pcd_as_stan_data: Prepare data for primarycensored Stan model

In primarycensored: Primary Event Censored Distributions

Prepare data for primarycensored Stan model

Description

This function takes in delay data and prepares it for use with the primarycensored Stan model.

Usage

pcd_as_stan_data(
  data,
  delay = "delay",
  delay_upper = "delay_upper",
  n = "n",
  pwindow = "pwindow",
  relative_obs_time = "relative_obs_time",
  dist_id,
  primary_id,
  param_bounds,
  primary_param_bounds,
  priors,
  primary_priors,
  compute_log_lik = FALSE,
  use_reduce_sum = FALSE,
  truncation_check_multiplier = 2
)

Arguments

data	A data frame containing the delay data.
delay	Column name for observed delays (default: "delay")
delay_upper	Column name for upper bound of delays (default: "delay_upper")
n	Column name for count of observations (default: "n")
pwindow	Column name for primary window (default: "pwindow")
relative_obs_time	Column name for relative observation time (default: "relative_obs_time")
dist_id	Integer identifying the delay distribution: You can use pcd_stan_dist_id() to get the dist ID for a distribution or look at the pcd_distributions data set.
primary_id	Integer identifying the primary distribution: You can use pcd_stan_dist_id() to get the primary dist ID for a distribution (make sure to select the "primary" type) or look at the pcd_primary_distributions data set.
param_bounds	A list with elements lower and upper, each a numeric vector specifying bounds for the delay distribution parameters.
primary_param_bounds	A list with elements lower and upper, each a numeric vector specifying bounds for the primary distribution parameters.
priors	A list with elements location and scale, each a numeric vector specifying priors for the delay distribution parameters.
primary_priors	A list with elements location and scale, each a numeric vector specifying priors for the primary distribution parameters.
compute_log_lik	Logical; compute log likelihood? (default: FALSE)
use_reduce_sum	Logical; use reduce_sum for performance? (default: FALSE)
truncation_check_multiplier	Numeric multiplier to use for checking if the truncation time D is appropriate relative to the maximum delay for each unique D value. Set to NULL to skip the check. Default is 2.

Value

A list containing the data formatted for use with pcd_cmdstan_model()

See Also

Modelling wrappers for external fitting packages fitdistdoublecens(), pcd_cmdstan_model()

Examples

data <- data.frame(
  delay = c(1, 2, 3),
  delay_upper = c(2, 3, 4),
  n = c(10, 20, 15),
  pwindow = c(1, 1, 2),
  relative_obs_time = c(10, 10, 10)
)
stan_data <- pcd_as_stan_data(
  data,
  dist_id = 1,
  primary_id = 1,
  param_bounds = list(lower = c(0, 0), upper = c(10, 10)),
  primary_param_bounds = list(lower = numeric(0), upper = numeric(0)),
  priors = list(location = c(1, 1), scale = c(1, 1)),
  primary_priors = list(location = numeric(0), scale = numeric(0))
)

primarycensored documentation built on April 3, 2025, 6:24 p.m.