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Plot the variability of an object of class "probability" as a histogram

Source: R/util_plotfunctions.R
hist.probability.Rd

The posterior probabilities calculated with the Pr() function, and outputted as a probability object, have an associated variability that comes from the finite size of the data sample. This variability can be interpreted in two ways:

  • How the probabilities would change, if we could collect a very large (infinite) amount of additional data, and how likely would such change be;

  • The relative frequency of a particular variate value in the full (sampled and unsampled) population is unknown; we can quantify our uncertainty about this relative frequency with a probability distribution.

The hist() method for a probability object is a utility to visualize this kind of variability, in the form of a distribution.

Usage

# S3 method for class 'probability'
hist(
  x,
  subset = NULL,
  breaks = NULL,
  legend = "top",
  lty = c(1, 2, 4, 3, 6, 5),
  lwd = 2,
  col = palette(),
  alpha.f = 1,
  fill.alpha.f = 0.125,
  showmean = TRUE,
  xlab = NULL,
  ylab = NULL,
  xlim = NULL,
  ylim = c(0, NA),
  main = NULL,
  grid = TRUE,
  add = FALSE,
  ...
)

Arguments

x

Object of class "probability", obtained with Pr().

subset

Named list or named vector: which variate values to display. For the variates corresponding to the names in this list, only the vector of values corresponding to that variate is displayed.

breaks

NULL or as in function graphics::hist(). If NULL (default), an optimal number of breaks for each probability distribution is computed.

legend

One of the values "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", "center" (see graphics::legend()): plot a legend at that position. A value FALSE or any other does not plot any legend. Default "top".

lty, lwd, col, alpha.f, xlab, ylab, xlim, ylim, main, grid, add

see analogous arguments in graphics::matplot()

fill.alpha.f

Numeric, default 0.125: opacity of the histogram filling. 0 means no filling.

showmean

Logical, default TRUE: show the means of the probability distributions? The means correspond to the probabilities about the next observed unit.

...

Other parameters to be passed to flexiplot().

Value

Invisibly, an object of class "histogram".

See also

Pr() to calculate posterior probabilities and quantiles.

plot.probability() to plot the posterior probabilities.

flexiplot() (on which hist.probability() is based) for more general plots.

plotquantiles() to plot quantile ranges.

Examples

## Load the example `learnt` object calculated from the "penguins" dataset;
## variates: 'species' and 'bill_len'
learnt <- learntExample

## calculate the probability, and its variability,
## for the value 'Adelie' of the "species" variate
probs <- Pr(Y = data.frame(species = 'Adelie'), learnt = learnt, parallel = 1)
probs$values
#>         
#> species      [,1]
#>   Adelie 0.440685

## show the variability of this probability; equivalently show
## the probability distribution for the relative frequency of
## 'Adelie' penguins in the full population
hist(probs, legend = 'topright')