traceplot {BCClong}

Trace plot function

Description

To visualize the MCMC chain for model parameters

Usage

traceplot(
  fit,
  cluster.indx = 1,
  feature.indx = 1,
  parameter = "PPI",
  xlab = NULL,
  ylab = NULL,
  ylim = NULL,
  xlim = NULL,
  title = NULL
)

Arguments

fit

an objective output from BCC.multi() function.

cluster.indx

a numeric value. For cluster-specific parameters, specifying cluster.indx will generate the trace plot for the corresponding cluster.

feature.indx

a numeric value. For cluster-specific parameters, specifying feature.indx will generate the trace plot for the corresponding cluster.

parameter

a character value. Specify which parameter for which the trace plot will be generated. The value can be "PPI" for pi, alpha for alpha, "GA" for gamma, "SIGMA.SQ.U" for Sigma and "SIGMA.SQ.E" for sigma.

xlab

Label for x axis

ylab

Label for y axis

ylim

The range for y axis

xlim

The range for x axis

title

Title for the trace plot

Value

void function with no return value, only show plots

Examples

# get data from the package
filePath <- system.file("extdata", "epil1.rds", package = "BCClong")
fit.BCC <- readRDS(filePath)
traceplot(fit=fit.BCC, parameter="PPI",ylab="pi",xlab="MCMC samples")