Package 'starnet'

Stacked Elastic Net Regression

Description

The R package starnet implements stacked elastic net regression. The elastic net generalises ridge and lasso regularisation. Instead of fixing or tuning the mixing parameter alpha, we combine multiple alphas by stacked generalisation.

Details

Use function starnet for model fitting. Type library(starnet) and then ?starnet or help("starnet)" to open its help file.

See the vignette for further examples. Type vignette("starnet") or browseVignettes("starnet") to open the vignette.

References

A Rauschenberger, E Glaab, and MA van de Wiel (2020). "Predictive and interpretable models via the stacked elastic net". Bioinformatics. In press. doi:10.1093/bioinformatics/btaa535. [email protected]

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glmnet::cv.glmnet

Description

Wrapper for cv.glmnet, with different handling of sparsity constraints.

Usage

.cv.glmnet(..., nzero)

Arguments

...	see cv.glmnet
nzero	maximum number of non-zero coefficients: positive integer

Value

Object of class cv.glmnet.

Examples

NA

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Loss

Description

Calculate loss from predicted and observed values

Usage

.loss(y, x, family, type.measure, foldid = NULL, grouped = TRUE)

Arguments

y	observed values: numeric vector of length $n$
x	predicted values: numeric vector of length $n$
family	character "gaussian", "binomial", "poisson", "mgaussian", or "multinomial" (to implement: "cox")
type.measure	character "deviance", "mse", "mae", "class", or "auc"
foldid	fold identifiers: integer vector of length $n$, or NULL
grouped	logical (for "cox" only)

Examples

NA

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Simulation

Description

Functions for simulating data

Usage

.simulate.block(n, p, mode, family = "gaussian")

Arguments

n	sample size: positive integer
p	dimensionality: positive integer
mode	character "sparse", "dense" or "mixed"
family	character "gaussian", "binomial" or "poisson"

Value

List of vector y and matrix X.

Examples

NA

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Extract Coefficients

Description

Extracts pooled coefficients. (The meta learners weights the coefficients from the base learners.)

Usage

## S3 method for class 'starnet'
coef(object, nzero = NULL, ...)

Arguments

object	starnet object
nzero	maximum number of non-zero coefficients: positive integer, or NULL
...	further arguments (not applicable)

Value

List of scalar alpha and vector beta, containing the pooled intercept and the pooled slopes, respectively.

Examples

set.seed(1)
n <- 50; p <- 100
y <- rnorm(n=n)
X <- matrix(rnorm(n*p),nrow=n,ncol=p)
object <- starnet(y=y,X=X)
coef <- coef(object)

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Model comparison

Description

Compares stacked elastic net, tuned elastic net, ridge and lasso.

Usage

cv.starnet(
  y,
  X,
  family = "gaussian",
  nalpha = 21,
  alpha = NULL,
  nfolds.ext = 10,
  nfolds.int = 10,
  foldid.ext = NULL,
  foldid.int = NULL,
  type.measure = "deviance",
  alpha.meta = 1,
  nzero = NULL,
  intercept = NULL,
  upper.limit = NULL,
  unit.sum = NULL,
  ...
)

Arguments

y	response: numeric vector of length $n$
X	covariates: numeric matrix with $n$ rows (samples) and $p$ columns (variables)
family	character "gaussian", "binomial" or "poisson"
nalpha	number of alpha values
alpha	elastic net mixing parameters: vector of length nalpha with entries between $0$ (ridge) and $1$ (lasso); or NULL (equidistance)
nfolds.ext, nfolds.int, foldid.ext, foldid.int	number of folds (nfolds): positive integer; fold identifiers (foldid): vector of length $n$ with entries between $1$ and nfolds, or NULL, for hold-out (single split) instead of cross-validation (multiple splits): set foldid.ext to $0$ for training and to $1$ for testing samples
type.measure	loss function: character "deviance", "class", "mse" or "mae" (see cv.glmnet)
alpha.meta	meta-learner: value between $0$ (ridge) and $1$ (lasso) for elastic net regularisation; NA for convex combination
nzero	number of non-zero coefficients: scalar/vector including positive integer(s) or NA; or NULL (no post hoc feature selection)
intercept	settings for meta-learner: logical, or NULL (intercept=!is.na(alpha.meta), upper.limit=TRUE, unit.sum=is.na(alpha.meta))
upper.limit	settings for meta-learner: logical, or NULL (intercept=!is.na(alpha.meta), upper.limit=TRUE, unit.sum=is.na(alpha.meta))
unit.sum	settings for meta-learner: logical, or NULL (intercept=!is.na(alpha.meta), upper.limit=TRUE, unit.sum=is.na(alpha.meta))
...	further arguments (not applicable)

Value

List containing the cross-validated loss (or out-of sample loss if nfolds.ext equals two, and foldid.ext contains zeros and ones). The slot meta contains the loss from the stacked elastic net (stack), the tuned elastic net (tune), ridge, lasso, and the intercept-only model (none). The slot base contains the loss from the base learners. And the slot extra contains the loss from the restricted stacked elastic net (stack), lasso, and lasso-like elastic net (enet), with the maximum number of non-zero coefficients shown in the column name.

Examples

loss <- cv.starnet(y=y,X=X)

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glmnet:::auc

Description

Import of auc (internal function)

Usage

glmnet.auc(y, prob, w)

Arguments

y	observed classes
prob	predicted probabilities
w	(ignored here)

Value

area under the ROC curve

Examples

NA

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Makes Predictions

Description

Predicts outcome from features with stacked model.

Usage

## S3 method for class 'starnet'
predict(object, newx, type = "response", nzero = NULL, ...)

Arguments

object	starnet object
newx	covariates: numeric matrix with $n$ rows (samples) and $p$ columns (variables)
type	character "link" or "response"
nzero	maximum number of non-zero coefficients: positive integer, or NULL
...	further arguments (not applicable)

Value

Matrix of predicted values, with samples in the rows, and models in the columns. Included models are alpha (fixed elastic net), ridge (i.e. alpha0), lasso (i.e. alpha1), tune (tuned elastic net), stack (stacked elastic net), and none (intercept-only model).

Examples

set.seed(1)
n <- 50; p <- 100
y <- rnorm(n=n)
X <- matrix(rnorm(n*p),nrow=n,ncol=p)
object <- starnet(y=y,X=X)
y_hat <- predict(object,newx=X[c(1),,drop=FALSE])

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Print Values

Description

Prints object of class starnet.

Usage

## S3 method for class 'starnet'
print(x, ...)

Arguments

x	starnet object
...	further arguments (not applicable)

Value

Prints "stacked gaussian/binomial/poisson elastic net".

Examples

set.seed(1)
n <- 50; p <- 100
y <- rnorm(n=n)
X <- matrix(rnorm(n*p),nrow=n,ncol=p)
object <- starnet(y=y,X=X)
print(object)

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Stacked Elastic Net Regression

Description

Implements stacked elastic net regression.

Usage

starnet(
  y,
  X,
  family = "gaussian",
  nalpha = 21,
  alpha = NULL,
  nfolds = 10,
  foldid = NULL,
  type.measure = "deviance",
  alpha.meta = 1,
  penalty.factor = NULL,
  intercept = NULL,
  upper.limit = NULL,
  unit.sum = NULL,
  ...
)

Arguments

y	response: numeric vector of length $n$
X	covariates: numeric matrix with $n$ rows (samples) and $p$ columns (variables)
family	character "gaussian", "binomial" or "poisson"
nalpha	number of alpha values
alpha	elastic net mixing parameters: vector of length nalpha with entries between $0$ (ridge) and $1$ (lasso); or NULL (equidistance)
nfolds	number of folds
foldid	fold identifiers: vector of length $n$ with entries between $1$ and nfolds; or NULL (balance)
type.measure	loss function: character "deviance", "class", "mse" or "mae" (see cv.glmnet)
alpha.meta	meta-learner: value between $0$ (ridge) and $1$ (lasso) for elastic net regularisation; NA for convex combination
penalty.factor	differential shrinkage: vector of length $n$ with entries between $0$ (include) and $Inf$ (exclude), or NULL (all $1$)
intercept, upper.limit, unit.sum	settings for meta-learner: logical, or NULL (intercept=!is.na(alpha.meta), upper.limit=TRUE, unit.sum=is.na(alpha.meta))
...	further arguments passed to glmnet

Details

Post hoc feature selection: consider argument nzero in functions coef and predict.

Value

Object of class starnet. The slots base and meta contain cv.glmnet-like objects, for the base and meta learners, respectively.

References

A Rauschenberger, E Glaab, and MA van de Wiel (2020). "Predictive and interpretable models via the stacked elastic net". Bioinformatics. In press. doi:10.1093/bioinformatics/btaa535. [email protected]

Examples

set.seed(1)
n <- 50; p <- 100
y <- rnorm(n=n)
X <- matrix(rnorm(n*p),nrow=n,ncol=p)
object <- starnet(y=y,X=X,family="gaussian")

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Extract Weights

Description

Extracts coefficients from the meta learner, i.e. the weights for the base learners.

Usage

## S3 method for class 'starnet'
weights(object, ...)

Arguments

object	starnet object
...	further arguments (not applicable)

Value

Vector containing intercept and slopes from the meta learner.

Examples

set.seed(1)
n <- 50; p <- 100
y <- rnorm(n=n)
X <- matrix(rnorm(n*p),nrow=n,ncol=p)
object <- starnet(y=y,X=X)
weights(object)

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