plotComb: Display a posterior probability distribution from the comb...

In wiqid: Quick and Dirty Estimates for Wildlife Populations

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, ...)

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.

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.

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.

Author(s)

Mike Meredith

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')

wiqid documentation built on Nov. 18, 2022, 1:07 a.m.