rgl: plot3d.lm – R documentation

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rgl

plot3d.lm

Method for plotting simple linear fit

Description

This function provides several plots of the result of fitting a two-predictor model.

Usage

## S3 method for class 'lm'
plot3d(x, 
       which = 1, 
       plane.col = "gray", plane.alpha = 0.5,
       sharedMouse = TRUE, 
       use_surface3d, 
       do_grid = TRUE,
       grid.col = "black", 
       grid.alpha = 1,
       grid.steps = 5,
       sub.steps = 4,
       vars = get_all_vars(terms(x), x$model),
       clip_to_density = 0,
       ...)

Arguments

`x`	An object inheriting from class `"lm"` obtained by fitting a two-predictor model.
`which`	Which plot to show? See Details below.
`plane.col, plane.alpha`	These parameters control the colour and transparency of a plane or surface.
`sharedMouse`	If multiple plots are requested, should they share mouse controls, so that they move in sync?
`use_surface3d`	Use the `surface3d` function to plot the surface rather than `planes3d`. This allows curved surfaces to be shown. The default is `FALSE` if the model looks like a simple 2 parameter linear fit, otherwise `TRUE`.
`do_grid`	Plot a grid.
`grid.col, grid.alpha, grid.steps`	Characteristics of the grid.
`sub.steps`	If `use_surface3d` is `TRUE`, use an internal grid of `grid.steps*sub.steps` to draw the surface. `sub.steps > 1` allows curvature within facets. Similarly, if `do_grid` is `TRUE`, it allows curvature within grid lines.
`vars`	A dataframe containing the variables to plot in the first three columns, with the response assumed to be in column 1. See the Note below.
`clip_to_density`	If positive, the surface, plane or grid will be clipped to a region with sufficient data.
`...`	Other parameters to pass to the default `plot3d` method, to control the appearance of aspects of the plot other than the plane.

Details

Three plots are possible, depending on the value(s) in which:

(default) Show the points and the fitted plane or surface.
Show the residuals and the plane at z = 0.
Show the predicted values on the fitted plane or surface.

If clip_to_density is positive, then the surface, plane or grid will be clipped to the region where a non-parametric density estimate (using MASS::kde2d), normalized to have a maximum value of 1, is greater than the given value. This will suppress parts of the plot that aren't supported by the observed data.

Value

Called for the side effect of drawing one or more plots.

Invisibly returns a high-level vector of object ids. Names of object ids have the plot number (in drawing order) appended.

Note

The default value for the vars argument will handle simple linear models with a response and two predictors, and some models with functions of those two predictors. For models that fail (e.g. models using poly), you can include the observed values as in the third example below.

If clip_to_density > 0,

The clipping is approximate, so it may not agree perfectly between surfaces, planes and grids.
This option requires the suggested packages MASS and akima, and will be ignored with a warning if either is not installed.

Author(s)

Duncan Murdoch

Examples

open3d()
ids <- plot3d(lm(mpg ~ wt + qsec, data = mtcars), which = 1:3)
names(ids)

open3d()
plot3d(lm(mpg ~ wt + I(wt^2) + qsec, data = mtcars))

open3d()
# Specify vars in the order:  response, pred1, pred2.
plot3d(lm(mpg ~ poly(wt, 3) + qsec, data = mtcars), 
       vars = mtcars[,c("mpg", "wt", "qsec")])
       
open3d()
# Clip parts of the plot with few (wt, qsec) points
plot3d(lm(mpg ~ poly(wt, 3) + qsec, data = mtcars), 
       vars = mtcars[,c("mpg", "wt", "qsec")],
       clip_to_density = 0.1)

rgl

3D Visualization Using OpenGL

v0.106.8

GPL

Authors

Duncan Murdoch [aut, cre], Daniel Adler [aut], Oleg Nenadic [ctb], Simon Urbanek [ctb], Ming Chen [ctb], Albrecht Gebhardt [ctb], Ben Bolker [ctb], Gabor Csardi [ctb], Adam Strzelecki [ctb], Alexander Senger [ctb], The R Core Team [ctb, cph], Dirk Eddelbuettel [ctb], The authors of Shiny [cph], The authors of knitr [cph], Jeroen Ooms [ctb], Yohann Demont [ctb], Joshua Ulrich [ctb], Xavier Fernandez i Marin [ctb], George Helffrich [ctb], Ivan Krylov [ctb]

Initial release