plot.logit.spike.fit.summary: Plot Logit or Probit Fit Summary

In BoomSpikeSlab: MCMC for Spike and Slab Regression

Plot Logit or Probit Fit Summary

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,
    ...)

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

Arguments

model	A model object inheriting from logit.spike or probit.spike.
burn	The number of MCMC iterations in the object 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.spike or probit.spike in order to keep permanent object sizes small.
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/probit or probability) scale.
number.of.buckets	The number of buckets to use in the Hosmer-Lemeshow plot.
...	Additional arguments to be passed to barplot.

Author(s)

Steven L. Scott

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)

BoomSpikeSlab documentation built on May 29, 2024, 5:07 a.m.