BoomSpikeSlab (version 0.5.2)

plot.logit.spike.fit.summary: Fit summary for logit.spike models

Description

Two plots can be accessed by this function. The first is a time series plot of the "deviance R-square" statistic, by MCMC iteration. The second is a Hosmer-Lemeshow plot in which the data is divided into 10 groups based on predicted probabilities, and the empirical success probabilities for that group are plotted against the expected probabilities from the model.

Usage

PlotLogitSpikeFitSummary(
    model,
    burn = 0,
    which.summary = c("both", "r2", "bucket"),
    scale = c("logit", "probability"),
    cutpoint.basis = c("sample.size", "equal.range"),
    number.of.buckets = 10,
    ...)

Arguments

model

A model object inheriting from logit.spike.

burn

The number of MCMC iterations in the ojbect to be discarded as burn-in. Note that this only affects the deviance R-square plot. The fit summaries in the Hosmer-Lemeshow plot are constructed by logit.

which.summary

Which plot is desired?

scale

The scale to use for the predicted probabilities in the Hosmer-Lemeshow plot.

cutpoint.basis

How should cutpoints be determined for the Hosmer-Lemeshow plot? If "sample.size" then each bucket will have equal sample size. If "equal.range" then each bucket will occupy the same size on the chosen (logit or pro

number.of.buckets

The number of buckets to use in the Hosmer-Lemeshow plot.

...

Additional arguments to be passed to barplot.

See Also

lm.spike SpikeSlabPrior summary.lm.spike predict.lm.spike

Examples

simulate.logit.spike <- function(n = 100, p = 10, ngood = 3,
                              niter=1000){
  x <- cbind(1, matrix(rnorm(n * (p-1)), nrow=n))
  beta <- c(rnorm(ngood), rep(0, p - ngood))
  prob <- plogis(x %*% beta)
  y <- runif(n) < prob
  x <- x[,-1]
  draws <- logit.spike(y ~ x, niter=niter)
  plot.ts(draws$beta)
  return(invisible(draws))
}
model <- simulate.logit.spike()
plot(model, "fit")
plot(model, "fit", scale = "probability", number.of.buckets = 15)