R/bounds.R

In RNAdecay: Maximum Likelihood Decay Modeling of RNA Degradation Data

#' calculates bounds for modeled parameters
#'
#' Calculates maximum and minimum bounds for parameter alpha based on experimental
#'   time points (t_0, t_1, t_2, t_3, ..., t_max). If RNA level is too low at t_1,
#'   then the decay has happened before our observations began - there is an upper
#'   bound to the decay rate we can detect (a_high).
#' If RNA level is too high at t_max, then relatively little decay has happened and
#'   we can not distinguish the decay rate and the decay of the decay rate  - there
#'   is a lower bound to the base decay rate of the decaying decay model (a_low).
#'
#' Similarly, limits on beta are required to prevent precude ranges in which the
#'   decay rate and decaing decay are indistinguishable. See vignette
#'   "RNAdecay_workflow" for more information.
#'
#' @param t_min time of first experiemtal time point after inhibition of
#'   transcription (not T0)
#' @param t_max time of last experimental time point
#'
#' @export
#'
#' @return returns the lowest/highest parameter values to be used as bounds on
#'   modeled parameters
#'
#' @examples
#' a_high(7.5)
#' a_low(480)
#' b_low(480)


a_high <- function(t_min) {
  signif(-(1 / t_min) * log(0.005), 2)
}

#' @rdname a_high
#' @export

a_low <- function(t_max) {
  10 ^ (floor(log(-(1 / t_max) * log(0.95), base = 10)))
}


#' @rdname a_high
#' @export

b_low <- function(t_max) {
  10 ^ (floor(log((1 / t_max), base = 10)))
}