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In medical studies, repeated measurements of biomarkers and time-to-event data are often collected during the follow-up period. To assess the association between these two outcomes, joint models are frequently considered. The most common approach uses a linear mixed model for the longitudinal part and a proportional hazard model for the survival part. The latter assumes a linear relationship between the survival covariates and the log hazard. In this work, we propose an extension allowing the inclusion of nonlinear covariate effects in the survival model using Bayesian penalized B-splines. Our model is valid for non-Gaussian longitudinal responses since we use a generalized linear mixed model for the longitudinal process. A simulation study shows that our method gives good statistical performance and highlights the importance of taking into account the possible nonlinear effects of certain survival covariates. Data from patients with a first progression of glioblastoma are analysed to illustrate the method.

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Double-zero-event studies (DZS) pose a challenge for accurately estimating the overall treatment effect in meta-analysis. Current approaches, such as continuity correction or omission of DZS, are commonly employed, yet these ad hoc methods can yield biased conclusions. Although the standard bivariate generalized linear mixed model can accommodate DZS, it fails to address the potential systemic differences between DZS and other studies. In this paper, we propose a zero-inflated bivariate generalized linear mixed model (ZIBGLMM) to tackle this issue. This two-component finite mixture model includes zero-inflation for a subpopulation with negligible or extremely low risk. We develop both frequentist and Bayesian versions of ZIBGLMM and examine its performance in estimating risk ratios (RRs) against the bivariate generalized linear mixed model and conventional two-stage meta-analysis that excludes DZS. Through extensive simulation studies and real-world meta-analysis case studies, we demonstrate that ZIBGLMM outperforms the bivariate generalized linear mixed model and conventional two-stage meta-analysis that excludes DZS in estimating the true effect size with substantially less bias and comparable coverage probability.

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Linear mixed models (LMMs) are a commonly used method for genome-wide association studies (GWAS) that aim to detect associations between genetic markers and phenotypic measurements in a population of individuals while accounting for population structure and cryptic relatedness. In a standard GWAS, hundreds of thousands to millions of statistical tests are performed, requiring control for multiple hypothesis testing. Typically, static corrections that penalize the number of tests performed are used to control for the family-wise error rate, which is the probability of making at least one false positive. However, it has been shown that in practice this threshold is too conservative for normally distributed phenotypes and not stringent enough for non-normally distributed phenotypes. Therefore, permutation-based LMM approaches have recently been proposed to provide a more realistic threshold that takes phenotypic distributions into account. In this work, we discuss the advantages of permutation-based GWAS approaches, including new simulations and results from a re-analysis of all publicly available Arabidopsis phenotypes from the AraPheno database.

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The COVID-19 pandemic generated distinct mental health challenges, characterised by stress and anxiety due to its unpredictable duration and continuous threat. This study examined the role of meditation practice on anxiety symptoms and perceived stress, considering co-variables such as self-compassion, acceptance, awareness, brooding, lockdown duration, and sociodemographic characteristics. The study used a longitudinal design and data were collected through online surveys from April 2020 to January 2021 (at four different time points) and included 238 participants from Portugal (165 had prior experience with meditation practices, 73 were non-meditators) with a mean age of 43.08 years (SD = 10.96). Linear mixed models revealed that over time, during the lockdown, the non-meditators group demonstrated a greater increase of anxiety symptoms (ß = -0.226, SE = 0.06, p = 0.006) and perceived stress (ß = -0.20, SE = 0.06, p = 0.004), whereas the meditators group showed non-significant (p > 0.05) variations in anxiety and stress symptoms during the same period of time. The effect of meditation on anxiety symptoms was moderated by sex, days of lockdown, self-compassion, and acceptance. The effect of meditation on perceived stress was moderated by sex, years of education, days of lockdown, and levels of awareness. Additionally, the study explored the potential predictive effect of different meditation session lengths, indicating that longer meditation practices offered greater protection against an increase in anxiety symptoms. These findings highlight the importance of cultivating self-regulation skills and investing in preventive mental health strategies to promote well-being and autonomy. Mental health professionals should prioritise educating communities on evidence-based practices like meditation and compassion exercises to enhance overall health.

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Genome-wide association studies (GWAS) significantly enhance our ability to identify trait-associated genomic variants by considering the host genome. Moreover, the hologenome refers to the host organism's collective genetic material and its associated microbiome. In this study, we utilized the hologenome framework, called Hologenome-wide association studies (HWAS), to dissect the architecture of complex traits, including milk yield, methane emissions, rumen physiology in cattle, and gut microbial composition in pigs. We employed four statistical models: (1) GWAS, (2) Microbial GWAS (M-GWAS), (3) HWAS-CG (hologenome interaction estimated using COvariance between Random Effects Genome-based restricted maximum likelihood (CORE-GREML)), and (4) HWAS-H (hologenome interaction estimated using the Hadamard product method). We applied Bonferroni correction to interpret the significant associations in the complex traits. The GWAS and M-GWAS detected one and sixteen significant SNPs for milk yield traits, respectively, whereas the HWAS-CG and HWAS-H each identified eight SNPs. Moreover, HWAS-CG revealed four, and the remaining models identified three SNPs each for methane emissions traits. The GWAS and HWAS-CG detected one and three SNPs for rumen physiology traits, respectively. For the pigs' gut microbial composition traits, the GWAS, M-GWAS, HWAS-CG, and HWAS-H identified 14, 16, 13, and 12 SNPs, respectively. We further explored these associations through SNP annotation and by analyzing biological processes and functional pathways. Additionally, we integrated our GWA results with expression quantitative trait locus (eQTL) data using transcriptome-wide association studies (TWAS) and summary-based Mendelian randomization (SMR) methods for a more comprehensive understanding of SNP-trait associations. Our study revealed hologenomic variability in agriculturally important traits, enhancing our understanding of host-microbiome interactions.

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BACKGROUND: Our societies are facing mental health challenges, which have been compounded by the Covid-19. This event led people to isolate themselves and to stop seeking the help they needed. In response to this situation, the Health and Recovery Learning Center, applying the Recovery College (RC) model, modified its training program to a shorter online format. This study examines the effectiveness of a single RC training course delivered in a shortened online format to a diverse population at risk of mental health deterioration in the context of Covid-19. METHODS: This quasi-experimental study used a one-group pretest-posttest design with repeated measures. Three hundred and fifteen (n = 315) learners agreed to take part in the study and completed questionnaires on wellbeing, anxiety, resilience, self-management, empowerment and stigmatizing attitudes and behaviors. RESULTS: Analyses of variance using a linear mixed models revealed that attending a RC training course had, over time, a statistically significant effect on wellbeing (p = 0.004), anxiety (p < 0.001), self-esteem/self-efficacy (p = 0.005), disclosure/help-seeking (p < 0.001) and a slight effect on resilience (p = 0.019) and optimism/control over the future (p = 0.01). CONCLUSIONS: This study is the first to measure participation in a single online short-format RC training course, with a diversity of learners and a large sample. These results support the hypothesis that an online short-format training course can reduce psychological distress and increase self-efficacy and help-seeking. TRIAL REGISTRATION: This study was previously approved by two certified ethics committees: Comité d'éthique de la recherche du CIUSSS EMTL, which acted as the committee responsible for the multicenter study, reference number MP-12-2021-2421, and Comité d'éthique avec les êtres humains de l'UQTR, reference number CER-20-270-07.01.

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With the steadily increasing abundance of longitudinal neuroimaging studies with large sample sizes and multiple repeated measures, questions arise regarding the appropriate modeling of variance and covariance. The current study examined the influence of standard classes of variance-covariance structures in linear mixed effects (LME) modeling of fMRI data from patients with pediatric mild traumatic brain injury (pmTBI; N = 181) and healthy controls (N = 162). During two visits, participants performed a cognitive control fMRI paradigm that compared congruent and incongruent stimuli. The hemodynamic response function was parsed into peak and late peak phases. Data were analyzed with a 4-way (GROUP×VISIT×CONGRUENCY×PHASE) LME using AFNI's 3dLME and compound symmetry (CS), autoregressive process of order 1 (AR1), and unstructured (UN) variance-covariance matrices. Voxel-wise results dramatically varied both within the cognitive control network (UN>CS for CONGRUENCY effect) and broader brain regions (CS>UN for GROUP:VISIT) depending on the variance-covariance matrix that was selected. Additional testing indicated that both model fit and estimated standard error were superior for the UN matrix, likely as a result of the modeling of individual terms. In summary, current findings suggest that the interpretation of results from complex designs is highly dependent on the selection of the variance-covariance structure using LME modeling.

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BACKGROUND: A Generalized Linear Mixed Model (GLMM) is recommended to meta-analyze diagnostic test accuracy studies (DTAs) based on aggregate or individual participant data. Since a GLMM does not have a closed-form likelihood function or parameter solutions, computational methods are conventionally used to approximate the likelihoods and obtain parameter estimates. The most commonly used computational methods are the Iteratively Reweighted Least Squares (IRLS), the Laplace approximation (LA), and the Adaptive Gauss-Hermite quadrature (AGHQ). Despite being widely used, it has not been clear how these computational methods compare and perform in the context of an aggregate data meta-analysis (ADMA) of DTAs. METHODS: We compared and evaluated the performance of three commonly used computational methods for GLMM - the IRLS, the LA, and the AGHQ, via a comprehensive simulation study and real-life data examples, in the context of an ADMA of DTAs. By varying several parameters in our simulations, we assessed the performance of the three methods in terms of bias, root mean squared error, confidence interval (CI) width, coverage of the 95% CI, convergence rate, and computational speed. RESULTS: For most of the scenarios, especially when the meta-analytic data were not sparse (i.e., there were no or negligible studies with perfect diagnosis), the three computational methods were comparable for the estimation of sensitivity and specificity. However, the LA had the largest bias and root mean squared error for pooled sensitivity and specificity when the meta-analytic data were sparse. Moreover, the AGHQ took a longer computational time to converge relative to the other two methods, although it had the best convergence rate. CONCLUSIONS: We recommend practitioners and researchers carefully choose an appropriate computational algorithm when fitting a GLMM to an ADMA of DTAs. We do not recommend the LA for sparse meta-analytic data sets. However, either the AGHQ or the IRLS can be used regardless of the characteristics of the meta-analytic data.

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Accounting for zonal-level variations and identifying factors that have linear effects on crop production help to make better decisions and plan new policies for effective crop production and food security. The main objective of this study is to identify potential subsets of covariates and estimate their linear effects on crop production. A linear mixed effects model (random--intercept) is used on agricultural sample survey data for Meher seasons from 2012/13 to 2019/20 to explore and identify the best variance-covariance structure for the longitudinal data on 90 zones with eight repeated observations and different sampling weights. The minimum, mean, and maximum crop production by farmers across the country are 1.616, 8.693, and 147.843 quintals, respectively, and about 98 % of farmers produced less than 25 quintals. There is a small rate of increase in mean and median crop production by farmers across the years, and the variability between zones is highest in the year 2019/20 and in the Somali region. The histogram, kernel density, and P-P plots suggested a common logarithm transformation on the crop production variable. Results from the data exploration and variance-covariance structure selection methods suggested a heterogeneous compound symmetry (CSH) structure. Covariates region, year, proportion of farmers who practice pure-agriculture and other-agriculture types, proportion of farmers who use any type of fertilizer, farmer's age, area used, farmer association crop production, indigenous seed used, improved seed used, UREA fertilizer used, other fertilizers used, and percentage of crop damaged are significant in linearly explaining/affecting log crop production, and among these area used, farmers association crop production, UREA fertilizer used, and indigenous seed used have relatively highest effect on log crop production. Zones Wolayita, North-Shewa (Am), West-Arsi, West-Welega, Dawro, and Guji are top/good performers while zones Southwest-Shewa, Waghimra, Guraghe, South-Omo, Keffa, North-Wello, South-Wello, and Eastern Tigray are bottom/poor performers in crop production. Model assumptions and influence diagnostics results suggested the linearity of the model and normality of random effects and residuals are not violated, even though some zones have influences on either model parameters, precisions of estimates of these parameters, and predicted values.

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This paper presents a general framework for simulating plot data in multi-environment field trials with one or more traits. The framework is embedded within the R package FieldSimR, whose core function generates plot errors that capture global field trend, local plot variation, and extraneous variation at a user-defined ratio. FieldSimR's capacity to simulate realistic plot data makes it a flexible and powerful tool for a wide range of improvement processes in plant breeding, such as the optimisation of experimental designs and statistical analyses of multi-environment field trials. FieldSimR provides crucial functionality that is currently missing in other software for simulating plant breeding programmes and is available on CRAN. The paper includes an example simulation of field trials that evaluate 100 maize hybrids for two traits in three environments. To demonstrate FieldSimR's value as an optimisation tool, the simulated data set is then used to compare several popular spatial models for their ability to accurately predict the hybrids' genetic values and reliably estimate the variance parameters of interest. FieldSimR has broader applications to simulating data in other agricultural trials, such as glasshouse experiments.

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Popular statistical software provides the Bayesian information criterion (BIC) for multi-level models or linear mixed models. However, it has been observed that the combination of statistical literature and software documentation has led to discrepancies in the formulas of the BIC and uncertainties as to the proper use of the BIC in selecting a multi-level model with respect to level-specific fixed and random effects. These discrepancies and uncertainties result from different specifications of sample size in the BIC's penalty term for multi-level models. In this study, we derive the BIC's penalty term for level-specific fixed- and random-effect selection in a two-level nested design. In this new version of BIC, called BIC E 1 , this penalty term is decomposed into two parts if the random-effect variance-covariance matrix has full rank: (a) a term with the log of average sample size per cluster and (b) the total number of parameters times the log of the total number of clusters. Furthermore, we derive the new version of BIC, called BIC E 2 , in the presence of redundant random effects. We show that the derived formulae, BIC E 1 and BIC E 2 , adhere to empirical values via numerical demonstration and that BIC E ( E indicating either E 1 or E 2 ) is the best global selection criterion, as it performs at least as well as BIC with the total sample size and BIC with the number of clusters across various multi-level conditions through a simulation study. In addition, the use of BIC E 1 is illustrated with a textbook example dataset.

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BACKGROUND: Few studies have examined longitudinal changes in lifestyle-related factors and frailty. METHODS: We examined the association between individual lifestyle factors (exercise, diet, sleep, alcohol, smoking and body composition), their sum at baseline, their change over the 17-year follow-up and the rate of change in frailty index values using linear mixed models in a cohort of 2,000 participants aged 57-69 years at baseline. RESULTS: A higher number of healthy lifestyle-related factors at baseline was associated with lower levels of frailty but not with its rate of change from late midlife into old age. Participants who stopped exercising regularly (adjusted ß × Time = 0.19, 95%CI = 0.10, 0.27) and who began experiencing sleeping difficulties (adjusted ß × Time = 0.20, 95%CI = 0.10, 0.31) experienced more rapid increases in frailty from late midlife into old age. Conversely, those whose sleep improved (adjusted ß × Time = -0.10, 95%CI = -0.23, -0.01) showed a slower increase in frailty from late midlife onwards. Participants letting go of lifestyle-related factors (decline by 3+ factors vs. no change) became more frail faster from late midlife into old age (adjusted ß × Time = 0.16, 95% CI = 0.01, 0.30). CONCLUSIONS: Lifestyle-related differences in frailty were already evident in late midlife and persisted into old age. Adopting one new healthy lifestyle-related factor had a small impact on a slightly less steeply increasing level of frailty. Maintaining regular exercise and sleeping habits may help prevent more rapid increases in frailty.

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Motivated by measurement errors in radiographic diagnosis of osteoarthritis, we propose a Bayesian approach to identify latent classes in a model with continuous response subject to a monotonic, that is, non-decreasing or non-increasing, process with measurement error. A latent class linear mixed model has been introduced to consider measurement error while the monotonic process is accounted for via truncated normal distributions. The main purpose is to classify the response trajectories through the latent classes to better describe the disease progression within homogeneous subpopulations.

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When analyzing multivariate longitudinal binary data, we estimate the effects on the responses of the covariates while accounting for three types of complex correlations present in the data. These include the correlations within separate responses over time, cross-correlations between different responses at different times, and correlations between different responses at each time point. The number of parameters thus increases quadratically with the dimension of the correlation matrix, making parameter estimation difficult; the estimated correlation matrix must also meet the positive definiteness constraint. The correlation matrix may additionally be heteroscedastic; however, the matrix structure is commonly considered to be homoscedastic and constrained, such as exchangeable or autoregressive with order one. These assumptions are overly strong, resulting in skewed estimates of the covariate effects on the responses. Hence, we propose probit linear mixed models for multivariate longitudinal binary data, where the correlation matrix is estimated using hypersphere decomposition instead of the strong assumptions noted above. Simulations and real examples are used to demonstrate the proposed methods. An open source R package, BayesMGLM, is made available on GitHub at https://github.com/kuojunglee/BayesMGLM/ with full documentation to produce the results.

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Modern biomedical datasets are increasingly high-dimensional and exhibit complex correlation structures. Generalized linear mixed models (GLMMs) have long been employed to account for such dependencies. However, proper specification of the fixed and random effects in GLMMs is increasingly difficult in high dimensions, and computational complexity grows with increasing dimension of the random effects. We present a novel reformulation of the GLMM using a factor model decomposition of the random effects, enabling scalable computation of GLMMs in high dimensions by reducing the latent space from a large number of random effects to a smaller set of latent factors. We also extend our prior work to estimate model parameters using a modified Monte Carlo Expectation Conditional Minimization algorithm, allowing us to perform variable selection on both the fixed and random effects simultaneously. We show through simulation that through this factor model decomposition, our method can fit high-dimensional penalized GLMMs faster than comparable methods and more easily scale to larger dimensions not previously seen in existing approaches.

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Count outcomes are frequently encountered in single-case experimental designs (SCEDs). Generalized linear mixed models (GLMMs) have shown promise in handling overdispersed count data. However, the presence of excessive zeros in the baseline phase of SCEDs introduces a more complex issue known as zero-inflation, often overlooked by researchers. This study aimed to deal with zero-inflated and overdispersed count data within a multiple-baseline design (MBD) in single-case studies. It examined the performance of various GLMMs (Poisson, negative binomial [NB], zero-inflated Poisson [ZIP], and zero-inflated negative binomial [ZINB] models) in estimating treatment effects and generating inferential statistics. Additionally, a real example was used to demonstrate the analysis of zero-inflated and overdispersed count data. The simulation results indicated that the ZINB model provided accurate estimates for treatment effects, while the other three models yielded biased estimates. The inferential statistics obtained from the ZINB model were reliable when the baseline rate was low. However, when the data were overdispersed but not zero-inflated, both the ZINB and ZIP models exhibited poor performance in accurately estimating treatment effects. These findings contribute to our understanding of using GLMMs to handle zero-inflated and overdispersed count data in SCEDs. The implications, limitations, and future research directions are also discussed.

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PURPOSE: To investigate whether intraocular pressure (IOP) fluctuation is associated independently with the rate of visual field (VF) progression in the United Kingdom Glaucoma Treatment Study. DESIGN: Randomized, double-masked, placebo-controlled multicenter trial. PARTICIPANTS: Participants with ≥5 VFs (213 placebo, 217 treatment). METHODS: Associations between IOP metrics and VF progression rates (mean deviation [MD] and five fastest locations) were assessed with linear mixed models. Fluctuation variables were mean Pascal ocular pulse amplitude (OPA), standard deviation (SD) of diurnal Goldmann IOP (diurnal fluctuation), and SD of Goldmann IOP at all visits (long-term fluctuation). Fluctuation values were normalized for mean IOP to make them independent from the mean IOP. Correlated nonfluctuation IOP metrics (baseline, peak, mean, supine, and peak phasing IOP) were combined with principal component analysis, and principal component 1 (PC1) was included as a covariate. Interactions between covariates and time from baseline modeled the effect of the variables on VF rates. Analyses were conducted separately in the two treatment arms. MAIN OUTCOME MEASURES: Associations between IOP fluctuation metrics and rates of MD and the five fastest test locations. RESULTS: In the placebo arm, only PC1 was associated significantly with the MD rate (estimate, -0.19 dB/year [standard error (SE), 0.04 dB/year]; P < 0.001), whereas normalized IOP fluctuation metrics were not. No variable was associated significantly with MD rates in the treatment arm. For the fastest five locations in the placebo group, PC1 (estimate, -0.58 dB/year [SE, 0.16 dB/year]; P < 0.001), central corneal thickness (estimate, 0.26 dB/year [SE, 0.10 dB/year] for 10 µm thicker; P = 0.01) and normalized OPA (estimate, -3.50 dB/year [SE, 1.04 dB/year]; P = 0.001) were associated with rates of progression; normalized diurnal and long-term IOP fluctuations were not. In the treatment group, only PC1 (estimate, -0.27 dB/year [SE, 0.12 dB/year]; P = 0.028) was associated with the rates of progression. CONCLUSIONS: No evidence supports that either diurnal or long-term IOP fluctuation, as measured in clinical practice, are independent factors for glaucoma progression; other aspects of IOP, including mean IOP and peak IOP, may be more informative. Ocular pulse amplitude may be an independent factor for faster glaucoma progression. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

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Purpose: To compare how linear mixed models (LMMs) using Gaussian, Student t, and log-gamma (LG) random effect distributions estimate rates of structural loss in a glaucomatous population using OCT and to compare model performance to ordinary least squares (OLS) regression. Design: Retrospective cohort study. Subjects: Patients in the Bascom Palmer Glaucoma Repository (BPGR). Methods: Eyes with ≥ 5 reliable peripapillary retinal nerve fiber layer (RNFL) OCT tests over ≥ 2 years were identified from the BPGR. Retinal nerve fiber layer thickness values from each reliable test (signal strength ≥ 7/10) and associated time points were collected. Data were modeled using OLS regression as well as LMMs using different random effect distributions. Predictive modeling involved constructing LMMs with (n - 1) tests to predict the RNFL thickness of subsequent tests. A total of 1200 simulated eyes of different baseline RNFL thickness values and progression rates were developed to evaluate the likelihood of declared progression and predicted rates. Main Outcome Measures: Model fit assessed by Watanabe-Akaike information criterion (WAIC) and mean absolute error (MAE) when predicting future RNFL thickness values; log-rank test and median time to progression with simulated eyes. Results: A total of 35 862 OCT scans from 5766 eyes of 3491 subjects were included. The mean follow-up period was 7.0 ± 2.3 years, with an average of 6.2 ± 1.4 tests per eye. The Student t model produced the lowest WAIC. In predictive models, all LMMs demonstrated a significant reduction in MAE when estimating future RNFL thickness values compared with OLS (P < 0.001). Gaussian and Student t models were similar and significantly better than the LG model in estimating future RNFL thickness values (P < 0.001). Simulated eyes confirmed LMM performance in declaring progression sooner than OLS regression among moderate and fast progressors (P < 0.01). Conclusions: LMMs outperformed conventional approaches for estimating rates of OCT RNFL thickness loss in a glaucomatous population. The Student t model provides the best model fit for estimating rates of change in RNFL thickness, although the use of the Gaussian or Student t distribution in models led to similar improvements in accurately estimating RNFL loss. Financial Disclosures: Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

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BACKGROUND: We examined the trajectory of estimated glomerular filtrate rate (eGFR), associated risk factors, and its relationship with end-stage kidney disease (ESKD) among a multiethnic patient population with type 2 diabetes in Singapore. METHODS: A follow-up study included 62 080 individuals with type 2 diabetes aged ≥18 years in a multi-institutional SingHealth Diabetes Registry between 2013 and 2019. eGFR trajectories were analyzed using latent class linear mixed models. Factors associated with eGFR trajectories were evaluated using multinomial logistic regression. The association of eGFR trajectories with ESKD was assessed via competing risk models. RESULTS: Trajectory of kidney function, determined by eGFR, was nonlinear. The trajectory pattern was classified as stable initially then gradual decline (75%), progressive decline (21.9%), and rapid decline (3.1%). Younger age, female sex, Malay ethnicity, lower-income housing type, current smoking, higher glycated hemoglobin, lower low-density lipoprotein, higher triglyceride, uncontrolled blood pressure, albuminuria, cardiovascular disease, hypertension, and higher eGFR levels each were associated with progressive or rapid decline. Compared with the trajectory of stable initially then gradual eGFR decline, progressive decline increased the hazard of ESKD by 6.14-fold (95% confidence interval [CI]: 4.96-7.61)) and rapid decline by 82.55 folds (95% CI: 55.90-121.89). CONCLUSIONS: Three nonlinear trajectory classes of kidney function were identified among multiethnic individuals with type 2 diabetes in Singapore. About one in four individuals had a progressive or rapid decline in eGFR. Our results suggest that eGFR trajectories are correlated with multiple social and modifiable risk factors and inform the risk of ESKD.

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Postmarket drug safety database like vaccine adverse event reporting system (VAERS) collect thousands of spontaneous reports annually, with each report recording occurrences of any adverse events (AEs) and use of vaccines. We hope to identify signal vaccine-AE pairs, for which certain vaccines are statistically associated with certain adverse events (AE), using such data. Thus, the outcomes of interest are multiple AEs, which are binary outcomes and could be correlated because they might share certain latent factors; and the primary covariates are vaccines. Appropriately accounting for the complex correlation among AEs could improve the sensitivity and specificity of identifying signal vaccine-AE pairs. We propose a two-step approach in which we first estimate the shared latent factors among AEs using a working multivariate logistic regression model, and then use univariate logistic regression model to examine the vaccine-AE associations after controlling for the latent factors. Our simulation studies show that this approach outperforms current approaches in terms of sensitivity and specificity. We apply our approach in analyzing VAERS data and report our findings.

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