Estimating a covariate-adjusted survival function using current status data • survML

library(survML)
#> Loading required package: SuperLearner
#> Loading required package: nnls
#> Loading required package: gam
#> Loading required package: splines
#> Loading required package: foreach
#> Loaded gam 1.22-5
#> Super Learner
#> Version: 2.0-29
#> Package created on 2024-02-06
library(ggplot2)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
set.seed(102524)

Introduction

Current status data arise in the analysis of time-to-event variables when each study participant’s event status is observed at only a single monitoring time. The current status sampling scheme represents a particular form of interval censoring: each participant’s event time is known to lie either between the event time support’s lower bound and the monitoring time, or between the monitoring time and the even time support’s upper bound. Traditional nonparametric methods for estimating the event time distribution under current status sampling require independence between the event time and the monitoring time, which may be unrealistic. The function currstatCIR() implements a nonparametric estimation approach that requires only conditional independence between the event time and the monitoring times given measured baseline covariates.

The method implemented in currstatCIR() is called extended causal isotonic regression, or extended CIR for short, due to its connection to the causal isotonic regression procedure proposed by Westling et al. (2020). Specifically, estimation of a survival function using current status data subject to covariate-informed monitoring is analogous to estimation of a monotone causal dose-response curve under covariate-induced confounding. Below, we describe this method and provide an example analysis using simulated data.

Current status data structure

Suppose we are interested in estimating the survival function of a time-to-event outcome $T$ . However, we do not directly observe $T$ ; rather, for each study participant, we observe a monitoring time $Y$ and an indicator of whether or not $T$ is smaller than $Y$ , denoted $\Delta := I(T \leq Y)$ . In addition, we observe a baseline covariate vector $X$ . This data structure is commonly referred to as current status data, and it represents an extreme form of interval censoring.

The extended CIR method implemented in survML was originally devised to analyze symptom survey data from a long COVID study conducted at the University of Washington. Study participants who tested positive for SARS-CoV-2 infection were sent an email survey 28 days after the positive test, and were queried for the presence of persistent COVID-19 symptoms at the time of survey response. Because participants could choose when to respond to the survey, there was substantial variation in response time. In this example, the event time $T$ represents the duration of COVID-19 symptoms after infection, and the monitoring time $Y$ represents the number of days since the positive test at which a participant chose to complete the survey. Baseline covariate information included demographics (sex, age, etc.), preexisting comorbidities, and characteristics of the participant’s acute infection (symptoms, viral load, etc.)

One key complication of the long COVID study was survey nonresponse. By the time data collection ended, fewer than half of the surveyed individuals had responded to the email survey. We use $c_0$ to denote the time — measured since the positive test — at which follow-up ends for a study participant. In many cases, $c_0$ must be determined by the investigator. We consider a participant who has not responded to the survey by time $c_0$ to be a nonrespondent.

Because the long COVID data are not publicly available, in this vignette, we will analyze a simple simulated dataset, generated below. Note that both the event time $T$ and monitoring time $Y$ depend on covariates $X_1$ and $X_2$ . The maximum follow-up time $c_0$ is set to 1.65, so both $Y$ and $Delta$ are set to NA for individuals who have not responded by that time.

# Simulate some current status data
n <- 250
x <- cbind(2*rbinom(n, size = 1, prob = 0.5)-1,
           2*rbinom(n, size = 1, prob = 0.5)-1)
t <- rweibull(n,
              shape = 0.75,
              scale = exp(0.8*x[,1] - 0.4*x[,2]))
y <- rweibull(n,
              shape = 0.75,
              scale = exp(0.8*x[,1] - 0.4*x[,2]))

# Round y to nearest quantile of y, just so there aren't so many unique values
# This will speed computation in this example analysis
quants <- quantile(y, probs = seq(0, 1, by = 0.025), type = 1)
for (i in 1:length(y)){
  y[i] <- quants[which.min(abs(y[i] - quants))]
}
delta <- as.numeric(t <= y)

dat <- data.frame(y = y, delta = delta, x1 = x[,1], x2 = x[,2])

dat$delta[dat$y > 1.65] <- NA
dat$y[dat$y > 1.65] <- NA

Extended CIR method

Details of the extended method can be found in the corresponding manuscript (Wolock et al., 2024). In essence, the procedure consists of the steps outlined below. These steps involve two nuisance functions that must be estimated: (1) $\mu(y,x) := E(\Delta \mid Y = y, X = x)$ , the conditional mean of $\Delta$ given $Y$ and $X$ ; and (2) $g(y,x) := \pi(y \mid x)/E\{\pi(y \mid X)\}$ , a standardization of the conditional density of $Y$ given $X$ . For those familiar with causal inference for continuous exposures, these two nuisance functions can be thought of as analogous to the outcome regression and (standardized) propensity score.

Extended CIR procedure:

Construct estimates $\mu_n$ and $g_n$ of $\mu$ and $g$ , respectively.
Construct pseudo-outcomes $\Gamma_n(\Delta_1, Y_1, X_1), \ldots, \Gamma_n(\Delta_n, Y_n, X_n)$ , defined pointwise as $\Gamma_n(\delta, y, x) = \frac{\delta - \mu_n(y,x)}{g_n(y,x)} + \frac{1}{n}\sum_{j=1}^{n}\mu_n(y, X_j)$ .
Regress these pseudo-outcomes against $Y_1, \ldots, Y_n$ using isotonic regression.

The isotonic regression step requires the investigator to choose a region over which to perform the regression. We denote this region $[t_0,t_1]$ . The endpoints of this region should be chosen so that $t_0$ is larger than the lower bound of the support of $Y$ , and so that $t_1$ is smaller than $c_0$ . Isotonic regression is known to perform poorly near the boundaries of the support of $Y$ , so choosing $t_0$ and $t_1$ to lie slightly inside those boundaries (for example, at the 2.5th and 97.5th percentiles of the distribution of $Y$ ) may be wise. More details are provided in the manuscript.

The currstatCIR() function uses SuperLearner() to estimate $\mu$ and haldensify to estimate $g$ . Control parameters for these functions can be passed using the arguments SL_control and HAL_control. The isotonic regression bounds $[t_0,t_1]$ are specified using the argument eval_region. The n_eval_pts argument specifies the number of time points, evenly spaced on the quantile scale of $Y$ , at which to estimate the survival function.

Below, we analyze the simulated data using currstatCIR. The control parameters for nuisance function estimate are chosen to speed computation for the purpose of this illustration; in real data analyses it is generally advisable to use a larger number of cross-validation folds and a larger SuperLearner() library.

eval_region <- c(0.02, 1.5)
res <- currstatCIR(time = dat$y,
                   event = dat$delta,
                   X = dat[,3:4],
                   SL_control = list(SL.library = c("SL.mean", "SL.glm"),
                                     V = 2),
                   HAL_control = list(n_bins = c(5),
                                      grid_type = c("equal_mass", "equal_range"),
                                      V = 2),
                   eval_region = eval_region,
                   n_eval_pts = 1000)
#> Warning in (function (X, Y, formula = NULL, X_unpenalized = NULL, max_degree = ifelse(ncol(X) >= : Some fit_control arguments are neither default nor glmnet/cv.glmnet arguments: n_folds; 
#> They will be removed from fit_control
#> 20% of observations outside training support...predictions trimmed.

We can plot the estimated survival function, along with a pointwise 95% confidence band, and compare it to the true survival function, shown below in red.

# use Monte Carlo to approximate the true survival function
n_test <- 5e5
x_test <- cbind(2*rbinom(n_test, size = 1, prob = 0.5)-1,
                2*rbinom(n_test, size = 1, prob = 0.5)-1)
t_test <- rweibull(n_test,
                   shape = 0.75,
                   scale = exp(0.8*x_test[,1] - 0.4*x_test[,2]))

S0 <- function(x){
  return(mean(t_test > x))
}

other_data <- data.frame(t = seq(min(res$t), max(res$t), length.out = 1000))
other_data$y <- apply(as.matrix(other_data$t), MARGIN = 1, FUN = S0)

# plot the results
p1 <- ggplot(data = res, aes(x = t)) +
  geom_step(aes(y = S_hat_est)) +
  geom_step(aes(y = S_hat_cil), linetype = "dashed") +
  geom_step(aes(y = S_hat_ciu), linetype = "dashed") +
  geom_smooth(data = other_data, aes(x = t, y = y), color = "red") +
  theme_bw() +
  ylab("Estimated survival probability") +
  xlab("Time") + 
  scale_y_continuous(limits = c(0, 1)) +
  ggtitle("Covariate-adjusted survival curve")
p1
#> `geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'

References

For details of extended CIR, please see the following paper:

Charles J. Wolock, Susan Jacob, Julia C. Bennett, Anna Elias-Warren, Jessica O’Hanlon, Avi Kenny, Nicholas P. Jewell, Andrea Rotnitzky, Stephen R. Cole, Ana A. Weil, Helen Y. Chu and Marco Carone. “Investigating symptom duration using current status data: a case study of post-acute COVID-19 syndrome.” arXiv:2407.04214 (2024).

Other references:

Ted Westling, Peter Gilbert and Marco Carone. “Causal isotonic regression.” Journal of the Royal Statistical Society Series B: Statistical Methodology (2020).

Mark J. van der Laan, Eric C. Polley and Alan E. Hubbard. “Super learner.” Statistical Applications in Genetics and Molecular Biology (2007).

Nima S. Hejazi, Mark J. van der Laan and David Benkeser. “haldensify: Highly adaptive lasso conditional density estimation in R.” The Journal of Open Source Software (2022).