Supplemental Material for An Introduction to Modeling Longitudinal Data With Generalized Additive Models: Applications to Single-Case Designs

2014 ◽  
Keyword(s):  
Longitudinal Data ◽  
Single Case ◽  
Generalized Additive Models ◽  
Additive Models ◽  
Single Case Designs

scholarly journals Using generalized additive models to analyze biomedical non-linear longitudinal data

2021 ◽  
Author(s):  
Ariel I. Mundo ◽  
John R. Tipton ◽  
Timothy J. Muldoon
Keyword(s):  
Longitudinal Data ◽  
Biomedical Research ◽  
Repeated Measures ◽  
Generalized Additive Models ◽  
Simulated Data ◽  
Additive Models ◽  
Biomedical Literature ◽  
Missing Observations ◽  
Non Linear ◽  
Biased Estimates

In biomedical research, the outcome of longitudinal studies has been traditionally analyzed using the repeated measures analysis of variance (rm-ANOVA) or more recently, linear mixed models (LMEMs). Although LMEMs are less restrictive than rm-ANOVA in terms of correlation and missing observations, both methodologies share an assumption of linearity in the measured response, which results in biased estimates and unreliable inference when they are used to analyze data where the trends are non-linear, which is a common occurrence in biomedical research. In contrast, generalized additive models (GAMs) relax the linearity assumption, and allow the data to determine the fit of the model while permitting missing observations and different correlation structures. Therefore, GAMs present an excellent choice to analyze non-linear longitudinal data in the context of biomedical research. This paper summarizes the limitations of rm-ANOVA and LMEMs and uses simulated data to visually show how both methods produce biased estimates when used on non-linear data. We also present the basic theory of GAMs, and using trends of oxygen saturation in tumors reported in the biomedical literature, we simulate example longitudinal data (2 treatment groups, 10 subjects per group, 6 repeated measures for each group) to demonstrate how these models can be computationally implemented. We show that GAMs are able to produce estimates that are consistent with the trends of biomedical non-linear data even in the case when missing observations exist (with 40% of the observations missing), allowing reliable inference from the data. To make this work reproducible, the code and data used in this paper are available at: https://github.com/aimundo/GAMs-biomedical-research.

Generalized additive models for longitudinal data

1998 ◽  
Vol 26 (4) ◽  
pp. 517-535 ◽  
Author(s):  
Kiros Berhane ◽  
Robert J. Tibshirani
Keyword(s):  
Longitudinal Data ◽  
Generalized Additive Models ◽  
Additive Models

scholarly journals Predicting Malaria Transmission Dynamics in Dangassa, Mali: A Novel Approach Using Functional Generalized Additive Models

2020 ◽  
Vol 17 (17) ◽  
pp. 6339
Author(s):  
François Freddy Ateba ◽  
Manuel Febrero-Bande ◽  
Issaka Sagara ◽  
Nafomon Sogoba ◽  
Mahamoudou Touré ◽  
...  
Keyword(s):  
Wind Speed ◽  
Malaria Incidence ◽  
Generalized Additive Models ◽  
Community Health Center ◽  
Additive Model ◽  
Additive Models ◽  
Functional Regression ◽  
Novel Approach ◽  
Malaria Incidence Rate ◽  
Mean Wind Speed

Mali aims to reach the pre-elimination stage of malaria by the next decade. This study used functional regression models to predict the incidence of malaria as a function of past meteorological patterns to better prevent and to act proactively against impending malaria outbreaks. All data were collected over a five-year period (2012–2017) from 1400 persons who sought treatment at Dangassa’s community health center. Rainfall, temperature, humidity, and wind speed variables were collected. Functional Generalized Spectral Additive Model (FGSAM), Functional Generalized Linear Model (FGLM), and Functional Generalized Kernel Additive Model (FGKAM) were used to predict malaria incidence as a function of the pattern of meteorological indicators over a continuum of the 18 weeks preceding the week of interest. Their respective outcomes were compared in terms of predictive abilities. The results showed that (1) the highest malaria incidence rate occurred in the village 10 to 12 weeks after we observed a pattern of air humidity levels >65%, combined with two or more consecutive rain episodes and a mean wind speed <1.8 m/s; (2) among the three models, the FGLM obtained the best results in terms of prediction; and (3) FGSAM was shown to be a good compromise between FGLM and FGKAM in terms of flexibility and simplicity. The models showed that some meteorological conditions may provide a basis for detection of future outbreaks of malaria. The models developed in this paper are useful for implementing preventive strategies using past meteorological and past malaria incidence.

The Relationship between Mobility and COVID-19 in Germany: Modeling Case Occurrence using Apple's Mobility Trends Data

2021 ◽  
Author(s):  
Mark David Walker ◽  
Mihály Sulyok
Keyword(s):  
Generalized Additive Models ◽  
Information Criterion ◽  
Additive Models ◽  
Online Data ◽  
German Government ◽  
Explanatory Variables ◽  
Mobility Data ◽  
Community Mobility ◽  
The Relationship ◽  
Potential Use

Abstract Background Restrictions on social interaction and movement were implemented by the German government in March 2020 to reduce the transmission of coronavirus disease 2019 (COVID-19). Apple's “Mobility Trends” (AMT) data details levels of community mobility; it is a novel resource of potential use to epidemiologists. Objective The aim of the study is to use AMT data to examine the relationship between mobility and COVID-19 case occurrence for Germany. Is a change in mobility apparent following COVID-19 and the implementation of social restrictions? Is there a relationship between mobility and COVID-19 occurrence in Germany? Methods AMT data illustrates mobility levels throughout the epidemic, allowing the relationship between mobility and disease to be examined. Generalized additive models (GAMs) were established for Germany, with mobility categories, and date, as explanatory variables, and case numbers as response. Results Clear reductions in mobility occurred following the implementation of movement restrictions. There was a negative correlation between mobility and confirmed case numbers. GAM using all three categories of mobility data accounted for case occurrence as well and was favorable (AIC or Akaike Information Criterion: 2504) to models using categories separately (AIC with “driving,” 2511. “transit,” 2513. “walking,” 2508). Conclusion These results suggest an association between mobility and case occurrence. Further examination of the relationship between movement restrictions and COVID-19 transmission may be pertinent. The study shows how new sources of online data can be used to investigate problems in epidemiology.

scholarly journals Comparing Charlson and Elixhauser comorbidity indices with different weightings to predict in-hospital mortality: an analysis of national inpatient data

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Narayan Sharma ◽  
René Schwendimann ◽  
Olga Endrich ◽  
Dietmar Ausserhofer ◽  
Michael Simon
Keyword(s):  
Hospital Mortality ◽  
Patient Population ◽  
Generalized Additive Models ◽  
Routine Data ◽  
Predictive Performance ◽  
Population Based ◽  
Mortality Prediction ◽  
Additive Models ◽  
General Hospitals ◽  
Net Reclassification Improvement

Abstract Background Understanding how comorbidity measures contribute to patient mortality is essential both to describe patient health status and to adjust for risks and potential confounding. The Charlson and Elixhauser comorbidity indices are well-established for risk adjustment and mortality prediction. Still, a different set of comorbidity weights might improve the prediction of in-hospital mortality. The present study, therefore, aimed to derive a set of new Swiss Elixhauser comorbidity weightings, to validate and compare them against those of the Charlson and Elixhauser-based van Walraven weights in an adult in-patient population-based cohort of general hospitals. Methods Retrospective analysis was conducted with routine data of 102 Swiss general hospitals (2012–2017) for 6.09 million inpatient cases. To derive the Swiss weightings for the Elixhauser comorbidity index, we randomly halved the inpatient data and validated the results of part 1 alongside the established weighting systems in part 2, to predict in-hospital mortality. Charlson and van Walraven weights were applied to Charlson and Elixhauser comorbidity indices. Derivation and validation of weightings were conducted with generalized additive models adjusted for age, gender and hospital types. Results Overall, the Elixhauser indices, c-statistic with Swiss weights (0.867, 95% CI, 0.865–0.868) and van Walraven’s weights (0.863, 95% CI, 0.862–0.864) had substantial advantage over Charlson’s weights (0.850, 95% CI, 0.849–0.851) and in the derivation and validation groups. The net reclassification improvement of new Swiss weights improved the predictive performance by 1.6% on the Elixhauser-van Walraven and 4.9% on the Charlson weights. Conclusions All weightings confirmed previous results with the national dataset. The new Swiss weightings model improved slightly the prediction of in-hospital mortality in Swiss hospitals. The newly derive weights support patient population-based analysis of in-hospital mortality and seek country or specific cohort-based weightings.

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