Skip to contents

bmcm_stan

Source: R/bmcm_stan.R
bmcm_stan.Rd

Jointly estimates all treatments and generates Stan code for Bayesian relative mixture cure modeling. It supports various latent and cure model configurations and allows the use of precompiled models or on-the-fly compilation.

Usage

bmcm_stan(
  input_data,
  formula,
  cureformula = ~1,
  family_latent = "exponential",
  prior_latent = NA,
  prior_cure = list(),
  centre_coefs = FALSE,
  bg_model = c("bg_distn", "bg_fixed"),
  bg_varname = "bg_rate",
  bg_hr = 1,
  t_max = 70,
  save_stan_code = FALSE,
  read_stan_code = FALSE,
  precompiled_model_path = NA,
  use_cmdstanr = FALSE,
  ...
)

Arguments

input_data

A long-format data frame containing the input data.

formula

An R formula object specifying the latent model component.

cureformula

An R formula object specifying the cure fraction model component. Default is ~ 1.

family_latent

A string or vector specifying the distribution(s) for the latent model component. Supported values are "exp", "weibull", "gompertz", "lognormal", "loglogistic", and "gengamma".

prior_latent

An optional prior specification for the latent model component. Default is NA.

prior_cure

An optional list specifying priors for the cure fraction model component. Default is an empty list.

centre_coefs

Logical. If TRUE, coefficients will be centered. Default is FALSE.

bg_model

A string specifying the background model type. Supported values are "bg_distn" and "bg_fixed".

bg_varname

A string specifying the background variable name in input_data. Default is "bg_rate".

bg_hr

A numeric value for the background hazard ratio adjustment. Default is 1.

t_max

A numeric value specifying the maximum time horizon for the model. Default is 70.

save_stan_code

Logical. If TRUE, saves the Stan model code to a file. Default is FALSE.

read_stan_code

Logical. If TRUE, reads the Stan model code from a file instead of generating it dynamically. Default is FALSE.

precompiled_model_path

A string specifying the path to a precompiled model. Default is NA.

use_cmdstanr

Logical. If TRUE, the cmdstanr package is used to fit the model. Default is FALSE.

...

Additional parameters to pass to the Stan sampler.

Value

A list of class bmcm containing the Stan model output, MCMC parameters, function call, distributions used, model inputs, input data, and formulas for the cure and latent components.