randomForest (version 4.5-35)

partialPlot: Partial dependence plot

Description

Partial dependence plot gives a graphical depiction of the marginal effect of a variable on the class probability (classification) or response (regression).

Usage

## S3 method for class 'randomForest':
partialPlot(x, pred.data, x.var, which.class,
      w, plot = TRUE, add = FALSE,
      n.pt = min(length(unique(pred.data[, xname])), 51),
      rug = TRUE, xlab=deparse(substitute(x.var)), ylab="",
      main=paste("Partial Dependence on", deparse(substitute(x.var))),
      ...)

Arguments

x
an object of class randomForest, which contains a forest component.
pred.data
a data frame used for contructing the plot, usually the training data used to contruct the random forest.
x.var
name of the variable for which partial dependence is to be examined.
which.class
For classification data, the class to focus on (default the first class).
w
weights to be used in averaging; if not supplied, mean is not weighted
plot
whether the plot should be shown on the graphic device.
add
whether to add to existing plot (TRUE).
n.pt
if x.var is continuous, the number of points on the grid for evaluating partial dependence.
rug
whether to draw hash marks at the bottom of the plot indicating the deciles of x.var.
xlab
label for the x-axis.
ylab
label for the y-axis.
main
main title for the plot.
...
other graphical parameters to be passed on to plot or lines.

Value

  • A list with two components: x and y, which are the values used in the plot.

Details

The function being plotted is defined as: $$\tilde{f}(x) = \frac{1}{n} \sum_{i=1}^n f(x, x_{iC}),$$ where $x$ is the variable for which partial dependence is sought, and $x_{iC}$ is the other variables in the data. The summand is the predicted regression function for regression, and logits (i.e., log of fraction of votes) for which.class for classification: $$f(x) = \log p_k(x) - \frac{1}{K} \sum_{j=1}^K \log p_j(x),$$ where $K$ is the number of classes, $k$ is which.class, and $p_j$ is the proportion of votes for class $j$.

References

Friedman, J. (2001). Greedy function approximation: the gradient boosting machine, Ann. of Stat.

See Also

randomForest

Examples

Run this code
data(airquality)
airquality <- na.omit(airquality)
set.seed(131)
ozone.rf <- randomForest(Ozone ~ ., airquality)
partialPlot(ozone.rf, airquality, Temp)

data(iris)
set.seed(543)
iris.rf <- randomForest(Species~., iris)
partialPlot(iris.rf, iris, Petal.Width, "versicolor")

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