Description Usage Arguments Details Value Author(s) References See Also Examples
Extends R package ncvreg to the proportional subdistribution hazards model. Penalties include LASSO, SCAD, and MCP. User-specified weights can be assigned to the penalty for each coefficient.
1 2 3 4 |
time |
vector of failure/censoring times |
fstatus |
vector with a unique code for each failure type and a separate code for censored observations |
X |
design matrix; |
failcode |
code of fstatus that denotes the failure type of interest |
cencode |
code of fstatus that denotes censored observations |
penalty |
penalty to be applied to the model. Either "LASSO", "SCAD", or "MCP" |
gamma |
tuning parameter of the MCP/SCAD penalty. Default is 2.7 for MCP and 3.7 for SCAD |
alpha |
tuning parameter indicating contributions from the MCP/SCAD penalty and the L2
penalty. |
lambda.min |
the smallest value for |
nlambda |
number of |
lambda |
a user-specified sequence of |
eps |
iteration stops when the relative change in any coefficient is less than |
max.iter |
maximum number of iterations. Default is 1000 |
penalty.factor |
a vector of weights applied to the penalty for each coefficient.
The length of the vector must be equal to the number of columns of |
weighted |
if |
The crrp
function penalizes the partial likelihood of the proportional subdistribution hazards model from Fine and Gray(1999) with penalty LASSO, SCAD, and MCP. The coordinate algorithm is used for implementation. The criteria BIC
and GCV
are used to select the optimal tuning parameter.
Return a list of class crrp
with components
$beta |
fitted coefficients matrix with |
$iter |
number of iterations until convergence for each |
$lambda |
sequence of tuning parameter values |
$penalty |
same as above |
$gamma |
same as above |
$alpha |
same as above |
$loglik |
log likelihood of the fitted model at each value of
|
$GCV |
generalized cross validation of the fitted model at each value of
|
$BIC |
Bayesian information criteria of the fitted model at each value of
|
$SE |
matrix of standard errors with |
Zhixuan Fu <zhixuan.fu@yale.edu>
Breheny, P. and Huang, J. (2011) Coordinate descent algorithms for nonconvex penalized regression, with applications to biological feature selection. Ann. Appl. Statist., 5: 232-253.
Fine J. and Gray R. (1999) A proportional hazards model for the subdistribution of a competing risk. JASA 94:496-509.
Fu Z., Parikh C. and Zhou B.(2015). Penalized variable selection in competing risks regression. Manuscript submitted for publication.
gcrrp, cmprsk, ncvreg
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | #simulate competing risks data
set.seed(10)
ftime <- rexp(200)
fstatus <- sample(0:2,200,replace=TRUE)
cov <- matrix(runif(1000),nrow=200)
dimnames(cov)[[2]] <- c('x1','x2','x3','x4','x5')
#fit LASSO
fit <- crrp(ftime, fstatus, cov, penalty="LASSO")
#use BIC to select tuning parameters
beta <- fit$beta[, which.min(fit$BIC)]
beta.se <- fit$SE[, which.min(fit$BIC)]
#fit adaptive LASSO
weight <- 1/abs(crr(ftime, fstatus, cov)$coef)
fit2 <-crrp(ftime, fstatus, cov, penalty="LASSO", penalty.factor=weight, weighted=TRUE)
beta2 <- fit2$beta[, which.min(fit2$BIC)]
beta2.se <- fit2$SE[, which.min(fit2$BIC)]
|
Loading required package: survival
Loading required package: Matrix
Loading required package: cmprsk
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