plot_matrix {BayesFBHborrow}

Plot smoothed baseline hazards

Description

Plot mean and given quantiles of a matrix. Can also be used to plot derivatives of the baseline hazard, such as estimated cumulative hazard and survival function.

Usage

plot_matrix(
  x_lim,
  y,
  percentiles = c(0.05, 0.95),
  title = "",
  xlab = "",
  ylab = "",
  color = "blue",
  fill = "blue",
  linewidth = 1,
  alpha = 0.2
)

Arguments

x_lim

time grid

y

samples

percentiles

percentiles to include in plot, default is c(0.025, 0.975)

title

optional, add title to plot

xlab

optional, add xlabel

ylab

optional, add ylabel

color

color of the mid line, default is blue

fill

color of the percentiles, default is blue

linewidth

thickness of the plotted line, default is 1

alpha

opacity of the percentiles, default is 0.2

Value

a ggplot2 object

Examples

data(weibull_cc, package = "BayesFBHborrow")

# Set your tuning parameters
tuning_parameters <- list("Jmax" = 5,
                          "pi_b" = 0.5,
                          "cprop_beta" = 0.5)
                          
# run the MCMC sampler
out <- BayesFBHborrow(weibull_cc, NULL, tuning_parameters, 
                      initial_values = NULL,
                      iter = 10, warmup_iter = 1)

# Visualize the smoothed baseline hazard
time_grid <- seq(0, max(weibull_cc$tte), length.out = 2000)
gg <- plot_matrix(time_grid, out$out_slam, 
                  title = "Example plot of smoothed baseline hazard",
                  xlab = "time", ylab = "baseline hazard")