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Trial-based economic evaluations are increasingly being conducted to support healthcare decision-making. When analysing trial-based economic evaluation data, different methodological challenges may be encountered, including (i) missing data, (ii) correlated costs and effects, (iii) baseline imbalances and (iv) skewness of costs and/or effects. Despite the broad range of methods available to account for these methodological challenges in effectiveness studies, they may not always be directly applicable in trial-based economic evaluations where costs and effects are analysed jointly, and more than one methodological challenge typically needs to be addressed simultaneously. The use of inappropriate methods can bias results and conclusions regarding the cost-effectiveness of healthcare interventions. Eventually, such low-quality evidence can hamper healthcare decision-making, which may in turn result in a waste of already scarce healthcare resources. Therefore, this tutorial aims to provide step-by-step guidance on how to combine appropriate statistical methods for handling the abovementioned methodological challenges using a ready-to-use R script. The theoretical background of the described methods is provided, and their application is illustrated using a simulated trial-based economic evaluation. [ABSTRACT FROM AUTHOR]