wiqid (version 0.3.3)

plotComb: Display a posterior probability distribution from the comb method

Description

Plot the posterior probability distribution for a single parameter calculated using the comb method described by Kruschke (2015).

Usage

plotComb(x, y, credMass = 0.95, plot = TRUE, showMode = FALSE, shadeHDI = NULL, ...)

Value

Returns a matrix with the upper and lower limits of the HDI. If the HDI is disjoint, this matrix will have more than 1 row. It has attributes credMass and height, giving the height of the probability curve corresponding to the ends of the HDI.

Arguments

x

A vector of equally-spaced possible values for the parameter. The range should cover all values of the parameter with non-negligible probability. (To restrict the range displayed in the plot, use xlim.)

y

A vector of probabilities corresponding to the values in x.

credMass

the probability mass to include in credible intervals; set to NULL to suppress plotting of credible intervals.

plot

logical: if TRUE, the posterior is plotted.

showMode

logical: if TRUE, the mode is displayed instead of the mean.

shadeHDI

specifies a colour to shade the area under the curve corresponding to the HDI; NULL for no shading. Usecolours() to see a list of possible colours.

...

additional graphical parameters.

Author

Mike Meredith

Details

The function calculates the Highest Density Interval (HDI). A multi-modal distribution may have a disjoint HDI, in which case the ends of each segment are calculated. No interpolation is done, and the end points correspond to values of the parameter in x; precision will be determined by the resolution of x.

If plot = TRUE, the probability density is plotted together with either the mean or the mode and the HDI.

See Also

For details of the HDI calculation, see hdi.

Examples

# Generate some data:
N <- 0:100
post <- dpois(N, 25)
# Do the plots:
plotComb(N, post)
plotComb(N, post, showMode=TRUE, shadeHDI='pink', xlim=c(10, 50))

# A bimodal distribution:
post2 <- (dnorm(N, 28, 8) + dnorm(N, 70, 11)) / 2
plotComb(N, post2, credMass=0.99, shade='pink')
plotComb(N, post2, credMass=0.80, shade='grey')