ggInteract_2D: ggInteract_2D
In JBjouffray/ggBRT: Explore and Visualise the Results of Boosted Regression Trees

ggInteract_2D

R Documentation

ggInteract_2D

Description

Function to draw 2D interaction plot showing predicted values for two predictors from a boosted regression trees obtained with the gbm.step routine in the dismo package. Values for all other variables are set at their mean by default.

Usage

ggInteract_2D(gbm.object, dat.rank = NULL, n.plots = NULL, x = 1, y = 2,
  col.gradient = c("lightskyblue", "#142c42"), palette = NULL,
  show.axis = F, show.dot = F, contour = T, label.contour = F,
  col.contour = "cadetblue2", col.dot = "grey10", alpha.dot = 0.9,
  cex.dot = 0.5, pred.means = NULL, x.label = NULL, y.label = NULL,
  legend = TRUE, z.label = "Fitted value", x.range = NULL, nrow = NULL,
  ncol = NULL, y.range = NULL, z.range = NULL, main = "",
  smooth = "none", ...)

Arguments

`gbm.object`	a gbm.step object (object of S3 class gbm)
`dat.rank`	allows to plot several interaction plots using a data frame of interaction size (e.g. obtained from ggInteract_list)
`n.plots`	number of interaction plots to display, ranked by decreasing interaction size
`x`	in case of a single plot, the first predictor. Can be either a character name (use "") or a number indicating its index
`y`	in case of a single plot, the second predictor. Can be either a character name (use "") or a number indicating its index
`col.gradient`	a vector of two colors to define the color gradient of the plot
`palette`	use a predefined color palette (default = NULL)
`show.dot`	Logical. If TRUE (default=FALSE), overlays the actual data points
`contour`	Logical. If TRUE (default), draw contours
`label.contour`	Logical. If TRUE (default=FALSE), adds labels to the contours
`col.contour`	color of the contour lines
`col.dot`	color of the dots
`alpha.dot`	transparency of the dots
`cex.dot`	size of the dots
`pred.means`	allows specification of values for other variables (see gbm.perspec in dismo)
`x.label`	title for the x-axis
`y.label`	title for the y-axis
`legend`	Logical. If TRUE (default) shows the legend
`z.label`	title for the z-axis
`x.range`	manual range for the x-axis
`nrow`	number of plots per row
`ncol`	number of plots per column
`y.range`	manual range for the y-axis
`z.range`	manual range for the z-axis
`main`	title for the plot
`smooth:`	controls smoothing of the predicted surface
`nrow`	number of plots per row
`ncol`	number of plots per column