diagnostic.bcmeta: Diagnostic function for bcmeta object in jarbes

In jarbes: Just a Rather Bayesian Evidence Synthesis

Diagnostic function for bcmeta object in jarbes

Description

This function performers an approximated Bayesian cross-validation for a bcmeta object and specially designed diagnostics to detect the existence of a biased component.

Usage

## S3 method for class 'bcmeta'
diagnostic(
  object,
  post.p.value.cut = 0.05,
  study.names = NULL,
  size.forest = 0.4,
  lwd.forest = 0.2,
  shape.forest = 23,
  bias.plot = TRUE,
  cross.val.plot = TRUE,
  level = c(0.5, 0.75, 0.95),
  x.lim = c(0, 1),
  y.lim = c(0, 10),
  x.lab = "P(Bias)",
  y.lab = "Mean Bias",
  title.plot = paste("Bias Diagnostics Contours (50%, 75% and 95%)"),
  kde2d.n = 25,
  marginals = TRUE,
  bin.hist = 30,
  color.line = "black",
  color.hist = "white",
  color.data.points = "black",
  alpha.data.points = 0.1,
  S = 5000,
  ...
)

Arguments

object	The object generated by the function b3lmeta.
post.p.value.cut	Posterior p-value cut point to assess outliers.
study.names	Character vector containing names of the studies used.
size.forest	Size of the center symbol mark in the forest-plot lines
lwd.forest	Thickness of the lines in the forest-plot
shape.forest	Type of symbol for the center mark in the forest-plot lines
bias.plot	Display the bias plot. The default is TRUE.
cross.val.plot	Display the cross validation plot. The default is TRUE.
level	Vector with the probability levels of the contour plot. The default values are: 0.5, 0.75, and 0.95.
x.lim	Numeric vector of length 2 specifying the x-axis limits.
y.lim	Numeric vector of length 2 specifying the y-axis limits.
x.lab	Text with the label of the x-axis.
y.lab	Text with the label of the y-axis.
title.plot	Text for setting a title in the bias plot.
kde2d.n	The number of grid points in each direction for the non-parametric density estimation. The default is 25.
marginals	If TRUE the marginal histograms of the posteriors are added to the plot.
bin.hist	The number of bins in for the histograms. The default value is 30.
color.line	The color of the contour lines. The default is "black.
color.hist	The color of the histogram bars. The default is "white".
color.data.points	The color of the data points. The default is "black".
alpha.data.points	Transparency of the data points.
S	The number of sample values from the joint posterior distribution used to approximate the contours. The default is S=5000.
...	...

jarbes documentation built on June 28, 2025, 1:07 a.m.