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Time‐varying covariates can be important predictors when model based predictions are considered. A Cox model that includes time‐varying covariates is usually referred to as an extended Cox model. When only right censoring is presented in the observed survival times, the conventional partial likelihood method is still applicable to estimate the regression coefficients of an extended Cox model. However, if there are interval‐censored survival times, then the partial likelihood method is not directly available unless an imputation, such as the middle point imputation, is used to replaced the left‐ and interval‐censored data. However, such imputation methods are well known for causing biases. This paper considers fitting of the extended Cox models using the maximum penalised likelihood method allowing observed survival times to be partly interval censored, where a penalty function is used to regularise the baseline hazard estimate. We present simulation studies to demonstrate the performance of our proposed method, and illustrate our method with applications to two real datasets from medical research. [ABSTRACT FROM AUTHOR]

Time‐to‐event data in medical studies may involve some patients who are cured and will never experience the event of interest. In practice, those cured patients are right censored. However, when data contain a cured fraction, standard survival methods such as Cox proportional hazards models can produce biased results and therefore misleading interpretations. In addition, for some outcomes, the exact time of an event is not known; instead an interval of time in which the event occurred is recorded. This article proposes a new computational approach that can deal with both the cured fraction issues and the interval censoring challenge. To do so, we extend the traditional mixture cure Cox model to accommodate data with partly interval censoring for the observed event times. The traditional method for estimation of the model parameters is based on the expectation‐maximization (EM) algorithm, where the log‐likelihood is maximized through an indirect complete data log‐likelihood function. We propose in this article an alternative algorithm that directly optimizes the log‐likelihood function. Extensive Monte Carlo simulations are conducted to demonstrate the performance of the new method over the EM algorithm. The main advantage of the new algorithm is the generation of asymptotic variance matrices for all the estimated parameters. The new method is applied to a thin melanoma dataset to predict melanoma recurrence. Various inferences, including survival and hazard function plots with point‐wise confidence intervals, are presented. An R package is now available at Github and will be uploaded to R CRAN. [ABSTRACT FROM AUTHOR]