varimp: Variable Importance Indices

In npreg: Nonparametric Regression via Smoothing Splines

Variable Importance Indices

Description

Computes variable importance indices for terms of a smooth model.

Usage

varimp(object, newdata = NULL, combine = TRUE)

Arguments

object	an object of class "sm" output by the sm function or an object of class "gsm" output by the gsm function.
newdata	the data used for variable importance calculation (if NULL training data are used).
combine	a switch indicating if the parametric and smooth components of the importance should be combined (default) or returned separately.

Details

Suppose that the function can be written as

η = η_0 + η_1 + η_2 + ... + η_p

where η_0 is a constant (intercept) term, and η_j denotes the j-th effect function, which is assumed to have mean zero. Note that η_j could be a main or interaction effect function for all j = 1, ..., p.

The variable importance index for the j-th effect term is defined as

π_j = (η_j^\top η_*) / (η_*^\top η_*)

where η_* = η_1 + η_2 + ... + η_p. Note that ∑_{j = 1}^p π_j = 1 but there is no guarantee that π_j > 0.

If all π_j are non-negative, then π_j gives the proportion of the model's R-squared that can be accounted for by the j-th effect term. Thus, values of π_j closer to 1 indicate that η_j is more important, whereas values of π_j closer to 0 (including negative values) indicate that η_j is less important.

Value

If combine = TRUE, returns a named vector containing the importance indices for each effect function (in object$terms).

If combine = FALSE, returns a data frame where the first column gives the importance indices for the parametric components and the second column gives the importance indices for the smooth (nonparametric) components.

Note

When combine = FALSE, importance indices will be equal to zero for non-existent components of a model term. For example, a nominal effect does not have a parametric component, so the $p component of the importance index for a nominal effect will be zero.

Author(s)

Nathaniel E. Helwig <[e-mail]>

References

Gu, C. (2013). Smoothing spline ANOVA models, 2nd edition. New York: Springer. doi: 10.1007/978-1-4614-5369-7

Helwig, N. E. (2020). Multiple and Generalized Nonparametric Regression. In P. Atkinson, S. Delamont, A. Cernat, J. W. Sakshaug, & R. A. Williams (Eds.), SAGE Research Methods Foundations. doi: 10.4135/9781526421036885885

See Also

See summary.sm for more thorough summaries of smooth models.

See summary.gsm for more thorough summaries of generalized smooth models.

Examples

##########   EXAMPLE 1   ##########
### 1 continuous and 1 nominal predictor

# generate data
set.seed(1)
n <- 100
x <- seq(0, 1, length.out = n)
z <- factor(sample(letters[1:3], size = n, replace = TRUE))
fun <- function(x, z){
  mu <- c(-2, 0, 2)
  zi <- as.integer(z)
  fx <- mu[zi] + 3 * x + sin(2 * pi * x)
}
fx <- fun(x, z)
y <- fx + rnorm(n, sd = 0.5)

# define marginal knots
probs <- seq(0, 0.9, by = 0.1)
knots <- list(x = quantile(x, probs = probs),
              z = letters[1:3])

# fit correct (additive) model
sm.add <- sm(y ~ x + z, knots = knots)

# fit incorrect (interaction) model
sm.int <- sm(y ~ x * z, knots = knots)

# true importance indices
eff <- data.frame(x = 3 * x + sin(2 * pi * x), z = c(-2, 0, 2)[as.integer(z)])
eff <- scale(eff, scale = FALSE)
fstar <- rowSums(eff)
colSums(eff * fstar) / sum(fstar^2)

# estimated importance indices
varimp(sm.add)
varimp(sm.int)



##########   EXAMPLE 2   ##########
### 4 continuous predictors
### additive model

# generate data
set.seed(1)
n <- 100
fun <- function(x){
  sin(pi*x[,1]) + sin(2*pi*x[,2]) + sin(3*pi*x[,3]) + sin(4*pi*x[,4])
}
data <- as.data.frame(replicate(4, runif(n)))
colnames(data) <- c("x1v", "x2v", "x3v", "x4v")
fx <- fun(data)
y <- fx + rnorm(n)

# define ssa knot indices
knots.indx <- c(bin.sample(data$x1v, nbin = 10, index.return = TRUE)$ix,
                bin.sample(data$x2v, nbin = 10, index.return = TRUE)$ix,
                bin.sample(data$x3v, nbin = 10, index.return = TRUE)$ix,
                bin.sample(data$x4v, nbin = 10, index.return = TRUE)$ix)

# fit correct (additive) model
sm.add <- sm(y ~ x1v + x2v + x3v + x4v, data = data, knots = knots.indx)

# fit incorrect (interaction) model
sm.int <- sm(y ~ x1v * x2v + x3v + x4v, data = data, knots = knots.indx)

# true importance indices
eff <- data.frame(x1v = sin(pi*data[,1]), x2v = sin(2*pi*data[,2]),
                  x3v = sin(3*pi*data[,3]), x4v = sin(4*pi*data[,4]))
eff <- scale(eff, scale = FALSE)
fstar <- rowSums(eff)
colSums(eff * fstar) / sum(fstar^2)

# estimated importance indices
varimp(sm.add)
varimp(sm.int)

npreg documentation built on July 21, 2022, 1:06 a.m.