R/sequence_cor.R

In Sorbus-torminalis/twopointzerothree: Detects Duplicate Sequences of Offset Values

#' segment_cor
#' @description Finds correlation between all segments length n of a vector
#' @param vec numeric vector to test for possible offset duplicate sequences
#' @param n length of duplicate sequence to search for
#' @details Embeds the vector into low-dimensional Euclidean space and then finds correlation between all columns. Pairs of columns with a correlation of 1 are either duplicates or have an offset. 
#' @examples
#' set.seed(42) 
#' x <- rnorm(10)
#' x <- c(x, x[1:4] + 2.03)
#' sequence_cor(vec = x, n = 4)
#' @importFrom stats cor embed
#'    
#' @export

sequence_cor <- function(vec, n){ 
  if(!is.numeric(vec)){
    stop("vec must be numeric")
  }
  if(length(vec) <= n){
    stop("vec must be longer than n")
  }
  #embed
  em <- embed(vec, length(vec) - n + 1) 
  #reverse col order
  em <- em[, ncol(em):1]
  co <- cor(em)
  diag(co) <- NA
  attr(co, "len") <- n
  co
}