An R-based Plotting Tool (gofplot_msw) to Support the Multistage Weibull(MSW) Time-to-tumor Model

Background: Carcinogenicity data are heavily censored, and events (Incidental and Fatal observations) may be sparse in some dose groups. The multistage Weibull (MSW) Time-to-tumor model describes the probability of a test subject exhibiting a specific carcinogenic response by observation time t, when the subject is exposed to a carcinogen at dosage rate d. Methods similar to the chi-square goodness-of-fit test that is applied to EPA's BMDS quantal models do not apply to the EPA's MSW model with censored data. Development of a suitable goodness-of-fit test, especially for heavily censored and current-status data, is difficult. Objective: To develop graphical comparison of the MSW parametric model and the nonparametric model for judging goodness-of-fit. Results: An R-based plotting tool was developed to support externally peer reviewed and EPA BMDS website posted MSW Time-to-tumor model. It generates diagnostic plots with MSW outputs and assist internal & external users to assess goodness-of-fit for the MSW model. This MSW plotting tool includes several plot types found useful for evaluating goodness-of-fit of survival functions: Probability vs. Time plot, Dose-Response plot, Hazard plot, Quantile-Quantile plot, and Probability-Probability plot. Conclusions: The tool can be used to assess the goodness-of-fit of the (parametric) MSW model by comparing it to a nonparametric model fitted to the same data. The nonparametric model imposes only the most necessary restrictions (esp. monotonicity) on the relationship between time, dose, and probability of tumor onset or death, with no assumption made on the specific distributional form of the data. By minimizing the restrictions on the structure of the model, the empirical nonparametric model fits the data as "closely" as possible. Comparisons between the parametric MSW and nonparametric models provide a subjective assessment for goodness-of-fit of the MSW Time-to-tumor model to the data.

o Time-to-tumor model

o goodness-of-fit

o multistage Weibull(MSW) model

o diagnostic plots 

Beginner

Practice and Applications

Symposium on Data Science and Statistics (SDSS) 2023