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From Spreadsheets to Script: Experiences From Converting a Scottish Cardiovascular Disease Policy Model into R

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Abstract

Given the advantages in transparency, reproducibility, adaptability and computational efficiency in R, there is a growing interest in converting existing spreadsheet-based models into an R script for model re-use and upskilling training among health economic modellers. The objective of this exercise was to convert the Scottish Cardiovascular Disease (CVD) Policy Model from Excel to R and discuss the lessons learnt throughout this process. The CVD model is a competing risk state transition cohort model. Four health economists, with varied experience of R, attempted to replicate an identical model structure in R based on the model in Excel and reproduce the intermediate and final results. Replications varied in their use of specialist health economics packages in addition to standard data management packages. Two versions of the CVD model were created in R along with a Shiny app. Version 1 was developed without health economics specialist packages and produced identical results to the Excel version. Version 2 used the heemod package and did not achieve the same results, possibly due to the non-standard elements of the model and limited time to adapt the functions. The R model requires less than half the computational time than the Excel model. Conversion of the spreadsheet models to script models is feasible for health economists. A step-by-step guide for the conversion process is provided and modellers’ experience is discussed. Coding without specialist packages allows full flexibility, while specialist packages may add convenience if the model structure is suitable. Whichever approach is taken, transparency and replicability remain the key criteria in model programming. Model conversions must maintain standards in these areas regardless of the choice of software.

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Acknowledgements

The original development of the Scottish Cardiovascular Policy Model was funded by the Chief Scientist Office for Scotland CZH/4/557. Mr Jesus Rodriguez Perez from the School of Computing Science at the University of Glasgow provided us with training on the version control software. The work has been presented at the R for Health Technology Assessment (HTA) showcase event in October 2020 organised by the R for HTA consortium. The authors have no financial relationships to disclose. Dr. Yiqiao **n is an associate at Analysis Group, Ltd. Research for this article was undertaken when she was working at University of Glasgow. The views presented in this article are those of the authors only. We sincerely thank the peer reviewers for their insightful and valuable inputs for this paper.

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Authors and Affiliations

  1. Health Economics and Health Technology Assessment (HEHTA), Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK

    Yiqiao **n, Jose Antonio Robles-Zurita, Houra Haghpanahan, Robert Heggie, Ciaran Kohli-Lynch & Jim Lewsey

  2. Edinburgh Clinical Trials Unit (ECTU), University of Edinburgh, Edinburgh, UK

    Ewan Gray

  3. Center for Health Services and Outcomes Research, Northwestern University, Chicago, IL, USA

    Ciaran Kohli-Lynch

  4. Department of Health Services Research and Policy, London School of Hygiene and Tropical Medicine, London, UK

    Andrew Briggs

  5. Public Health, Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK

    David A. McAllister

  6. Brain and Mind Centre, Faculty of Medicine and Health, University of Sydney, Camperdown, Australia

    Kenny D. Lawson

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  1. Yiqiao **n
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  6. Ciaran Kohli-Lynch
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  9. Kenny D. Lawson
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  10. Jim Lewsey
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Correspondence to Yiqiao **n.

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Code availability

Code for the CVD model described in this article is available at https://github.com/yiqiaoxin/CVDmodel.

Authors’ contributions

YX, RH, EG, JL and AB conceptualized this project. YX, EG, JR, HH, JL, AB, CK, RH, KL and DM contributed to the model conversion process and the verification process between the Excel and R models. YX, EG, JR and HH conducted the actual R coding. YX and EG prepared the original draft and all authors critically reviewed the manuscript and provided editing and proofing.

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**n, Y., Gray, E., Robles-Zurita, J.A. et al. From Spreadsheets to Script: Experiences From Converting a Scottish Cardiovascular Disease Policy Model into R. Appl Health Econ Health Policy 20, 149–158 (2022). https://doi.org/10.1007/s40258-021-00684-y

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