Display results from the funnel plot asymmetry test

Generates a funnel plot for a fitted fat object.

Usage

# S3 method for fat
plot(
  x,
  ref,
  confint = TRUE,
  confint.level = 0.1,
  confint.col = "skyblue",
  confint.alpha = 0.5,
  confint.density = NULL,
  xlab = "Effect size",
  add.pval = TRUE,
  ...
)

Arguments

x: An object of class fat
ref: A numeric value indicating the fixed or random effects summary estimate. If no value is provided then it will be retrieved from a fixed effects meta-analysis (if possible).
confint: A logical indicator. If TRUE, a confidence interval will be displayed for the estimated regression model (based on a Student-T distribution)
confint.level: Significance level for constructing the confidence interval.
confint.col: The color for filling the confidence interval. Choose NA to leave polygons unfilled. If confint.density is specified with a positive value this gives the color of the shading lines.
confint.alpha: A numeric value between 0 and 1 indicating the opacity for the confidence region.
confint.density: The density of shading lines, in lines per inch. The default value of NULL means that no shading lines are drawn. A zero value of density means no shading nor filling whereas negative values and NA suppress shading (and so allow color filling).
xlab: A title for the x axis
add.pval: Logical to indicate whether a P-value should be added to the plot
...: Additional arguments.

Author

Thomas Debray <thomas.debray@gmail.com>

Frantisek Bartos <f.bartos96@gmail.com>

Examples

data(Fibrinogen)
b <- log(Fibrinogen$HR)
b.se <- ((log(Fibrinogen$HR.975) - log(Fibrinogen$HR.025))/(2*qnorm(0.975)))
n.total <- Fibrinogen$N.total

# A very simple funnel plot
plot(fat(b=b, b.se=b.se), xlab = "Log hazard ratio")


# Plot the funnel for an alternative test
plot(fat(b=b, b.se=b.se, n.total=n.total, method="M-FIV"), xlab = "Log hazard ratio")