make_IC_dmat {ICSKAT}

make_IC_dmat.R

Description

Puts together the entire design matrix for both the left and right ends of the interval, pasting together the non-genetic covariates with the cubic spline basis.

Usage

make_IC_dmat(xMat, lt, rt, obs_ind, tpos_ind, quant_r = NULL, nKnots = 1)

Arguments

xMat

n*p matrix of non-genetic covariates.

lt

n*1 vector with left end of intervals (min is 0).

rt

n*1 vector with right end of intervals.

obs_ind

n*1 vector of whether the event was observed before last follow-up.

tpos_ind

n*1 vector of whether the event was observed after follow-up started (t>0).

quant_r

Quantiles of time to use in constructing the spline, pass in if doing bootstrap.

nKnots

Number of knots to use for cubic spline basis (default is 1).

Value

A list with the elements:

right_dmat

n*(p+nKnots+2) design matrix for right end of interval.

left_dmat

n*(p+nKnots+2) design matrix for left end of interval.

quant_r

Quantiles used for constructing spline.

Examples

set.seed(0)
xMat <- matrix(data=rnorm(200), nrow=100)
bhFunInv <- function(x) {x}
obsTimes <- 1:5
etaVec <- rep(0, 100)
outcomeDat <- gen_IC_data(bhFunInv = bhFunInv, obsTimes = obsTimes, windowHalf = 0.1,
probMiss = 0.1, etaVec = etaVec)
lt <- outcomeDat$leftTimes
rt <- outcomeDat$rightTimes
tpos_ind <- as.numeric(lt > 0)
obs_ind <- as.numeric(rt != Inf)
make_IC_dmat(xMat = xMat, lt = lt, rt = rt, obs_ind = obs_ind, tpos_ind = tpos_ind)