IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0303254.html

A joint penalized spline smoothing model for the number of positive and negative COVID-19 tests

Author

Listed:
  • Dries De Witte
  • Ariel Alonso Abad
  • Thomas Neyens
  • Geert Verbeke
  • Geert Molenberghs

Abstract

One of the key tools to understand and reduce the spread of the SARS-CoV-2 virus is testing. The total number of tests, the number of positive tests, the number of negative tests, and the positivity rate are interconnected indicators and vary with time. To better understand the relationship between these indicators, against the background of an evolving pandemic, the association between the number of positive tests and the number of negative tests is studied using a joint modeling approach. All countries in the European Union, Switzerland, the United Kingdom, and Norway are included in the analysis. We propose a joint penalized spline model in which the penalized spline is reparameterized as a linear mixed model. The model allows for flexible trajectories by smoothing the country-specific deviations from the overall penalized spline and accounts for heteroscedasticity by allowing the autocorrelation parameters and residual variances to vary among countries. The association between the number of positive tests and the number of negative tests is derived from the joint distribution for the random intercepts and slopes. The correlation between the random intercepts and the correlation between the random slopes were both positive. This suggests that, when countries increase their testing capacity, both the number of positive tests and negative tests will increase. A significant correlation was found between the random intercepts, but the correlation between the random slopes was not significant due to a wide credible interval.

Suggested Citation

  • Dries De Witte & Ariel Alonso Abad & Thomas Neyens & Geert Verbeke & Geert Molenberghs, 2024. "A joint penalized spline smoothing model for the number of positive and negative COVID-19 tests," PLOS ONE, Public Library of Science, vol. 19(5), pages 1-21, May.
    • Handle: RePEc:plo:pone00:0303254
    DOI: 10.1371/journal.pone.0303254
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0303254
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0303254&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0303254?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Donald Hedeker & Robin J. Mermelstein & Hakan Demirtas, 2008. "An Application of a Mixed-Effects Location Scale Model for Analysis of Ecological Momentary Assessment (EMA) Data," Biometrics, The International Biometric Society, vol. 64(2), pages 627-634, June.
    2. Ruppert,David & Wand,M. P. & Carroll,R. J., 2003. "Semiparametric Regression," Cambridge Books, Cambridge University Press, number 9780521785167, January.
    3. I. D. Currie & M. Durban & P. H. C. Eilers, 2006. "Generalized linear array models with applications to multidimensional smoothing," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 68(2), pages 259-280, April.
    4. Ruppert,David & Wand,M. P. & Carroll,R. J., 2003. "Semiparametric Regression," Cambridge Books, Cambridge University Press, number 9780521780506, January.
    5. Inyoung Kim & Noah D. Cohen & Raymond J. Carroll, 2003. "Semiparametric Regression Splines in Matched Case-Control Studies," Biometrics, The International Biometric Society, vol. 59(4), pages 1158-1169, December.
    6. Lee, Dae-Jin & Durbán, María, 2009. "Smooth-CAR mixed models for spatial count data," Computational Statistics & Data Analysis, Elsevier, vol. 53(8), pages 2968-2979, June.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Francesca Bruno & Fedele Greco & Massimo Ventrucci, 2016. "Non-parametric regression on compositional covariates using Bayesian P-splines," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 25(1), pages 75-88, March.
    2. Basile, Roberto & Durbán, María & Mínguez, Román & María Montero, Jose & Mur, Jesús, 2014. "Modeling regional economic dynamics: Spatial dependence, spatial heterogeneity and nonlinearities," Journal of Economic Dynamics and Control, Elsevier, vol. 48(C), pages 229-245.
    3. Mariola Sánchez-González & María Durbán & Dae-Jin Lee & Isabel Cañellas & Hortensia Sixto, 2017. "Smooth additive mixed models for predicting aboveground biomass," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 22(1), pages 23-41, March.
    4. Martin Siebenborn & Julian Wagner, 2021. "A multigrid preconditioner for tensor product spline smoothing," Computational Statistics, Springer, vol. 36(4), pages 2379-2411, December.
    5. Otto-Sobotka, Fabian & Salvati, Nicola & Ranalli, Maria Giovanna & Kneib, Thomas, 2019. "Adaptive semiparametric M-quantile regression," Econometrics and Statistics, Elsevier, vol. 11(C), pages 116-129.
    6. Arthur Charpentier & Emmanuel Flachaire & Antoine Ly, 2017. "Econom\'etrie et Machine Learning," Papers 1708.06992, arXiv.org, revised Mar 2018.
    7. Hyunju Son & Youyi Fong, 2021. "Fast grid search and bootstrap‐based inference for continuous two‐phase polynomial regression models," Environmetrics, John Wiley & Sons, Ltd., vol. 32(3), May.
    8. Welham, S.J. & Thompson, R., 2009. "A note on bimodality in the log-likelihood function for penalized spline mixed models," Computational Statistics & Data Analysis, Elsevier, vol. 53(4), pages 920-931, February.
    9. Michael Wegener & Göran Kauermann, 2017. "Forecasting in nonlinear univariate time series using penalized splines," Statistical Papers, Springer, vol. 58(3), pages 557-576, September.
    10. Bernhard Baumgartner & Daniel Guhl & Thomas Kneib & Winfried J. Steiner, 2018. "Flexible estimation of time-varying effects for frequently purchased retail goods: a modeling approach based on household panel data," OR Spectrum: Quantitative Approaches in Management, Springer;Gesellschaft für Operations Research e.V., vol. 40(4), pages 837-873, October.
    11. Zi Ye & Giles Hooker & Stephen P. Ellner, 2021. "Generalized Single Index Models and Jensen Effects on Reproduction and Survival," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 26(3), pages 492-512, September.
    12. Ferraccioli, Federico & Sangalli, Laura M. & Finos, Livio, 2022. "Some first inferential tools for spatial regression with differential regularization," Journal of Multivariate Analysis, Elsevier, vol. 189(C).
    13. Vahid Goodarzi Vanani & Davood Shahsavani & Mohammad Kazemi, 2025. "A robust partial linear model combining modified Huber loss function and variable selection," Statistical Papers, Springer, vol. 66(6), pages 1-28, October.
    14. Alexander Dokumentov & Rob J. Hyndman, 2022. "STR: Seasonal-Trend Decomposition Using Regression," INFORMS Joural on Data Science, INFORMS, vol. 1(1), pages 50-62, April.
    15. Akdeniz Duran, Esra & Härdle, Wolfgang Karl & Osipenko, Maria, 2012. "Difference based ridge and Liu type estimators in semiparametric regression models," Journal of Multivariate Analysis, Elsevier, vol. 105(1), pages 164-175.
    16. Kalogridis, Ioannis & Van Aelst, Stefan, 2023. "Robust penalized estimators for functional linear regression," Journal of Multivariate Analysis, Elsevier, vol. 194(C).
    17. Krisztin, Tamás, 2018. "Semi-parametric spatial autoregressive models in freight generation modeling," Transportation Research Part E: Logistics and Transportation Review, Elsevier, vol. 114(C), pages 121-143.
    18. Goepp, Vivien & Bouaziz, Olivier & Nuel, Grégory, 2025. "Spline regression with automatic knot selection," Computational Statistics & Data Analysis, Elsevier, vol. 202(C).
    19. Lauren N. Berry & Nathaniel E. Helwig, 2021. "Cross-Validation, Information Theory, or Maximum Likelihood? A Comparison of Tuning Methods for Penalized Splines," Stats, MDPI, vol. 4(3), pages 1-24, September.
    20. Nagler Thomas & Schellhase Christian & Czado Claudia, 2017. "Nonparametric estimation of simplified vine copula models: comparison of methods," Dependence Modeling, De Gruyter, vol. 5(1), pages 99-120, January.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0303254. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.