Package 'aftPenCDA'

Penalized AFT estimation for right-censored data

Description

Fits a penalized accelerated failure time (AFT) model for right-censored survival data using induced smoothing and a penalized coordinate descent algorithm. Supported penalties include BAR, LASSO, adaptive LASSO, and SCAD.

Usage

aftpen(
  dt,
  lambda,
  se,
  type = c("BAR", "LASSO", "ALASSO", "SCAD"),
  r = 3.7,
  eps = 1e-08,
  max.iter = 100
)

Arguments

dt	A data frame whose first two columns are y and d, where y is the observed survival or censoring time and d is the event indicator (1 for observed event and 0 for right-censoring). The remaining columns are treated as covariates.
lambda	A nonnegative tuning parameter controlling the amount of penalization.
se	A character string specifying the variance estimation method. "CF" Closed-form (plug-in) variance estimator based on the analytic expression of the estimating function (see Equation (6)). "ZL" Perturbation-based variance estimator using the resampling approach of Zeng and Lin (2008).
type	Penalty type. One of "BAR", "LASSO", "ALASSO", or "SCAD".
r	A positive tuning constant used in the SCAD penalty. Ignored unless type = "SCAD". The default is 3.7.
eps	Convergence tolerance for the outer penalized coordinate descent iterations. The default is 1e-8.
max.iter	Maximum number of iterations for the outer penalized coordinate descent algorithm. The default is 100.

Details

The function first calls the Rcpp backend is_aft_cpp() to obtain an initial estimator together with gradient and Hessian information. A Cholesky-based transformation is then applied, followed by coordinate-wise penalized updates.

For type = "BAR", the update uses the internal BAR_threshold() operator. For type = "LASSO", "ALASSO", and "SCAD", soft-thresholding-based updates are used.

Value

A list containing the following components:

• beta: final coefficient estimate on the original scale.

Examples

n = 100
p = 10
beta0 = c(rep(1,3),rep(0,7))
x = matrix(rnorm(n * p), n, p)
T = exp(x%*%beta0 + rnorm(n))
C = rexp(n, rate = exp(-2))
d = 1*(T<C)
y = pmin(T,C)
dt = data.frame(y,d,x)
fit <- aftpen(dt, lambda = 0.1, se = "CF", type = "BAR")
fit$beta

---

Penalized AFT estimation for clustered-partly interval censored data

Description

Fits a penalized accelerated failure time (AFT) model for partly interval censored survival data using induced smoothing and a penalized coordinate descent algorithm. Supported penalties include BAR, LASSO, adaptive LASSO, and SCAD.

Usage

aftpen_pic(
  dt,
  lambda,
  se,
  type = c("BAR", "LASSO", "ALASSO", "SCAD"),
  r = 3.7,
  eps = 1e-08,
  max.iter = 100
)

Arguments

dt	A data frame containing PIC survival data. It must include L, R, delta, and id, where L and R define the observation interval, delta indicates whether the failure time is exactly observed (1) or censored (0), and id is the cluster identifier. The remaining columns are treated as covariates.
lambda	A nonnegative tuning parameter controlling the amount of penalization.
se	A character string specifying the variance estimation method. "CF" Closed-form (analytic plug-in) variance estimator based on the estimating function. "ZL" Perturbation-resampling variance estimator following Zeng and Lin (2008).
type	Penalty type. One of "BAR", "LASSO", "ALASSO", or "SCAD".
r	A positive tuning constant used in the SCAD penalty. Ignored unless type = "SCAD". The default is 3.7.
eps	Convergence tolerance for the outer penalized coordinate descent iterations. The default is 1e-8.
max.iter	Maximum number of iterations for the outer penalized coordinate descent algorithm. The default is 100.

Details

The input data dt are assumed to arise from clustered partly interval-censored survival data with informative cluster sizes.

Specifically, observations are grouped into clusters, where each cluster shares a latent frailty variable that affects both the failure times and the cluster size. As a result, the number of observations within each cluster is not fixed but depends on the underlying frailty, leading to an informative cluster size structure.

For each subject, the failure time follows an accelerated failure time (AFT) model, and the observed data consist of an interval $(L, R)$ together with an indicator delta. When $L = R$ (i.e., delta = 1), the observation is exact; otherwise (delta = 0), the observation is censored and may correspond to left-censoring, right-censoring, or interval-censoring depending on the relationship between the true failure time and the inspection times.

The function first calls the Rcpp backend is_aftp_pic_cpp() to obtain an initial estimator together with gradient and Hessian information. A Cholesky-based transformation is then applied, followed by coordinate-wise penalized updates.

For type = "BAR", the update uses the internal BAR_threshold() operator. For "LASSO", "ALASSO", and "SCAD", soft-thresholding-based updates are used.

Value

A list containing the following components:

• beta: final coefficient estimate on the original scale.

Examples

set.seed(1)

## simplified generator for clustered partly interval-censored data
n <- 50
p <- 2
beta0 <- c(1, 1)
clu_rate <- 0.5
exactrates <- 0.8
left <- 0.001
right <- 0.01

## cluster-level frailty and informative cluster sizes
eta <- 1 / clu_rate
v <- rgamma(n, shape = eta, rate = eta)
m <- ifelse(v > median(v), 5, 3)
id <- rep(seq_len(n), m)
vi <- rep(v, m)

## subject-level covariates and failure times
N <- sum(m)
x <- matrix(rnorm(N * p), ncol = p)
T <- as.vector(exp(x %*% beta0 + vi * log(rexp(N))))

## build (L, R, delta)
L <- R <- delta <- numeric(N)
index <- rbinom(N, 1, exactrates)

for (i in seq_len(N)) {
  if (index[i] == 1) {
    L[i] <- T[i]
    R[i] <- T[i]
    delta[i] <- 1
  } else {
    U <- cumsum(c(1e-8, runif(10, left, right)))
    LL <- U[-length(U)]
    RR <- U[-1]

    if (T[i] < min(LL)) {
      L[i] <- 1e-8
      R[i] <- min(LL)
      delta[i] <- 0
    } else if (T[i] > max(RR)) {
      L[i] <- max(RR)
      R[i] <- 1e8
      delta[i] <- 0
    } else {
      idd <- which(T[i] > LL & T[i] < RR)
      if (length(idd) == 1) {
        L[i] <- LL[idd]
        R[i] <- RR[idd]
        delta[i] <- 0
      } else {
        L[i] <- T[i]
        R[i] <- T[i]
        delta[i] <- 1
      }
    }
  }
}

dt <- data.frame(
  L = L, R = R, delta = delta, id = id,
  x1 = x[, 1], x2 = x[, 2]
)

fit <- aftpen_pic(dt, lambda = 0.001, se = "CF", type = "BAR")
fit$beta

---

Simulated clustered partly interval-censored data

Description

Example dataset for penalized AFT model fitting with clustered partly interval-censored survival data.

Usage

simdat_pic

Format

A data frame with 6 variables:

L

Left endpoint of observation interval

R

Right endpoint of observation interval

delta

Exact observation indicator (1 = exact, 0 = interval)

id

Cluster identifier

x1

First covariate

x2

Second covariate

Source

Simulated data

---

Simulated right-censored data

Description

Example dataset for penalized AFT model fitting with right-censored survival data.

Usage

simdat_rc

Format

A data frame with 100 rows and 12 variables:

y

Observed survival or censoring time

d

Censoring indicator (1 = event observed, 0 = censored)

X1

First covariate

X2

Second covariate

X3

Third covariate

X4

Fourth covariate

X5

Fifth covariate

X6

Sixth covariate

X7

Seventh covariate

X8

Eighth covariate

X9

Ninth covariate

X10

Tenth covariate

Source

Simulated data

---