inst/examples/ex-cox_cure_net.R

In intsurv: Integrative Survival Modeling

library(intsurv)

### 1. Regularized Cox cure rate model with elastic-net penalty
## simulate a toy right-censored data with a cure fraction
set.seed(123)
n_obs <- 100
p <- 10
x_mat <- matrix(rnorm(n_obs * p), nrow = n_obs, ncol = p)
colnames(x_mat) <- paste0("x", seq_len(p))
surv_beta <- c(rep(0, p - 5), rep(1, 5))
cure_beta <- c(rep(1, 2), rep(0, p - 2))
dat <- simData4cure(nSubject = n_obs, lambda_censor = 0.01,
                    max_censor = 10, survMat = x_mat,
                    survCoef = surv_beta, cureCoef = cure_beta,
                    b0 = 0.5, p1 = 1, p2 = 1, p3 = 1)

## model-fitting for the given design matrices
fit1 <- cox_cure_net.fit(x_mat, x_mat, dat$obs_time, dat$obs_event,
                         surv_net = list(nlambda = 10, alpha = 1),
                         cure_net = list(nlambda = 10, alpha = 0.8))

## model-fitting for the given model formula
fm <- paste(paste0("x", seq_len(p)), collapse = " + ")
surv_fm <- as.formula(sprintf("~ %s", fm))
cure_fm <- surv_fm
fit2 <- cox_cure_net(surv_fm, cure_fm, data = dat,
                     time = obs_time, event = obs_event)

## summary of BIC's
BIC(fit1)
BIC(fit2)
BIC(fit1)[which.min(BIC(fit1)[, "BIC"]), ]
BIC(fit2)[which.min(BIC(fit2)[, "BIC"]), ]

## list of coefficient estimates based on BIC
coef(fit1)
coef(fit2)


### 2. regularized Cox cure model for uncertain event status
## simulate a toy data
set.seed(123)
n_obs <- 100
p <- 5
x_mat <- matrix(rnorm(n_obs * p), nrow = n_obs, ncol = p)
colnames(x_mat) <- paste0("x", seq_len(p))
surv_beta <- c(rep(0, p - 3), rep(1, 3))
cure_beta <- c(rep(1, 2), rep(0, p - 2))
dat <- simData4cure(nSubject = n_obs, lambda_censor = 0.01,
                    max_censor = 10, survMat = x_mat,
                    survCoef = surv_beta, cureCoef = cure_beta,
                    b0 = 0.5, p1 = 0.95, p2 = 0.95, p3 = 0.95)

## model-fitting from given design matrices
fit1 <- cox_cure_net.fit(
    x_mat, x_mat,
    dat$obs_time, dat$obs_event,
    surv_net = list(nlambda = 5, alpha = 0.5)
)

## model-fitting from given model formula
fm <- paste(paste0("x", seq_len(p)), collapse = " + ")
surv_fm <- as.formula(sprintf("~ %s", fm))
cure_fm <- surv_fm
fit2 <- cox_cure_net(
    surv_fm,
    cure_fm,
    data = dat,
    time = obs_time,
    event = obs_event,
    surv_net = list(nlambda = 5, alpha = 0.9),
    cure_net = list(nlambda = 5, alpha = 0.9)
)

## summary of BIC's
BIC(fit1)
BIC(fit2)

## list of coefficient estimates based on BIC
coef(fit1)
coef(fit2)