R/model-sigmoid-prior.R

In maomlab/BayesPharma: Tools for Bayesian Analysis of Non-Linear Pharmacology Models

#' Create a Prior an Agonist Sigmoid Model
#'
#' @description
#' Creates a `data.frame` of priors for the sigmoid agonist model
#'
#' If the function arguments `ec50`, `hill`, `top`, `bottom` are `NULL`, default
#' normal distribution priors will be set.
#'
#' If you would like to set a parameter as a constant, enter a numeric
#' value for the function argument.
#'
#' For other distribution options, reference [brms::prior] and [Prior Choice
#' Recommendations
#' ](https://github.com/stan-dev/stan/wiki/Prior-Choice-Recommendations)
#'
#'
#' @param ec50 [brms::brmsprior] or `numeric`. Prior for the `ec50`
#'  parameter. Setting ec50 to a numeric value constrains it to a constant
#'  value. Default: normal(-6, 2.5) where the mean -6 corresponds to a
#'  concentration of 1e-6 or 1 μM.
#' @param hill [brms::brmsprior] or `numeric`. Prior for the `hill`
#'  parameter. Default: `normal(1, 1)` with and a lower bound of
#'  `-0.1`.
#' @param top [brms::brmsprior] or `numeric` giving the prior for the `top`
#'  parameter. Setting `top` to a `numeric` constrains it to a constant
#'  value.
#' @param bottom [brms::brmsprior] or `numeric` giving the prior for the
#'  `bottom` parameter. Setting `bottom` to `numeric` constrains it to a
#'  constant value.
#' @param ... additional [brms::brmsprior] objects.
#' @returns [brms::brmsprior]
#'
#' @seealso [sigmoid_agonist_formula], [sigmoid_agonist_init], and
#'   [sigmoid_model]
#'
#' @examples
#'\dontrun{
#' # Consider an activator that has a max response around 50%, EC50 is estimated
#' # to be around 1 nM, and minimum response is known to be 0.
#' priors <- sigmoid_agonist_prior(
#'   ec50 = brms::prior(prior = normal(-9, 0.5), nlpar = "ec50"),
#'   top = brms::prior(prior = normal(0.5, 0.2), nlpar = "top"),
#'   bottom = 0)
#'}
#' @export
sigmoid_agonist_prior <- function(
  ec50 = brms::prior(prior = normal(-6, 2.5), nlpar = "ec50"),
  hill = brms::prior(prior = normal(1, 1), nlpar = "hill", lb = -0.01),
  top = brms::prior(prior = normal(1, 0.5), nlpar = "top"),
  bottom = brms::prior(prior = normal(0, 0.5), nlpar = "bottom"),
  ...) {

  c(
    prepare_prior(prior = ec50, nlpar = "ec50"),
    prepare_prior(prior = hill, nlpar = "hill"),
    prepare_prior(prior = top, nlpar = "top"),
    prepare_prior(prior = bottom, nlpar = "bottom"),
    ...)
}

#' Create a Prior an Antagonist Sigmoid Model
#'
#' @description Creates a `data.frame` of priors for the sigmoid antagonist
#' model
#'
#' If the function arguments ic50, hill, top, bottom = NULL, default
#' normal distribution priors will be set.
#'
#' If you would like to set a parameter as a constant, enter a numeric value for
#' the function argument.
#'
#' For other distribution options, reference [brms::prior] and [Prior Choice
#' Recommendations
#' ](https://github.com/stan-dev/stan/wiki/Prior-Choice-Recommendations)
#'
#' @param ic50 [brms::brmsprior()] or `numeric`. Prior for the
#'   `ic50` parameter. (Default: `normal(-6, 2.5)` where the mean
#'   `-6` corresponds to a concentration of 1e-6 or 1 μM. Setting
#'   `ic50` to a numeric value constrains it to a constant value.
#' @param hill [brms::brmsprior()] or `numeric`. Prior for the
#'   `hill` parameter. (Default: `normal(-1, 1)` upper bounded by
#'   `0.1`).
#' @param top `brmsprior` or `numeric` giving the prior for the `top`
#'  parameter. Setting `top` to a `numeric` constrains it to a constant
#'  value.
#' @param bottom `brmsprior` or `numeric` giving the prior for the `bottom`
#'  parameter. Setting `bottom` to `numeric` constrains it to a constant
#'  value.
#' @param ... additional [brms::brmsprior] objects.
#' @returns [brms::brmsprior]
#'
#' @examples
#'\dontrun{
#' # Consider an activator that has a max response around 50%, EC50 is estimated
#' # to be around 1 μM, and minimum response is known to be 0.
#' priors <- sigmoid_antagonist_prior(
#'   ic50 = brms::prior(prior = normal(-6, 0.5), nlpar = "ic50"),
#'   top = brms::prior(prior = normal(0.5, 0.5), nlpar = "top"),
#'   bottom = 0)
#'}
#' @export
sigmoid_antagonist_prior <- function(
  ic50 = brms::prior(prior = normal(-6, 2.5), nlpar = "ic50"),
  hill = brms::prior(prior = normal(-1, 1), nlpar = "hill", ub = 0.01),
  top = brms::prior(prior = normal(1, 0.5), nlpar = "top"),
  bottom = brms::prior(prior = normal(0, 0.5), nlpar = "bottom"),
  ...) {

  c(
    prepare_prior(prior = ic50, nlpar = "ic50"),
    prepare_prior(prior = hill, nlpar = "hill"),
    prepare_prior(prior = top, nlpar = "top"),
    prepare_prior(prior = bottom, nlpar = "bottom"))
}