BGPhazard (version 2.1.1)

CCuPloth: Plots for the Hazard and Survival Funcion Estimates

Description

Plots the resulting hazard function and the survival function estimates defined by the bayesian semiparametric cure rate model with an unknown threshold (Nieto-Barajas & Yin, 2008).

Usage

CCuPloth(
  M,
  new_obs = NULL,
  type.h = "segment",
  qn = 0.5,
  intervals = T,
  confidence = 0.95,
  summary = FALSE
)

Value

SUM.h

Numeric tibble. Summary for the mean, median, and a confint / 100 confidence interval for each segment of the hazard function. If summary = TRUE

SUM.S

Numeric tibble. Summary for the mean, median, and a confint / 100 confidence interval for each segment of the survival function. If summary = TRUE

Arguments

M

tibble. Contains the output generated by CuMRres.

new_obs

tibble. Contains the covariate information for new observations.

type.h

character. "segment"= use segments to plot hazard rates, "line" = link hazard rates by a line

qn

Numeric. Quantile for Tao (cure time) that should be visualized on the plot.

intervals

logical. If TRUE, plots credible intervals.

confidence

Numeric. Confidence level.

summary

Logical. If TRUE, a summary for the hazard and survival functions is returned as a tibble.

Details

This function returns estimators plots for the hazard rate as it is computed by CCuMRes and the cure time (quantile of Tao specified by the user) together with credible intervals. Additionally, it plots the survival function and the cure proportion estimates with their corresponding credible intervals.

References

- Nieto-Barajas, L. E. (2003). Discrete time Markov gamma processes and time dependent covariates in survival analysis. Bulletin of the International Statistical Institute 54th Session. Berlin. (CD-ROM).

-Nieto-Barajas, L. E., & Yin, G. (2008). Bayesian semiparametric cure rate model with an unknown threshold. Scandinavian Journal of Statistics, 35(3), 540-556. https://doi.org/10.1111/j.1467-9469.2007.00589.x

See Also

CCuMRes,

Examples

## Simulations may be time intensive. Be patient.

## Example 1
# data(BMTKleinbook)
    # res <- CCuMRes(BMTKleinbook, covs.x = c("tTransplant","hodgkin","karnofsky","waiting"),
    #                covs.y = c("tTransplant","hodgkin","karnofsky","waiting"),
    #                        type.t = 2, K = 72, length = 30,
    #                        alpha = rep(2,72), beta = rep(2,72), c.r = rep(50, 71), type.c = 2,
    #                        var.delta.str = .1, var.theta.str = 1,
    #                        var.delta.ini = 100, var.theta.ini = 100,
    #                        iterations = 100, burn.in = 10, thinning = 1)
    # 
    # CCuPloth(res, type.h = "segment",qn=.5, summary = T)
    # 
    # new_obs <- tibble(tTransplant=c(0,0,0,0),
    #                       hodgkin=c(0,1,0,1),
    #                       karnofsky=c(90,90,60,60),
    #                       waiting=c(36,36,36,36)
    # )
    # 
    # ind <- CCuPloth(res, new_obs, qn = .5)
    # ind