Arothron: Geometric Morphometrics Analyses

#' dec.curve
#'
#' This function computes the order of points on a open 3D curve and finds intermediate points
#' @param mat_input numeric: a kx3 matrix
#' @param mag numeric: how many times will be divided by the number of initial points
#' @param plot logical: if TRUE will be plotted the starting and final point matrices
#' @return matt numeric: a kx3 matrix with points coordinates 
#' @author Antonio Profico, Alessio Veneziano, Marina Melchionna, Pasquale Raia
#' @examples
#' \dontrun{
#' ## Create and plot a 3D curve
#' require(compositions)
#' curve_3D<-cbind(1:10,seq(1,5,length=10),rnorm(10,sd = 0.2))
#' plot3D(curve_3D,bbox=FALSE)
#' rgl.close()
#' ## Create and plot the new 3D curve (with intermediate points)
#' dec_curve_3D<-dec.curve(curve_3D, 2, plot = TRUE)
#' }
#' @export
dec.curve<-function(mat_input,mag,plot=TRUE){
matt<-mat_input
for(j in 1:mag){
magn_j=NULL
for(i in 1:((dim(matt)[1])-1)){
magn_j<-c((as.numeric(matt[i,])+as.numeric(matt[i+1,]))/2,magn_j)
}
matt_1_junk<-matrix(magn_j,ncol=3,byrow=T)
matt_1_mat<-rbind(matt,matt_1_junk)
orig<-1:dim(matt)[1]
deri<-(dim(matt)[1]*2-1):(dim(matt)[1]+1)
reordered<-NULL
for(i in 1:dim(matt)[1]){
reordered<-c(reordered,orig[i],deri[i])
}
reordered<-reordered[-length(reordered)]
matt<-matt_1_mat[reordered,]
}
if(plot=="TRUE"){
compositions::plot3D(mat_input,cex=1,col=2) 
compositions::plot3D(matt,cex=0.5,col=3,add=TRUE)}
return(matt)}