gbm.persp: gbm perspective plot

In dismo: Species Distribution Modeling

Description

Takes a gbm boosted regression tree object produced by gbm.step and plots a perspective plot showing predicted values for two predictors as specified by number using x and y. Values for all other variables are set at their mean by default but values can be specified by giving a list consisting of the variable name and its desired value, e.g., c(name1 = 12.2, name2 = 57.6)

Usage

gbm.perspec(gbm.object, x = 1, y = 2, pred.means = NULL, x.label = NULL, x.range = NULL,
 y.label = NULL, z.label = "fitted value", y.range = NULL, z.range = NULL, 
 leg.coords = NULL, ticktype = "detailed", theta = 55, phi = 40, smooth = "none",
 mask = FALSE, perspective = TRUE, ...)

Arguments

gbm.object	object of class gbm
x	the first variable to be plotted
y	the second variable to be plotted
pred.means	allows specification of values for other variables
x.label	allows manual specification of the x label
x.range	manual range specification for the x variable
y.label	and y label
z.label	default z label
y.range	and the y
z.range	allows control of the vertical axis
leg.coords	can specify coords (x, y) for legend
ticktype	specifiy detailed types - otherwise "simple"
theta	rotation
phi	and elevation
smooth	controls smoothing of the predicted surface
mask	controls masking using a sample intensity model
perspective	controls whether a contour or perspective plot is drawn
...	allows the passing of additional arguments to plotting routine useful options include shade, ltheta, lphi for controlling illumination and cex for controlling text size - cex.axis and cex.lab have no effect

Author(s)

John R. Leathwick and Jane Elith

References

Elith, J., J.R. Leathwick and T. Hastie, 2009. A working guide to boosted regression trees. Journal of Animal Ecology 77: 802-81

dismo documentation built on May 2, 2019, 6:07 p.m.