cv.grpnet: Cross-Validation for grpnet

Description

Implements k-fold cross-validation for grpnet to find the regularization parameters that minimize the prediction error (deviance, mean squared error, mean absolute error, or misclassification rate).

Usage

cv.grpnet(x, ...)
# S3 method for default
cv.grpnet(x, 
          y, 
          group,
          weights = NULL,
          offset = NULL,
          alpha = c(0.01, 0.25, 0.5, 0.75, 1),
          gamma = c(3, 4, 5),
          type.measure = NULL,
          nfolds = 10, 
          foldid = NULL,
          same.lambda = FALSE,
          parallel = FALSE, 
          cluster = NULL, 
          verbose = interactive(), 
          adaptive = FALSE,
          power = 1,
          ...)
           
# S3 method for formula
cv.grpnet(formula,
          data, 
          use.rk = TRUE,
          weights = NULL,
          offset = NULL,
          alpha = c(0.01, 0.25, 0.5, 0.75, 1),
          gamma = c(3, 4, 5),
          type.measure = NULL,
          nfolds = 10, 
          foldid = NULL, 
          same.lambda = FALSE,
          parallel = FALSE, 
          cluster = NULL, 
          verbose = interactive(), 
          adaptive = FALSE,
          power = 1,
          ...)

Value

lambda: regularization parameter sequence for the full data
cvm: mean cross-validation error for each lambda
cvsd: estimated standard error of cvm
cvup: upper curve: cvm + cvsd
cvlo: lower curve: cvm - cvsd
nzero: number of non-zero groups for each lambda
grpnet.fit: fitted grpnet object for the full data
lambda.min: value of lambda that minimizes cvm
lambda.1se: largest lambda such that cvm is within one cvsd from the minimum (see Note)
index: two-element vector giving the indices of lambda.min and lambda.1se in the lambda vector, i.e., c(minid, se1id) as defined in the Note
type.measure: loss function for cross-validation (used for plot label)
call: matched call
time: runtime in seconds to perform k-fold CV tuning
tune: data frame containing the tuning results, i.e., min(cvm) for each combination of alpha and/or gamma

Arguments

x: Model (design) matrix of dimension nobs by nvars ( $n \times p$ ).
y: Response vector of length $n$ or matrix of dimension $n \times m$ . Note that matrix inputs are (i) required for multigaussian family, (ii) allowed for binomial and multinomial families (see "Binomial and multinomial" section in grpnet), and (iii) not permitted for other families.
group: Group label vector (factor, character, or integer) of length $p$ . Predictors with the same label are grouped together for regularization.
formula: Model formula: a symbolic description of the model to be fitted. Uses the same syntax as lm and glm.
data: Optional data frame containing the variables referenced in formula.
use.rk: If TRUE (default), the rk.model.matrix function is used to build the model matrix. Otherwise, the model.matrix function is used to build the model matrix. Additional arguments to the rk.model.matrix function can be passed via the ... argument.
weights: Optional vector of length $n$ with non-negative weights to use for weighted (penalized) likelihood estimation. Defaults to a vector of ones.
offset: Optional vector of length $n$ with an a priori known term to be included in the model's linear predictor. Defaults to a vector of zeros.
alpha: Scalar or vector specifying the elastic net tuning parameter $α$ . If alpha is a vector (default), then (a) the same foldid is used to compute the cross-validation error for each $α$ , and (b) the solution for the optimal $α$ is returned.
gamma: Scalar or vector specifying the penalty hyperparameter $γ$ for MCP or SCAD. If gamma is a vector (default), then (a) the same foldid is used to compute the cross-validation error for each $γ$ , and (b) the solution for the optimal $γ$ is returned.
type.measure: Loss function for cross-validation. Options include: "deviance" for model deviance, "mse" for mean squared error, "mae" for mean absolute error, or "class" for classification error. Note that "class" is only available for binomial and multinomial families. The default is classification error (for binomial and multinomial) or mean absolute error (others).
nfolds: Number of folds for cross-validation.
foldid: Optional vector of length $n$ giving the fold identification for each observation. Must be coercible into a factor. After coersion, the nfolds argument is defined as nfolds = nlevels(foldid).
same.lambda: Logical specfying if the same $λ$ sequence should be used for fitting the model to each fold's data. If FALSE (default), the $λ$ sequence is determined separately holding out each fold, and the $λ$ sequence from the full model is used to align the predictions. If TRUE, the $λ$ sequence from the full model is used to fit the model for each fold. The default often provides better (i.e., more stable) computational performance.
parallel: Logical specifying if sequential computing (default) or parallel computing should be used. If TRUE, the fitting for each fold is parallelized.
cluster: Optional cluster to use for parallel computing. If parallel = TRUE and cluster = NULL, then the cluster is defined cluster = makeCluster(2L), which uses two cores. Recommended usage: cluster = makeCluster(detectCores())
verbose: Logical indicating if the fitting progress should be printed. Defaults to TRUE in interactive sessions and FALSE otherwise.
adaptive: Logical indicating if the adaptive group elastic net should be used (see Note).
power: If adaptive = TRUE, then the adaptive penalty weights are defined by dividing the original penalty weights by tapply(coef, group, norm, type = "F")^power.
...: Optional additional arguments for grpnet (e.g., standardize, penalty.factor, etc.)

Author

Nathaniel E. Helwig <helwig@umn.edu>

Details

This function calls the grpnet function nfolds+1 times: once on the full dataset to obtain the lambda sequence, and once holding out each fold's data to evaluate the prediction error. The syntax of (the default S3 method for) this function closely mimics that of the cv.glmnet function in the glmnet package (Friedman, Hastie, & Tibshirani, 2010).

Let $D_{u} = {y_{u}, X_{u}}$ denote the $u$ -th fold's data, let $D_{[u]} = {y_{[u]}, X_{[u]}}$ denote the full dataset excluding the $u$ -th fold's data, and let $β_{λ [u]}$ denote the coefficient estimates obtained from fitting the model to $D_{[u]}$ using the regularization parameter $λ$ .

The cross-validation error for the $u$ -th fold is defined as $E_{u} (λ) = C (β_{λ [u]}, D_{u})$ where $C (\cdot, \cdot)$ denotes the cross-validation loss function that is specified by type.measure. For example, the "mse" loss function is defined as $C (β_{λ [u]}, D_{u}) = ‖ y_{u} - X_{u} β_{λ [u]} ‖^{2}$ where $‖ \cdot ‖$ denotes the L2 norm.

The mean cross-validation error cvm is defined as $\bar{E} (λ) = \frac{1}{v} \sum_{u = 1}^{v} E_{u} (λ)$ where $v$ is the total number of folds. The standard error cvsd is defined as $S (λ) = \sqrt{\frac{1}{v (v - 1)} \sum_{u = 1}^{v} (E_{u} (λ) - \bar{E} (λ))^{2}}$ which is the classic definition of the standard error of the mean.

References

Friedman, J., Hastie, T., & Tibshirani, R. (2010). Regularization paths for generalized linear models via coordinate descent. Journal of Statistical Software, 33(1), 1-22. tools:::Rd_expr_doi("10.18637/jss.v033.i01")

Helwig, N. E. (2025). Versatile descent algorithms for group regularization and variable selection in generalized linear models. Journal of Computational and Graphical Statistics, 34(1), 239-252. tools:::Rd_expr_doi("10.1080/10618600.2024.2362232")

Examples

Run this code

# \donttest{
######***######   family = "gaussian"   ######***######

# load data
data(auto)

# 10-fold cv (formula method, response = mpg)
set.seed(1)
mod <- cv.grpnet(mpg ~ ., data = auto)

# print min and 1se solution info
mod

# plot cv error curve
plot(mod)



######***######   family = "multigaussian"   ######***######

# load data
data(auto)

# 10-fold cv (formula method, response = (mpg, displacement))
y <- as.matrix(auto[,c(1,3)])
set.seed(1)
mod <- cv.grpnet(y ~ ., data = auto[,-c(1,3)], family = "multigaussian",
                 standardize.response = TRUE)

# print min and 1se solution info
mod

# plot cv error curve
plot(mod)



######***######   family = "svm1"   ######***######

# load data
data(auto)

# redefine origin (Domestic vs Foreign)
auto$origin <- ifelse(auto$origin == "American", "Domestic", "Foreign")

# 10-fold cv (default method, response = origin with 2 levels)
set.seed(1)
mod <- cv.grpnet(origin ~ ., data = auto, family = "svm1")

# print min and 1se solution info
mod

# plot cv error curve
plot(mod)



######***######   family = "svm2"   ######***######

# load data
data(auto)

# redefine origin (Domestic vs Foreign)
auto$origin <- ifelse(auto$origin == "American", "Domestic", "Foreign")

# 10-fold cv (default method, response = origin with 2 levels)
set.seed(1)
mod <- cv.grpnet(origin ~ ., data = auto, family = "svm2")

# print min and 1se solution info
mod

# plot cv error curve
plot(mod)



######***######   family = "logit"   ######***######

# load data
data(auto)

# redefine origin (Domestic vs Foreign)
auto$origin <- ifelse(auto$origin == "American", "Domestic", "Foreign")

# 10-fold cv (default method, response = origin with 2 levels)
set.seed(1)
mod <- cv.grpnet(origin ~ ., data = auto, family = "logit")

# print min and 1se solution info
mod

# plot cv error curve
plot(mod)


######***######   family = "binomial"   ######***######

# load data
data(auto)

# redefine origin (Domestic vs Foreign)
auto$origin <- ifelse(auto$origin == "American", "Domestic", "Foreign")

# 10-fold cv (default method, response = origin with 2 levels)
set.seed(1)
mod <- cv.grpnet(origin ~ ., data = auto, family = "binomial")

# print min and 1se solution info
mod

# plot cv error curve
plot(mod)



######***######   family = "multinomial"   ######***######

# load data
data(auto)

# 10-fold cv (formula method, response = origin with 3 levels)
set.seed(1)
mod <- cv.grpnet(origin ~ ., data = auto, family = "multinomial")

# print min and 1se solution info
mod

# plot cv error curve
plot(mod)



######***######   family = "poisson"   ######***######

# load data
data(auto)

# 10-fold cv (formula method, response = horsepower)
set.seed(1)
mod <- cv.grpnet(horsepower ~ ., data = auto, family = "poisson")

# print min and 1se solution info
mod

# plot cv error curve
plot(mod)



######***######   family = "negative.binomial"   ######***######

# load data
data(auto)

# 10-fold cv (formula method, response = horsepower)
set.seed(1)
mod <- cv.grpnet(horsepower ~ ., data = auto, family = "negative.binomial")

# print min and 1se solution info
mod

# plot cv error curve
plot(mod)



######***######   family = "Gamma"   ######***######

# load data
data(auto)

# 10-fold cv (formula method, response = origin)
set.seed(1)
mod <- cv.grpnet(mpg ~ ., data = auto, family = "Gamma")

# print min and 1se solution info
mod

# plot cv error curve
plot(mod)



######***######   family = "inverse.gaussian"   ######***######

# load data
data(auto)

# 10-fold cv (formula method, response = origin)
set.seed(1)
mod <- cv.grpnet(mpg ~ ., data = auto, family = "inverse.gaussian")

# print min and 1se solution info
mod

# plot cv error curve
plot(mod)

# }

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