diff --git a/NEWS.md b/NEWS.md
diff --git a/R/autocor.r b/R/autocor.r
@@ -1,123 +1,191 @@
-#
-#  growth : A Library of Normal Distribution Growth Curve Models
-#  Copyright (C) 1998, 1999, 2000, 2001 J.K. Lindsey
-#
-#  This program is free software; you can redistribute it and/or modify
-#  it under the terms of the GNU General Public Licence as published by
-#  the Free Software Foundation; either version 2 of the Licence, or
-#  (at your option) any later version.
-#
-#  This program is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#  GNU General Public Licence for more details.
-#
-#  You should have received a copy of the GNU General Public Licence
-#  along with this program; if not, write to the Free Software
-#  Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-#
-#  SYNOPSIS
-#
-#     pergram(y)
-#     corgram(y, wt=1, add=FALSE, lty=1, xlim=NULL, ylim=NULL, xlab=NULL,
-#		ylab=NULL, main=NULL)
-#
-#  DESCRIPTION
-#
-#    Functions to compute and plot correlograms and periodograms
-
-### periodogram functions
-###
-pergram <- function(y){
-	ll <- length(y)
-	len <- trunc(ll/2)
-	len1 <- if(ll==2*len)len+1 else len+2
-	fc <- fft(y)
-	z <- cbind(2*pi*(1:len)/ll,
-		(Re(fc[ll:len1])^2+Im(fc[ll:len1])^2)*ll/4/pi)
-	class(z) <- "pergram"
-	z}
-
-#pergram <- function(y){
-#	ll <- length(y)
-#	len <- trunc(ll/2)
-#	fc <- matrix(0,ncol=2,nrow=ll)
-#	for(i in 1:ll){
-#		a <- 2*pi*i*(0:(ll-1))/ll
-#		fc[i,1] <- sum(y*sin(a))
-#		fc[i,2] <- sum(y*cos(a))}
-#	invisible(cbind(2*pi*(1:len)/ll,(fc[,1]^2+fc[,2]^2)*ll/4/pi))}
-
-plot.pergram <- function(y, add=FALSE, lty=1, xlab="Frequency",
-	ylab="Periodogram", main="Periodogram", ylim=c(0,max(po[,2]))){
-	if(inherits(y,"pergram"))po <- y
-	else po <- pergram(y)
-	if(add)lines(po[,1],po[,2],lty=lty)
-	else plot(po[,1],po[,2],xlim=c(0,3.6),xlab=xlab,ylab=ylab,type="l",
-		lty=lty,ylim=ylim)
-	invisible(po)}
-
-plot.cum <- function(z, ...) 
-	UseMethod("plot.cum")
-
-plot.cum.pergram <- function(y, xlab="Frequency", ylab="Periodogram",
-	main="Cumulative periodogram",
-	ylim=c(0,max(cpo+1.358/(a+0.12+0.11/a)))){
-	if(inherits(y,"pergram")){
-		len <- 2*dim(y)[1]
-		po <- y}
-	else {
-		len <- length(y)
-		po <- pergram(y)}
-	cpo <- cumsum(po[,2])
-	cpo <- cpo/max(cpo)
-	a <- sqrt(len)
-	pa <- 2*pi*(1:length(cpo))/len
-	x <- (1:dim(po)[1])/dim(po)[1]
-	plot(po[,1],cpo,xlim=c(0,3.6),xlab=xlab,ylab=ylab,type="l",
-		ylim=ylim,main=main)
-	lines(po[,1],x+1.358/(a+0.12+0.11/a),lty=3)
-	lines(po[,1],x-1.358/(a+0.12+0.11/a),lty=3)}
-###
-### correlogram function
-###
-corgram <- function(y, wt=1, maxlag=NULL, partial=FALSE, add=FALSE, lty=1,
-	xlim=NULL, ylim=NULL, xlab=NULL, ylab=NULL, main=NULL, ...){
-	if(any(wt!=0&&wt!=1))stop("weigts must be 0 or 1")
-	len <- length(y)
-	if(length(wt)==1)wt <- rep(1,len)
-	if(any(is.na(y)))wt[is.na(y)] <- 0
-	wt <- wt>0
-	num <- sum(wt)
-	limit <- 2/sqrt(num)
-	if(is.null(maxlag))maxlag <- trunc(num/4)
-	ave <- sum(y*wt,na.rm=TRUE)/num
-	var <- sum((y-ave)^2*wt,na.rm=TRUE)/(num-1)
-	co <- rep(1,maxlag+1)
-	for(lag in 1:maxlag)
-		co[lag+1] <- sum((y[1:(len-lag)]-ave)*(y[(lag+1):len]-ave)*
-			wt[1:(len-lag)]*wt[(lag+1):len],na.rm=TRUE)/
-			var/(sum(wt[1:(len-lag)]*wt[(lag+1):len],na.rm=TRUE)-1)
-	if(partial){
-		a <- tmp <- rep(0,maxlag)
-		a[1] <- tmp[1] <- co[2]
-		for(lag in 2:maxlag){
-			a[lag] <- tmp[lag] <- (co[lag+1]-sum(a[1:(lag-1)]*
-				co[lag:2]))/(1-sum(a[1:(lag-1)]*co[2:lag]))
-			a[1:(lag-1)] <- a[1:(lag-1)]-a[lag]*a[(lag-1):1]}
-		co <- tmp}
-	start <- if(partial)1 else 0
-	if(is.null(xlim))xlim <- c(0,maxlag)
-	if(is.null(ylim))ylim <- c(if(min(co)<0)min(c(min(co),-limit))else 0,1)
-	if(is.null(xlab))xlab <- "Lag"
-	if(is.null(ylab))ylab <- expression(rho)
-	if(is.null(main))main <- if(partial)"Partial Correlogram"
-		else"Correlogram"
-	if(add)lines(start:maxlag,co,lty=lty)
-	else {
-		plot(start:maxlag,co,type="l",lty=lty,xlim=xlim,ylim=ylim,
-			xlab=xlab,ylab=ylab,main=main,...)
-		abline(h=limit,lty=3)
-		if(min(co)<0)abline(h=-limit,lty=3)
-	abline(h=0)}
-	invisible(cbind(start:maxlag,co))}
+#
+#  growth : A Library of Normal Distribution Growth Curve Models
+#  Copyright (C) 1998, 1999, 2000, 2001 J.K. Lindsey
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public Licence as published by
+#  the Free Software Foundation; either version 2 of the Licence, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public Licence for more details.
+#
+#  You should have received a copy of the GNU General Public Licence
+#  along with this program; if not, write to the Free Software
+#  Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
+#
+#  SYNOPSIS
+#
+#     pergram(y)
+#     corgram(y, wt=1, add=FALSE, lty=1, xlim=NULL, ylim=NULL, xlab=NULL,
+#		ylab=NULL, main=NULL)
+#
+#  DESCRIPTION
+#
+#    Functions to compute and plot correlograms and periodograms
+
+### periodogram functions
+###
+
+
+#' Calculate and Plot a Periodogram
+#' 
+#' \code{pergram} calculates the values of a periodogram, \code{plot.pergram}
+#' plots it, and \code{plot.cum.pergram} plots the corresponding cumulative
+#' periodogram.
+#' 
+#' 
+#' @aliases pergram plot.pergram plot_cum plot_cum.pergram
+#' @param y A time series vector.
+#' @param add If TRUE, adds a new periodogram to an existing plot.
+#' @param x Plotting parameters
+#' @param lty Plotting parameters
+#' @param xlab Plotting parameters
+#' @param ylab Plotting parameters
+#' @param main Plotting parameters
+#' @param ylim Plotting parameters
+#' @param ... Plotting parameters
+#' @return \code{pergram} prints and returns a two-column matrix of class,
+#' \code{pergram}, containing the periodogram.
+#' @author J.K. Lindsey
+#' @keywords hplot
+#' @examples
+#' 
+#' y <- rnorm(100)
+#' print(z <- pergram(y))
+#' plot(z)
+#' plot_cum(z)
+#' 
+#' @export
+pergram <- function(y){
+	ll <- length(y)
+	len <- trunc(ll/2)
+	len1 <- if(ll==2*len)len+1 else len+2
+	fc <- fft(y)
+	z <- cbind(2*pi*(1:len)/ll,
+		(Re(fc[ll:len1])^2+Im(fc[ll:len1])^2)*ll/4/pi)
+	class(z) <- "pergram"
+	z}
+
+#pergram <- function(y){
+#	ll <- length(y)
+#	len <- trunc(ll/2)
+#	fc <- matrix(0,ncol=2,nrow=ll)
+#	for(i in 1:ll){
+#		a <- 2*pi*i*(0:(ll-1))/ll
+#		fc[i,1] <- sum(y*sin(a))
+#		fc[i,2] <- sum(y*cos(a))}
+#	invisible(cbind(2*pi*(1:len)/ll,(fc[,1]^2+fc[,2]^2)*ll/4/pi))}
+#' @describeIn pergram Plot method
+#' @export 
+plot.pergram <- function(x, add=FALSE, lty=1, xlab="Frequency",
+	ylab="Periodogram", main="Periodogram", ylim=c(0,max(po[,2])), ...){
+  y <- x
+	if(inherits(y,"pergram"))po <- y
+	else po <- pergram(y)
+	if(add)lines(po[,1],po[,2],lty=lty)
+	else plot(po[,1],po[,2],xlim=c(0,3.6),xlab=xlab,ylab=ylab,type="l",
+		lty=lty,ylim=ylim)
+	invisible(po)}
+
+#' @export 
+plot_cum <- function(x, ...) UseMethod("plot_cum")
+
+#' @describeIn pergram Plot_cum method
+#' @export 
+plot_cum.pergram <- function(x, xlab="Frequency", ylab="Periodogram",
+	main="Cumulative periodogram",
+	ylim=c(0,max(cpo+1.358/(a+0.12+0.11/a))), ...){
+  y <- x
+	if(inherits(y,"pergram")){
+		len <- 2*dim(y)[1]
+		po <- y}
+	else {
+		len <- length(y)
+		po <- pergram(y)}
+	cpo <- cumsum(po[,2])
+	cpo <- cpo/max(cpo)
+	a <- sqrt(len)
+	pa <- 2*pi*(1:length(cpo))/len
+	x <- (1:dim(po)[1])/dim(po)[1]
+	plot(po[,1],cpo,xlim=c(0,3.6),xlab=xlab,ylab=ylab,type="l",
+		ylim=ylim,main=main)
+	lines(po[,1],x+1.358/(a+0.12+0.11/a),lty=3)
+	lines(po[,1],x-1.358/(a+0.12+0.11/a),lty=3)}
+###
+### correlogram function
+###
+
+
+#' Calculate and Plot a Correlogram
+#' 
+#' \code{corgram} calculates the values of a correlogram (autocorrelation
+#' function or ACF) and plots it.
+#' 
+#' 
+#' @param y A time series vector.
+#' @param maxlag Maximum number of lags for which the correlation is to be
+#' calculated.
+#' @param partial If TRUE, the partial autocorrelation function (PACF) is
+#' plotted.
+#' @param wt Indicator vector with zeros for values to be ignored.
+#' @param add If TRUE, adds a new correlogram to an existing plot.
+#' @param xlim Plotting parameters
+#' @param lty Plotting parameters
+#' @param xlab Plotting parameters
+#' @param ylab Plotting parameters
+#' @param main Plotting parameters
+#' @param ylim Plotting parameters
+#' @param ... Plotting parameters
+#' @return \code{corgram} returns a two-column matrix containing the (partial)
+#' correlogram coordinates.
+#' @author J.K. Lindsey
+#' @keywords hplot
+#' @examples
+#' 
+#' y <- rnorm(100)
+#' corgram(y)
+#' corgram(y, partial=TRUE)
+#' @export
+corgram <- function(y, wt=1, maxlag=NULL, partial=FALSE, add=FALSE, lty=1,
+	xlim=NULL, ylim=NULL, xlab=NULL, ylab=NULL, main=NULL, ...){
+	if(any(wt!=0&&wt!=1))stop("weights must be 0 or 1")
+	len <- length(y)
+	if(length(wt)==1)wt <- rep(1,len)
+	if(any(is.na(y)))wt[is.na(y)] <- 0
+	wt <- wt>0
+	num <- sum(wt)
+	limit <- 2/sqrt(num)
+	if(is.null(maxlag))maxlag <- trunc(num/4)
+	ave <- sum(y*wt,na.rm=TRUE)/num
+	var <- sum((y-ave)^2*wt,na.rm=TRUE)/(num-1)
+	co <- rep(1,maxlag+1)
+	for(lag in 1:maxlag)
+		co[lag+1] <- sum((y[1:(len-lag)]-ave)*(y[(lag+1):len]-ave)*
+			wt[1:(len-lag)]*wt[(lag+1):len],na.rm=TRUE)/
+			var/(sum(wt[1:(len-lag)]*wt[(lag+1):len],na.rm=TRUE)-1)
+	if(partial){
+		a <- tmp <- rep(0,maxlag)
+		a[1] <- tmp[1] <- co[2]
+		for(lag in 2:maxlag){
+			a[lag] <- tmp[lag] <- (co[lag+1]-sum(a[1:(lag-1)]*
+				co[lag:2]))/(1-sum(a[1:(lag-1)]*co[2:lag]))
+			a[1:(lag-1)] <- a[1:(lag-1)]-a[lag]*a[(lag-1):1]}
+		co <- tmp}
+	start <- if(partial)1 else 0
+	if(is.null(xlim))xlim <- c(0,maxlag)
+	if(is.null(ylim))ylim <- c(if(min(co)<0)min(c(min(co),-limit))else 0,1)
+	if(is.null(xlab))xlab <- "Lag"
+	if(is.null(ylab))ylab <- expression(rho)
+	if(is.null(main))main <- if(partial)"Partial Correlogram"
+		else"Correlogram"
+	if(add)lines(start:maxlag,co,lty=lty)
+	else {
+		plot(start:maxlag,co,type="l",lty=lty,xlim=xlim,ylim=ylim,
+			xlab=xlab,ylab=ylab,main=main,...)
+		abline(h=limit,lty=3)
+		if(min(co)<0)abline(h=-limit,lty=3)
+	abline(h=0)}
+	invisible(cbind(start:maxlag,co))}
diff --git a/R/carma.r b/R/carma.r
diff --git a/R/elliptic.r b/R/elliptic.r
diff --git a/R/potthoff.r b/R/potthoff.r
diff --git a/R/rmaov.r b/R/rmaov.r
@@ -1,95 +1,135 @@
-#
-#  growth : A Library of Normal Distribution Growth Curve Models
-#  Copyright (C) 1998, 1999, 2000, 2001 J.K. Lindsey
-#
-#  This program is free software; you can redistribute it and/or modify
-#  it under the terms of the GNU General Public Licence as published by
-#  the Free Software Foundation; either version 2 of the Licence, or
-#  (at your option) any later version.
-#
-#  This program is distributed in the hope that it will be useful,
-#  but WITHOUT ANY WARRANTY; without even the implied warranty of
-#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#  GNU General Public Licence for more details.
-#
-#  You should have received a copy of the GNU General Public Licence
-#  along with this program; if not, write to the Free Software
-#  Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-#
-#  SYNOPSIS
-#
-#     rmaov(response, tvcov=NULL, ccov=NULL, analysis=TRUE)
-#
-#  DESCRIPTION
-#
-#    Function to calculate the ANOVA table for a balanced split-plot design
-#    Copyright (C) 1999 Ralf Goertz (ralf.goertz@uni-jena.de)
-
-rmaov <- function(response, tvcov=NULL, ccov=NULL, analysis=TRUE){
-	if(!is.matrix(response)||!is.numeric(response))stop("response must be a matrix")
-	if(is.null(tvcov)){
-		nfac <- 1
-		nrep <- nlev <- dim(response)[2]
-		rfacname <- "repfac"}
-	else if(is.vector(tvcov,mode="numeric")||is.factor(tvcov)){
-		nfac <- 1
-		nrep <- nlev <- length(unique(tvcov))
-		rfacname <- paste(deparse(substitute(tvcov)))
-		tvcov <- as.data.frame(tvcov)}
-	else if(is.data.frame(tvcov)||is.matrix(tvcov)){
-		nfac <- dim(tvcov)[2]
-		if(!is.null(colnames(tvcov)))rfacname <- colnames(tvcov)
-		else rfacname <- paste("repfac",1:dim(tvcov)[2],sep="")
-		nlev <- NULL
-		nrep <- 1
-		for(i in 1:dim(tvcov)[2]){
-			nlev <- c(nlev,length(unique(tvcov[,i])))
-			nrep <- nrep*nlev[i]}}
-	else stop("If specified, tvcov must be a vector, matrix, or dataframe containing the repeated factors")
-	if(is.vector(ccov,mode="numeric")||is.factor(ccov)){
-		tmp <- paste(deparse(substitute(ccov)))
-		ccov <- list(ccov)
-		names(ccov) <- tmp}
-	else if(is.matrix(ccov))ccov <- data.frame(ccov)
-	else if(is.list(ccov)&&!is.data.frame(ccov))for(i in 1:length(ccov))
-		if(is.matrix(ccov[[i]]))ccov[[i]] <- as.vector(t(ccov[[i]]))
-	else if(!is.null(ccov))print("ccov must be a vector, matrix, dataframe, or list of time-constant covariates")
-	ncases <- dim(response)[2]*dim(response)[1]
-	if(nrep!=dim(response)[2])
-		stop("Number of columns in response must match product of levels")
-	block <- gl(dim(response)[1],nrep)
-	nc <- n <- dim(response)[2]
-	response <- as.vector(t(response))
-	for(i in 1:nfac){
-		n <- n/nlev[i]
-		com <- paste("fm",as.character(i),"<-gl(nlev[i],n,ncases",sep="")
-		if(!is.null(levels(tvcov[,i])))
-			com <- paste(com,",labels=levels(tvcov[,i])",sep="")
-		com <- paste(com,")\n",sep="")
-		eval(parse(text=com))}
-	if(!is.null(ccov)){
-		tccov <- ccov
-		if(length(tccov[[1]])!=ncases)for(i in 1:length(tccov)){
-			if(!is.factor(tccov[[i]]))
-				tccov[[i]] <- as.factor(tccov[[i]])
-			ccov[[i]] <- gl(nlevels(tccov[[i]]),1,ncases,labels=levels(tccov[[i]]))
-			ccov[[i]][(rep(1:length(tccov[[i]]),rep(nc,length(tccov[[i]])))-1)*nc+rep(1:nc,length(tccov[[i]]))] <- tccov[[i]][rep(1:length(tccov[[i]]),rep(nc,length(tccov[[i]])))]}}
-	com <- paste("b<-data.frame(response=response,block=block")
-	for(i in 1:nfac)com <- paste(com,",",rfacname[i],"=fm",as.character(i),sep="")
-	if(!is.null(ccov)){
-		if(is.null(names(ccov)))
-			names(ccov) <- paste("ccov",1:length(ccov),sep="")
-		for(i in 1:length(ccov))
-			com <- paste(com,",",names(ccov)[i],"=ccov$",names(ccov)[i],sep="")}
-	com <- paste(com,")\n",sep="")
-	eval(parse(text=com))
-	if(!analysis)return(b)
-	efacterm <- facterm <- paste(rfacname,collapse="*")
-	if(!is.null(ccov))
-		for(i in 1:length(ccov))
-			facterm <- paste(facterm,names(ccov)[i],sep="*")
-	com <- paste("res<-aov(response~",facterm,"+Error(block/(",efacterm,")),data=b)\n",sep="")
-	eval(parse(text=com))
-	res}
-
-
+#
+#  growth : A Library of Normal Distribution Growth Curve Models
+#  Copyright (C) 1998, 1999, 2000, 2001 J.K. Lindsey
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public Licence as published by
+#  the Free Software Foundation; either version 2 of the Licence, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public Licence for more details.
+#
+#  You should have received a copy of the GNU General Public Licence
+#  along with this program; if not, write to the Free Software
+#  Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
+#
+#  SYNOPSIS
+#
+#     rmaov(response, tvcov=NULL, ccov=NULL, analysis=TRUE)
+#
+#  DESCRIPTION
+#
+#    Function to calculate the ANOVA table for a balanced split-plot design
+#    Copyright (C) 1999 Ralf Goertz (ralf.goertz@uni-jena.de)
+
+
+
+#' Split-plot ANOVA Model
+#' 
+#' \code{rmaov} performs the classical balanced split-plot ANOVA, with
+#' \code{summary} providing the table. This is the so-called repeated measures
+#' ANOVA.
+#' 
+#' For unbalanced data, \code{\link[growth]{elliptic}} will perform the
+#' analysis for one or two levels of nesting.
+#' 
+#' 
+#' @param response A matrix or dataframe of response values with units as rows
+#' and repeated measures as columns.
+#' @param tvcov A numeric vector or factor variable defining the clusters. If
+#' there are several levels of nesting, a matrix or dataframe with columns of
+#' such variables defining the nested clusters starting with the highest level
+#' (that is, from slowest to fastest varying). If not provided, each response
+#' value of a unit is assumed to belong to a different cluster (that is, one
+#' factor with \code{ncol(response)} levels is assumed).
+#' @param ccov A vector or factor variable for one inter-subject covariate or a
+#' matrix, dataframe, or list of several such variables.
+#' @param analysis If FALSE, the design matrix is set up, but the analysis is
+#' not performed.
+#' @return The fitted model is returned.
+#' @author Ralf Goertz (ralf.goertz@@uni-jena.de)
+#' @seealso \code{\link[growth]{carma}}, \code{\link[growth]{elliptic}},
+#' \code{\link{lm}}, \code{\link[growth]{potthoff}}.
+#' @keywords models
+#' @examples
+#' 
+#' # vision data for 7 individuals, with response a 7x8 matrix
+#' # two levels of nesting: 4 levels of power for each eye
+#' y <- matrix(rnorm(56),ncol=8)
+#' tvc <- data.frame(eye=c(rep(1,4),rep(2,4)),power=c(1:4,1:4))
+#' summary(rmaov(y, tvc))
+#' 
+#' @export rmaov
+rmaov <- function(response, tvcov=NULL, ccov=NULL, analysis=TRUE){
+	if(!is.matrix(response)||!is.numeric(response))stop("response must be a matrix")
+	if(is.null(tvcov)){
+		nfac <- 1
+		nrep <- nlev <- dim(response)[2]
+		rfacname <- "repfac"}
+	else if(is.vector(tvcov,mode="numeric")||is.factor(tvcov)){
+		nfac <- 1
+		nrep <- nlev <- length(unique(tvcov))
+		rfacname <- paste(deparse(substitute(tvcov)))
+		tvcov <- as.data.frame(tvcov)}
+	else if(is.data.frame(tvcov)||is.matrix(tvcov)){
+		nfac <- dim(tvcov)[2]
+		if(!is.null(colnames(tvcov)))rfacname <- colnames(tvcov)
+		else rfacname <- paste("repfac",1:dim(tvcov)[2],sep="")
+		nlev <- NULL
+		nrep <- 1
+		for(i in 1:dim(tvcov)[2]){
+			nlev <- c(nlev,length(unique(tvcov[,i])))
+			nrep <- nrep*nlev[i]}}
+	else stop("If specified, tvcov must be a vector, matrix, or dataframe containing the repeated factors")
+	if(is.vector(ccov,mode="numeric")||is.factor(ccov)){
+		tmp <- paste(deparse(substitute(ccov)))
+		ccov <- list(ccov)
+		names(ccov) <- tmp}
+	else if(is.matrix(ccov))ccov <- data.frame(ccov)
+	else if(is.list(ccov)&&!is.data.frame(ccov))for(i in 1:length(ccov))
+		if(is.matrix(ccov[[i]]))ccov[[i]] <- as.vector(t(ccov[[i]]))
+	else if(!is.null(ccov))print("ccov must be a vector, matrix, dataframe, or list of time-constant covariates")
+	ncases <- dim(response)[2]*dim(response)[1]
+	if(nrep!=dim(response)[2])
+		stop("Number of columns in response must match product of levels")
+	block <- gl(dim(response)[1],nrep)
+	nc <- n <- dim(response)[2]
+	response <- as.vector(t(response))
+	for(i in 1:nfac){
+		n <- n/nlev[i]
+		com <- paste("fm",as.character(i),"<-gl(nlev[i],n,ncases",sep="")
+		if(!is.null(levels(tvcov[,i])))
+			com <- paste(com,",labels=levels(tvcov[,i])",sep="")
+		com <- paste(com,")\n",sep="")
+		eval(parse(text=com))}
+	if(!is.null(ccov)){
+		tccov <- ccov
+		if(length(tccov[[1]])!=ncases)for(i in 1:length(tccov)){
+			if(!is.factor(tccov[[i]]))
+				tccov[[i]] <- as.factor(tccov[[i]])
+			ccov[[i]] <- gl(nlevels(tccov[[i]]),1,ncases,labels=levels(tccov[[i]]))
+			ccov[[i]][(rep(1:length(tccov[[i]]),rep(nc,length(tccov[[i]])))-1)*nc+rep(1:nc,length(tccov[[i]]))] <- tccov[[i]][rep(1:length(tccov[[i]]),rep(nc,length(tccov[[i]])))]}}
+b <- NULL
+		com <- paste("b<-data.frame(response=response,block=block")
+	for(i in 1:nfac)com <- paste(com,",",rfacname[i],"=fm",as.character(i),sep="")
+	if(!is.null(ccov)){
+		if(is.null(names(ccov)))
+			names(ccov) <- paste("ccov",1:length(ccov),sep="")
+		for(i in 1:length(ccov))
+			com <- paste(com,",",names(ccov)[i],"=ccov$",names(ccov)[i],sep="")}
+	com <- paste(com,")\n",sep="")
+	eval(parse(text=com))
+	if(!analysis)return(b)
+	efacterm <- facterm <- paste(rfacname,collapse="*")
+	if(!is.null(ccov))
+		for(i in 1:length(ccov))
+			facterm <- paste(facterm,names(ccov)[i],sep="*")
+	res <- NULL
+	com <- paste("res<-aov(response~",facterm,"+Error(block/(",efacterm,")),data=b)\n",sep="")
+	eval(parse(text=com))
+	res}
+
+
diff --git a/README.md b/README.md
@@ -0,0 +1,10 @@
+
+<!-- README.md is generated from README.Rmd. Please edit README.Rmd -->
+[![Travis-CI Build Status](https://travis-ci.org/swihart/growth.svg?branch=master)](https://travis-ci.org/swihart/growth) [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/growth)](https://cran.r-project.org/package=growth) ![downloads](http://cranlogs.r-pkg.org/badges/grand-total/growth)
+
+`growth` R package
+==================
+
+This package is intended to be the developmental version to the CRAN version of [Jim Lindsey's growth](http://www.commanster.eu/rcode.html). The .zip files listed on his homepage have been listed as version 1.0 since 2005. For the subsequent maintenance on this github and CRAN, we will start at 1.1.
+
+To compare this version with the static v1.0 files on [Jim Lindsey's Homepage](http://www.commanster.eu/rcode.html), it may be useful to use [the compare page for this repo's two branches](https://github.com/swihart/growth/compare/jim-lindsey-homepage-version-1.0...master?diff=split&name=master).
diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1,69 @@
+# growth R package
+Bruce Swihart  
+Feb 2019
+
+## Re-Submission 1
+
+  * fixed an `Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’` NOTE.  
+  * corrected Fatal error: length > 1 in coercion to logical (raised on R-devel check)
+
+## Test environments
+* local OS X install: R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
+* Ubuntu 14.04.5 LTS (on travis-ci): R version 3.5.2 (2017-01-27)
+* win-builder: R Under development (unstable) (2019-01-31 r76038)
+
+## R CMD check results
+There were no ERRORs or WARNINGs or NOTEs.
+
+
+## Downstream dependencies
+There are currently no downstream dependencies for this package.
+
+
+
+# growth R package
+Bruce Swihart  
+December 2016
+
+## Test environments
+* local OS X install: R version 3.3.2 (2016-10-31)
+* ubuntu 12.04 (on travis-ci): R version 3.3.1 (2016-06-21)
+* win-builder:        R Under development (unstable) (2016-12-05 r71733)
+
+## R CMD check results
+There were no ERRORs or WARNINGs. 
+
+There was 1 NOTE:
+
+* 1st submission (Package was archived on CRAN, see Miscellaneous)
+
+## Downstream dependencies
+There are currently no downstream dependencies for this package.
+
+## Miscellaneous
+As per the CRAN Repository Policy Version Revision 3577,
+
+  *  Explain any change in the maintainer’s email address and if possible send confirmation from the previous address (by a separate email to CRAN@R-project.org) or explain why it is not possible. 
+
+This Package was archived on CRAN.  I am resurrecting it.
+I have Jim Lindsey's permission to be maintainer of his packages on CRAN.  Currently he has them in .zip files on his homepage:  http://www.commanster.eu/rcode.html.  He does not have access to the original email address he used when this package was on CRAN, and thus cannot send a separate confirmation email.  However, you can contact him at James Lindsey <jlindsey@gen.unimaas.nl>.  
+
+He sent this confirmation message on 2016-11-24:
+
+---------- Forwarded message ----------
+From: James Lindsey <jlindsey@gen.unimaas.nl>
+Date: Thu, Nov 24, 2016 at 9:26 AM
+Subject: transferring maintainer role to Bruce Swihart for 'rmutil', 'repeated', 'gnlm', 'growth', 'event', 'stable'
+To: CRAN@r-project.org, ligges@statistik.tu-dortmund.de, Kurt.Hornik@wu.ac.at
+Cc: bruce.swihart@gmail.com
+
+
+Dear CRAN,
+
+Bruce Swihart is taking on the role of maintainer for my R-packages which have been available on my homepage, http://www.commanster.eu/rcode.html.  Some of these R-packages were on CRAN but have since been archived. 
+I know it is CRAN repository policy to email confirmation from the previous maintainer's email address (jlindsey@luc.ac.be), but alas I can't due to LUC changing its name.
+
+Please accept this email as confirmation of the maintainer role changing for R packages 'rmutil', 'repeated', 'gnlm', 'growth', 'event', 'stable'.
+
+Regards,
+Jim Lindsey
diff --git a/man/carma.Rd b/man/carma.Rd
diff --git a/man/corgram.Rd b/man/corgram.Rd
diff --git a/man/elliptic.Rd b/man/elliptic.Rd
diff --git a/man/growth.Rd b/man/growth.Rd
diff --git a/man/pergram.Rd b/man/pergram.Rd
diff --git a/man/potthoff.Rd b/man/potthoff.Rd
diff --git a/man/rmaov.Rd b/man/rmaov.Rd
diff --git a/src/Makefile b/src/Makefile
diff --git a/src/elliptic.f b/src/elliptic.f
diff --git a/src/growth_init.c b/src/growth_init.c
@@ -0,0 +1,33 @@
+#include <R_ext/RS.h>
+#include <stdlib.h> // for NULL
+#include <R_ext/Rdynload.h>
+
+/* FIXME: 
+   Check these declarations against the C/Fortran source code.
+*/
+
+/* .Fortran calls */
+extern void F77_NAME(back)(void *, void *);
+extern void F77_NAME(kalman)(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern void F77_NAME(plra)(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern void F77_NAME(resid)(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern void F77_NAME(resid2)(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern void F77_NAME(roots)(void *, void *, void *);
+extern void F77_NAME(ttvert)(void *, void *);
+
+static const R_FortranMethodDef FortranEntries[] = {
+    {"back",   (DL_FUNC) &F77_NAME(back),    2},
+    {"kalman", (DL_FUNC) &F77_NAME(kalman), 25},
+    {"plra",   (DL_FUNC) &F77_NAME(plra),   43},
+    {"resid",  (DL_FUNC) &F77_NAME(resid),  24},
+    {"resid2", (DL_FUNC) &F77_NAME(resid2), 16},
+    {"roots",  (DL_FUNC) &F77_NAME(roots),   3},
+    {"ttvert", (DL_FUNC) &F77_NAME(ttvert),  2},
+    {NULL, NULL, 0}
+};
+
+void R_init_growth(DllInfo *dll)
+{
+    R_registerRoutines(dll, NULL, NULL, FortranEntries, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}