cv.cox.interaction {AIM} | R Documentation |
Cross-validation for selecting the number of binary rules in interaction AIM with survival outcomes in the context of Cox regression.
cv.cox.interaction(x, trt, y, status, K.cv=5, num.replicate=1, nsteps, mincut=0.1, backfit=F, maxnumcut=1, dirp=0)
x |
n by p matrix. The covariate matrix |
trt |
n vector. The treatment indicator |
y |
n vector. The observed follow-up time |
status |
n 0/1 vector. The status indicator. 1=failure and 0=alive. |
K.cv |
K.cv-fold cross validation |
num.replicate |
number of independent replications of K-fold cross validations. |
nsteps |
the maximum number of binary rules to be included in the index |
backfit |
T/F. Whether the existing split points are adjusted after including a new binary rule |
mincut |
the minimum cutting proportion for the binary rule at either end. It typically is between 0 and 0.2. |
maxnumcut |
the maximum number of binary splits per predictor |
dirp |
p vector. The given direction of the binary split for each of the p predictors. 0 represents "no pre-given direction"; 1 represents "(x>cut)"; -1 represents "(x<cut)". Alternatively, "dirp=0" represents that there is no pre-given direction for any of the predictor. |
cv.cox.interaction
implements K-fold cross-validation for the interaction Cox AIM. It estimates the partial likelihood score test statistics for testing the treatment*index interaction in the test set. It also provides pre-validated fits for each observation and pre-validated partial likelihood score test statistics. The output can be used to select the optimal number of binary rules.
cv.cox.interaction
returns
kmax |
the optimal number of binary rules based the cross-validation |
meanscore |
nsteps-vector. The cross-validated partial likelihood score test statistics (significant at 0.05, if greater than 1.96) for the treatment*index interaction. |
pvfit.score |
nsteps-vector. The pre-validated partial likelihood score test statistics (significant at 0.05, if greater than 1.96) for the treatment*index interaction. |
preval |
nsteps by n matrix. Pre-validated fits for individual observation |
L Tian and R Tibshirani Adaptive index models for marker-based risk stratification, Tech Report, available at http://www-stat.stanford.edu/~tibs/AIM.
R Tibshirani and B Efron, Pre-validation and inference in microarrays, Statist. Appl. Genet. Mol. Biol., 1:1-18, 2002.
Lu Tian and Robert Tibshirani
## generate data set.seed(1) n=400 p=10 x=matrix(rnorm(n*p), n, p) z=(x[,1]<0.2)+(x[,5]>0.2) beta=1 trt=rbinom(n,1,0.5) fail.time=rexp(n)*exp(-beta*z*trt) cen.time=rexp(n)*1.25 y=pmin(fail.time, cen.time) y=round(y*10)/10 delta=1*(fail.time<cen.time) ## cross-validate the interaction Cox AIM model a=cv.cox.interaction(x, trt, y, delta, nsteps=10, K.cv=4, num.replicate=5) ## examine the score test statistics for the interaction in the test set par(mfrow=c(1,2)) plot(a$meanscore, type="l") plot(a$pvfit.score, type="l") ## construct the index with the optimal number of binary rules k.opt=a$kmax a=cox.interaction(x, trt, y, delta, nsteps=k.opt) print(a)