plot.af {mplot}

Plot diagnostics for an af object

Description

Summary plot of the bootstrap results of an af object.

Usage

## S3 method for class '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.