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This repo contains code for simulating forms of data bias encountered in real-world clinical practice that lead to misleading VPCs

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The VPC and Real World Data

The visual predictive check (VPC) is a standard tool for assessing pharmacometric model suitability, producing visualizations that compare observed data with simulated data such that both model structure and model variability terms can be assessed. However, real-world data commonly reflect clinical decision-making that adapts therapy in response to patient data. As a result, VPCs constructed from such data may display apparent model misspecification, even when models are well-specified. To illustrate possible confounders, four common real-world therapy adaptation scenarios were simulated: (1) varying dose amount with constant interval, (2) varying dosing interval with constant dose amount, (3) patient dropout after identification of a suitable maintenance dose, and (4) variability in sample timing and frequency based on drug concentration measurements. For all scenarios, simulated observations were generated using the same model used to produce the VPC simulations, ensuring that the model was unbiased. When only the dose amount varied, the prediction-corrected VPC (pcVPC) appropriately indicated a well-specified model. In all other cases, both VPC and pcVPC erroneously suggested a misspecified model. These simulated results, together with our broader experience with complex real-world data, demonstrate that VPCs can be misleading when applied to real-world data. We therefore recommend against relying on VPCs to assess model suitability in real-world settings if dosing interval, sample timing or sample frequency varies in response to measured drug concentrations.

knitr::include_graphics("figures/all_plots.png")

This figure shows a comparison of visual predictive check (VPC) and prediction-corrected VPC (pcVPC) for each considered case. Case 0: adaptive dosing with dose quantity adjustment, (a) VPC and (b) pcVPC. Case 1: adaptive dosing with dose interval adjustment, (c) VPC and (d) pcVPC. Case 2: adaptive dosing with dropout based identification of a suitable maintenance dose, (e) VPC and (f) pcVPC. Case 3: Sampling strategy varying based on measured values, (g) VPC, (h) pcVPC, (i) VPC with censoring model applied to simulated data. Points indicate individual observations. Solid black lines (dashed black lines) indicate the median (5th and 95th percentile) of the observed data. Dark blue (light blue) shaded regions indicate the 95% confidence interval for the predicted median (5th and 95th percentile) based on simulation. MTX: methotrexate.

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This repo contains code for simulating forms of data bias encountered in real-world clinical practice that lead to misleading VPCs

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