cox.fit {glmnet}

Fit a Cox regression model with elastic net regularization for a single value of lambda

Description

Fit a Cox regression model via penalized maximum likelihood for a single value of lambda. Can deal with (start, stop] data and strata, as well as sparse design matrices.

Usage

cox.fit(
  x,
  y,
  weights,
  lambda,
  alpha = 1,
  offset = rep(0, nobs),
  thresh = 1e-10,
  maxit = 1e+05,
  penalty.factor = rep(1, nvars),
  exclude = c(),
  lower.limits = -Inf,
  upper.limits = Inf,
  warm = NULL,
  from.cox.path = FALSE,
  save.fit = FALSE,
  trace.it = 0
)

Arguments

x

Input matrix, of dimension nobs x nvars; each row is an observation vector. If it is a sparse matrix, it is assumed to be unstandardized. It should have attributes xm and xs, where xm(j) and xs(j) are the centering and scaling factors for variable j respsectively. If it is not a sparse matrix, it is assumed that any standardization needed has already been done.

y

Survival response variable, must be a Surv or stratifySurv object.

weights

Observation weights. cox.fit does NOT standardize these weights.

lambda

A single value for the lambda hyperparameter.

alpha

See glmnet help file

offset

See glmnet help file

thresh

Convergence threshold for coordinate descent. Each inner coordinate-descent loop continues until the maximum change in the objective after any coefficient update is less than thresh times the null deviance. Default value is 1e-10.

maxit

Maximum number of passes over the data; default is 10^5. (If a warm start object is provided, the number of passes the warm start object performed is included.)

penalty.factor

See glmnet help file

exclude

See glmnet help file

lower.limits

See glmnet help file

upper.limits

See glmnet help file

warm

Either a glmnetfit object or a list (with name beta containing coefficients) which can be used as a warm start. Default is NULL, indicating no warm start. For internal use only.

from.cox.path

Was cox.fit() called from cox.path()? Default is FALSE.This has implications for computation of the penalty factors.

save.fit

Return the warm start object? Default is FALSE.

trace.it

Controls how much information is printed to screen. If trace.it=2, some information about the fitting procedure is printed to the console as the model is being fitted. Default is trace.it=0 (no information printed). (trace.it=1 not used for compatibility with glmnet.path.)

Details

WARNING: Users should not call cox.fit directly. Higher-level functions in this package call cox.fit as a subroutine. If a warm start object is provided, some of the other arguments in the function may be overriden.

cox.fit solves the elastic net problem for a single, user-specified value of lambda. cox.fit works for Cox regression models, including (start, stop] data and strata. It solves the problem using iteratively reweighted least squares (IRLS). For each IRLS iteration, cox.fit makes a quadratic (Newton) approximation of the log-likelihood, then calls elnet.fit to minimize the resulting approximation.

In terms of standardization: cox.fit does not standardize x and weights. penalty.factor is standardized so that they sum up to nvars.

Value

An object with class "coxnet", "glmnetfit" and "glmnet". The list returned contains more keys than that of a "glmnet" object.

a0

Intercept value, NULL for "cox" family.

beta

A nvars x 1 matrix of coefficients, stored in sparse matrix format.

df

The number of nonzero coefficients.

dim

Dimension of coefficient matrix.

lambda

Lambda value used.

dev.ratio

The fraction of (null) deviance explained. The deviance calculations incorporate weights if present in the model. The deviance is defined to be 2*(loglike_sat - loglike), where loglike_sat is the log-likelihood for the saturated model (a model with a free parameter per observation). Hence dev.ratio=1-dev/nulldev.

nulldev

Null deviance (per observation). This is defined to be 2*(loglike_sat -loglike(Null)). The null model refers to the 0 model.

npasses

Total passes over the data.

jerr

Error flag, for warnings and errors (largely for internal debugging).

offset

A logical variable indicating whether an offset was included in the model.

call

The call that produced this object.

nobs

Number of observations.

warm_fit

If save.fit=TRUE, output of C++ routine, used for warm starts. For internal use only.

family

Family used for the model, always "cox".

converged

A logical variable: was the algorithm judged to have converged?

boundary

A logical variable: is the fitted value on the boundary of the attainable values?

obj_function

Objective function value at the solution.