R/make_data.R

In circacompare: Analyses of Circadian Data

#' @title make_data
#' @name make_data
#'
#' @description Generate example circadian data with specified phase shift between groups
#'
#' @param k mesor of group 1.
#' @param k1 change in mesor in group 2 from group 1.
#' @param alpha amplitude rhythm for group 1.
#' @param alpha1 change in amplitude in group 2 from group 1
#' @param phi phase of rhythm, in radian-hours, in group 1.
#' @param phi1 change in phase, in radian-hours, in group 2 from group 1
#' @param tau period of the rhythm, shared between both groups.
#' @param hours the number of hours/datapoints to sample.
#' @param noise_sd the standard deviation of the noise term.
#' @param seed random seed for generating data.
#' @return data.frame
#' @export
#'
#' @examples
#' data <- make_data(k1 = 3, alpha1 = 4, phi1 = 6)
make_data <- function(k = 0, k1 = 3, alpha = 10, alpha1 = 4, phi = 0, phi1 = 3.15, tau = 24, hours = 48, noise_sd = 0.1, seed = NULL) {
  if (!is.null(seed)) {
    withr::with_seed(seed, {
      return(make_data(
        k = k,
        k1 = k1,
        alpha = alpha,
        alpha1 = alpha1,
        phi = phi,
        phi1 = phi1,
        tau = tau,
        hours = hours,
        noise_sd = noise_sd
      ))
    })
  }
  g1 <- data.frame(
    time = rep(NA, hours),
    measure = rep(NA, hours)
  )
  g2 <- data.frame(
    time = rep(NA, hours),
    measure = rep(NA, hours)
  )
  V <- c(k = k, k1 = k1, alpha = alpha, alpha1 = alpha1, phi = phi, phi1 = phi1, tau = tau)
  eq_expression <- create_formula(grouped_params = c("k", "alpha", "phi"))$f_equation
  eval(parse(text = eq_expression$g1))
  eval(parse(text = eq_expression$g2))
  g1$time <- 1:hours
  g1$measure <- eq_1(g1$time) + stats::rnorm(n = hours, mean = 0, sd = noise_sd)
  g1$group <- "g1"
  g2$time <- 1:hours
  g2$measure <- eq_2(g2$time) + stats::rnorm(n = hours, mean = 0, sd = noise_sd)
  g2$group <- "g2"

  return(rbind(g1, g2))
}