surface_matrix: Construct a set of (x, y, z) matrices for surface plotting a...

In ggRandomForests: Visually Exploring Random Forests

Construct a set of (x, y, z) matrices for surface plotting a gg_partial_coplot object

Description

Construct a set of (x, y, z) matrices for surface plotting a gg_partial_coplot object

Usage

surface_matrix(dta, xvar)

Arguments

dta	a gg_partial_coplot object containing at least 3 numeric columns of data
xvar	a vector of 3 column names from the data object, in (x, y, z) order

Details

To create a surface plot, the plot3D::surf3D function expects 3 matrices of n.x by n.y. Take the p+1 by n gg_partial_coplot object, and extract and construct the x, y and z matrices from the provided xvar column names.

Examples

## Not run: 
## From vignette(randomForestRegression, package="ggRandomForests")
data(Boston, package="MASS")
rfsrc_boston <- randomForestSRC::rfsrc(medv~., Boston)

varsel_boston <- var.select(rfsrc_boston)

 rm_pts <- quantile_pts(rfsrc_boston$xvar$rm,
    groups = 9, 
    intervals = TRUE)

 partial_boston_surf <- lapply(rm_pts, function(ct) {
  rfsrc_boston$xvar$rm <- ct
  randomForestSRC::plot.variable(
    rfsrc_boston,
    xvar.names = "lstat", 
    time = 1,
    npts = 10,
    show.plots = FALSE,
    partial = TRUE
   )
 })
   
# Instead of groups, we want the raw rm point values,
# To make the dimensions match, we need to repeat the values
# for each of the 50 points in the lstat direction
rm.tmp <- do.call(c,lapply(rm_pts,
                           function(grp) {rep(grp,
                           length(partial_boston_surf))}))

# Convert the list of plot.variable output to
partial_surf <- do.call(rbind,lapply(partial_boston_surf, gg_partial))

# attach the data to the gg_partial_coplot
partial_surf$rm <- rm.tmp

# Transform the gg_partial_coplot object into a list of three named matrices
# for surface plotting with plot3D::surf3D
srf <- surface_matrix(partial_surf, c("lstat", "rm", "yhat"))

## End(Not run)

## Not run: 
# surf3D is in the plot3D package.
library(plot3D)
# Generate the figure.
surf3D(x=srf$x, y=srf$y, z=srf$z, col=topo.colors(10),
       colkey=FALSE, border = "black", bty="b2",
       shade = 0.5, expand = 0.5,
       lighting = TRUE, lphi = -50,
       xlab="Lower Status", ylab="Average Rooms", zlab="Median Value"
)

## End(Not run)

ggRandomForests documentation built on Sept. 1, 2022, 5:07 p.m.