Plot diagnostics for an af object

Summary plot of the bootstrap results of an af object.

# S3 method for af
plot(
  x,
  pch,
  interactive = FALSE,
  classic = NULL,
  tag = NULL,
  shiny = FALSE,
  best.only = FALSE,
  width = 800,
  height = 400,
  fontSize = 12,
  left = 50,
  top = 30,
  chartWidth = "60%",
  chartHeight = "80%",
  backgroundColor = "transparent",
  legend.position = "top",
  model.wrap = NULL,
  legend.space = NULL,
  options = NULL,
  ...
)

Arguments

x	af object, the result of af
pch	plotting character, i.e., symbol to use
interactive	logical. If interactive=TRUE a googleVis plot is provided instead of the base graphics plot. Default is interactive=FALSE.
classic	logical. Depricated. If classic=TRUE a base graphics plot is provided instead of a googleVis plot. For now specifying classic will overwrite the default interactive behaviour, though this is likely to be removed in the future.
tag	Default NULL. Name tag of the objects to be extracted from a gvis (googleVis) object. The default tag for is NULL, which will result in R opening a browser window. Setting tag='chart' or setting options(gvis.plot.tag='chart') is useful when googleVis is used in scripts, like knitr or rmarkdown.
shiny	Default FALSE. Set to TRUE when using in a shiny interface.
best.only	logical determining whether the output used the standard fence approach of only considering the best models that pass the fence (TRUE) or if it should take into account all models that pass the fence at each boundary value (FALSE).
width	Width of the googleVis chart canvas area, in pixels. Default: 800.
height	Height of the googleVis chart canvas area, in pixels. Default: 400.
fontSize	font size used in googleVis chart. Default: 12.
left	space at left of chart (pixels?). Default: "50".
top	space at top of chart (pixels?). Default: "30".
chartWidth	googleVis chart area width. A simple number is a value in pixels; a string containing a number followed by % is a percentage. Default: "60%"
chartHeight	googleVis chart area height. A simple number is a value in pixels; a string containing a number followed by % is a percentage. Default: "80%"
backgroundColor	The background colour for the main area of the chart. A simple HTML color string, for example: 'red' or '#00cc00'. Default: 'transparent'
legend.position	legend position, e.g. "topleft" or "bottomright"
model.wrap	Optional parameter to split the legend names if they are too long for classic plots. model.wrap=2 means that there will be two variables per line, model.wrap=2 gives three variables per line and model.wrap=4 gives 4 variables per line.
legend.space	Optional parameter to add additional space between the legend items for the classic plot.
options	If you want to specify the full set of googleVis options.
...	further arguments (currently unused)

Details

For each value of \(c\) a parametric bootstrap is performed under the full model. For each bootstrap sample we identify the smallest model inside the fence, \(\hat{\alpha}(c)\). We calculate the empirical probability of selecting model \(\alpha\) for a given value of \(c\) as $$p^*(c,\alpha)=P^*\{\hat{\alpha}(c)=\alpha\}.$$ Hence, if \(B\) bootstrap replications are performed, \(p^*(c,\alpha)\) is the proportion of times that model \(\alpha\) is selected. Finally, define an overall selection probability, $$p^*(c)=\max_{\alpha\in\mathcal{A}}p^*(c,\alpha)$$ and we plot \(p^*(c)\) against \(c\). The points on the scatter plot are colour coded by the model that yielded the highest inclusion probability.