R/IS.R

In junruidi/actigraphy: Feature Extraction from Minute Level Actigraphy Data

#' @title Interdaily Statbility
#' @description This function calcualte interdaily stability, a nonparametric metric
#' of circadian rhtymicity
#'
#' @param x  \code{data.frame} of dimension p by 1440, representing the p days of activity data for one subjectect
#' @return IS
#'
#'
#' @export
#'
#'
#' @examples
#' data(example_activity_data)
#' count1 = example_activity_data$count[c(1,2,3),-c(1,2)]
#' is = IS(x = count1)
#'
#'

IS = function(x){
  p = ncol(x)
  xh = colMeans(x)

  v = c(t(x))
  n = length(v)

  numerator = sum((xh - mean(v))^2)/p
  denominator = sum((v - mean(v))^2)/n

  return(numerator/denominator)
}


# bin_data = function(x, window = c(10,30,60,120)){
#   return(colSums(matrix(x, nrow = window)))
# }



# convert_2_hr = function(x){
#   hr = NULL
#   for(i in 1:24){
#     temp = x[,(60*(i-1)+1):(60*i)]
#     temp.i = rowSums(temp,na.rm = T)
#     hr = cbind(hr,temp.i)
#   }
#   hr = data.frame(hr)
#   names(hr) = paste0("hr",c(1:24))
#   return(hr)
# }