        a<-LIE[[i]]$Prec[m]
                        b<-LIE[[i]]$Date[m]
                        if (b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Z[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Z[m], col=colors[r,b],...)}}}}}}
              
              if (all.equal(twod, c("y", "z"))==TRUE){
                
                plot(LIE[[i]]$Z[1], LIE[[i]]$Y[1], type="n", xlim=zlim1, ylim=ylim1, main=main1, ylab=ylab1, xlab=zlab1,...)
                r<-0
                for (k in 1:nrow(LIE[[i]])){
                  if(LIE[[i]]$Bran[k]=="true"){
                    r<-r+1
                    a<-LIE[[i]]$Prec[k]
                    b<-LIE[[i]]$Date[k]
                    if (a!=0 & b<=numdate[j]) {segments(x0=LIE[[i]]$Z[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$Z[k],y1=LIE[[i]]$Y[k], col=colors[r,b],...)}
                    m<-LIE[[i]]$Suiv[k]
                    if (m!=0){
                      while (LIE[[i]]$Apic[m]=="false"){
                        a<-LIE[[i]]$Prec[m]
                        b<-LIE[[i]]$Date[m]
                        if (b<=numdate[j]) {segments(x0=LIE[[i]]$Z[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$Z[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)}
                        m<-LIE[[i]]$Suiv[m]}
                      if (LIE[[i]]$Apic[m]=="true"){
                        a<-LIE[[i]]$Prec[m]
                        b<-LIE[[i]]$Date[m]
                        if (b<=numdate[j]) {segments(x0=LIE[[i]]$Z[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$Z[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)}}}}}}}}}}
      
      if (finalscale==FALSE){
        for (j in 1:length(numdate)){
          Date=NULL
          Num=NULL
          Suiv=NULL
          Prec=NULL
          X=NULL
          Y=NULL
          if ("Z" %in% colnames(LIE[[i]])) {Z=NULL}
          if (!("Z" %in% colnames(LIE[[i]]))) {subset.LIE<-subset(LIE[[i]], Date<=numdate[j], select=c(Num, Date, Suiv, Prec, X, Y))} else {subset.LIE<-subset(LIE[[i]], Date<=numdate[j], select=c(Num, Date, Suiv, Prec, X, Y, Z))}
          LIE[[i]]$X<-LIE[[i]]$X-min(subset.LIE$X)
          LIE[[i]]$Y<-LIE[[i]]$Y-min(subset.LIE$Y)
          if ("Z" %in% colnames(LIE[[i]])) {LIE[[i]]$Z<-LIE[[i]]$Z-min(subset.LIE$Z)}
          subset.LIE$X<-subset.LIE$X-min(subset.LIE$X)
          subset.LIE$Y<-subset.LIE$Y-min(subset.LIE$Y)
          if ("Z" %in% colnames(LIE[[i]])){subset.LIE$Z<-subset.LIE$Z-min(subset.LIE$Z)}
          minx<-min(subset.LIE$X)
          maxx<-max(subset.LIE$X)
          miny<-min(subset.LIE$Y)
          maxy<-max(subset.LIE$Y)
          if ("Z" %in% colnames(LIE[[i]])){
            minz<-min(subset.LIE$Z)
            maxz<-max(subset.LIE$Z)}
          if (is.null(main)==TRUE){main1<-paste(filenameslie[i], "-numdate=", numdate[j], sep="")} else {main1<-main}
          if (is.null(xlim)==TRUE){xlim1<-c(minx,maxx)} else {xlim1<-xlim}
          if (is.null(ylim)==TRUE){ylim1<-c(maxy,miny)} else {ylim1<-ylim}
          if ("Z" %in% colnames(LIE[[i]]) & is.null(zlim)==TRUE){zlim1<-c(minz,maxz)} else {zlim1<-zlim}
          if (is.null(xlab)==TRUE){xlab1<-paste("X (", unitlength, ")", sep="")} else {xlab1<-xlab}
          if (is.null(ylab)==TRUE){ylab1<-paste("Y (", unitlength, ")", sep="")} else {ylab1<-ylab}
          if ("Z" %in% colnames(LIE[[i]]) & is.null(zlab)==TRUE){zlab1<-paste("Z (", unitlength, ")", sep="")} else {zlab1<-zlab}
          
          if (!("Z" %in% colnames(LIE[[i]]))){
          
          plot(LIE[[i]]$X[1], LIE[[i]]$Y[1], type="n", xlim=xlim1, ylim=ylim1, main=main1, xlab=xlab1, ylab=ylab1,...)
          r<-0
          for (k in 1:nrow(LIE[[i]])){
            if(LIE[[i]]$Bran[k]=="true"){
              r<-r+1
              a<-LIE[[i]]$Prec[k]
              b<-LIE[[i]]$Date[k]
              if (a!=0 & b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[k],y1=LIE[[i]]$Y[k], col=colors[r,b],...)}
              m<-LIE[[i]]$Suiv[k]
              if (m!=0){
              while (LIE[[i]]$Apic[m]=="false"){
                a<-LIE[[i]]$Prec[m]
                b<-LIE[[i]]$Date[m]
                if (b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)}
                m<-LIE[[i]]$Suiv[m]}
              if (LIE[[i]]$Apic[m]=="true"){
                a<-LIE[[i]]$Prec[m]
                b<-LIE[[i]]$Date[m]
                if (b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)}}}}}}
          
          else {
            
            if (is.null(twod)==TRUE){
            
            LIE[[i]]$col<-colors[as.matrix(LIE[[i]][,c("root", "Date")])]
            dataroot1<-LIE[[i]][LIE[[i]]$Date<=numdate[j],]
            root<-sum(dataroot1$Bran=="true")
            if (root>1) {
              end<-which(dataroot1$Bran=="true")-1
              end<-end[-1]
              end[length(end)+1]<-nrow(dataroot1)}
            else {end<-nrow(dataroot1)}
            
            if (!requireNamespace("rgl", quietly = TRUE)) {
              stop("3D plotting with archigrow() requires package `rgl`. Please install it and try again.")}
            
            rgl::open3d()
            rgl::plot3d(x=LIE[[i]]$X[1], y=LIE[[i]]$Y[1], z=LIE[[i]]$Z[1], type="n", xlim=xlim1, ylim=ylim1, zlim=zlim1, main=main1, ylab=ylab1, xlab=xlab1, zlab=zlab1,...)
            
            for (k in 1:root){
              if (k==1) {
                dataroot<-as.matrix(dataroot1[k:end[k],c(7:9, ncol(LIE[[i]]))])} 
              else {
                if (dataroot1$Prec[end[k-1]+1]!=0){
                  dataroot<-as.matrix(dataroot1[(end[k-1]+1):end[k],c(7:9, ncol(LIE[[i]]))])
                  dataroot<-rbind(dataroot1[dataroot1$Num==dataroot1$Prec[end[k-1]+1],c(7:9, ncol(LIE[[i]]))], dataroot)}
                else{
                  dataroot<-as.matrix(dataroot1[(end[k-1]+1):end[k],c(7:9, ncol(LIE[[i]]))])}}
              
              rgl::lines3d(dataroot[,1:3], col=dataroot[,4], smooth=FALSE, ...)}}
            
            else {
              
              if (all.equal(twod, c("x", "y"))==TRUE) {
                
                plot(LIE[[i]]$X[1], LIE[[i]]$Y[1], type="n", xlim=xlim1, ylim=ylim1, main=main1, ylab=ylab1, xlab=xlab1,...)
                r<-0
                for (k in 1:nrow(LIE[[i]])){
                  if(LIE[[i]]$Bran[k]=="true"){
                    r<-r+1
                    a<-LIE[[i]]$Prec[k]
                    b<-LIE[[i]]$Date[k]
                    if (a!=0 & b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[k],y1=LIE[[i]]$Y[k], col=colors[r,b],...)}
                    m<-LIE[[i]]$Suiv[k]
                    if (m!=0){
                      while (LIE[[i]]$Apic[m]=="false"){
                        a<-LIE[[i]]$Prec[m]
                        b<-LIE[[i]]$Date[m]
                        if (b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)}
                        m<-LIE[[i]]$Suiv[m]}
                      if (LIE[[i]]$Apic[m]=="true"){
                        a<-LIE[[i]]$Prec[m]
                        b<-LIE[[i]]$Date[m]
                        if (b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)}}}}}}
              
              if (all.equal(twod, c("x", "z"))==TRUE){
                
                plot(LIE[[i]]$X[1], LIE[[i]]$Z[1], type="n", xlim=xlim1, ylim=zlim1, main=main1, ylab=zlab1, xlab=xlab1,...)
                r<-0
                for (k in 1:nrow(LIE[[i]])){
                  if(LIE[[i]]$Bran[k]=="true"){
                    r<-r+1
                    a<-LIE[[i]]$Prec[k]
                    b<-LIE[[i]]$Date[k]
                    if (a!=0 & b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Z[a],x1=LIE[[i]]$X[k],y1=LIE[[i]]$Z[k], col=colors[r,b],...)}
                    m<-LIE[[i]]$Suiv[k]
                    if (m!=0){
                      while (LIE[[i]]$Apic[m]=="false"){
                        a<-LIE[[i]]$Prec[m]
                        b<-LIE[[i]]$Date[m]
                        if (b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Z[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Z[m], col=colors[r,b],...)}
                        m<-LIE[[i]]$Suiv[m]}
                      if (LIE[[i]]$Apic[m]=="true"){
                        a<-LIE[[i]]$Prec[m]
                        b<-LIE[[i]]$Date[m]
                        if (b<=numdate[j]) {segments(x0=LIE[[i]]$X[a],y0=LIE[[i]]$Z[a],x1=LIE[[i]]$X[m],y1=LIE[[i]]$Z[m], col=colors[r,b],...)}}}}}}
              
              if (all.equal(twod, c("y", "z"))==TRUE){
                
                plot(LIE[[i]]$Z[1], LIE[[i]]$Y[1], type="n", xlim=zlim1, ylim=ylim1, main=main1, ylab=ylab1, xlab=zlab1,...)
                r<-0
                for (k in 1:nrow(LIE[[i]])){
                  if(LIE[[i]]$Bran[k]=="true"){
                    r<-r+1
                    a<-LIE[[i]]$Prec[k]
                    b<-LIE[[i]]$Date[k]
                    if (a!=0 & b<=numdate[j]) {segments(x0=LIE[[i]]$Z[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$Z[k],y1=LIE[[i]]$Y[k], col=colors[r,b],...)}
                    m<-LIE[[i]]$Suiv[k]
                    if (m!=0){
                      while (LIE[[i]]$Apic[m]=="false"){
                        a<-LIE[[i]]$Prec[m]
                        b<-LIE[[i]]$Date[m]
                        if (b<=numdate[j]) {segments(x0=LIE[[i]]$Z[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$Z[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)}
                        m<-LIE[[i]]$Suiv[m]}
                      if (LIE[[i]]$Apic[m]=="true"){
                        a<-LIE[[i]]$Prec[m]
                        b<-LIE[[i]]$Date[m]
                        if (b<=numdate[j]) {segments(x0=LIE[[i]]$Z[a],y0=LIE[[i]]$Y[a],x1=LIE[[i]]$Z[m],y1=LIE[[i]]$Y[m], col=colors[r,b],...)}}}}}}}}}}}}}
        
          return(GRlist)}