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Outcome trajectory estimation for optimal dynamic treatment regimes with repeated measures. 重复测量最佳动态治疗方案的结果轨迹估计。
IF 1.6 4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-05-22 eCollection Date: 2023-08-01 DOI: 10.1093/jrsssc/qlad037
Yuan Zhang, David M Vock, Megan E Patrick, Lizbeth H Finestack, Thomas A Murray
{"title":"Outcome trajectory estimation for optimal dynamic treatment regimes with repeated measures.","authors":"Yuan Zhang, David M Vock, Megan E Patrick, Lizbeth H Finestack, Thomas A Murray","doi":"10.1093/jrsssc/qlad037","DOIUrl":"10.1093/jrsssc/qlad037","url":null,"abstract":"<p><p>In recent sequential multiple assignment randomized trials, outcomes were assessed multiple times to evaluate longer-term impacts of the dynamic treatment regimes (DTRs). Q-learning requires a scalar response to identify the optimal DTR. Inverse probability weighting may be used to estimate the optimal outcome trajectory, but it is inefficient, susceptible to model mis-specification, and unable to characterize how treatment effects manifest over time. We propose modified Q-learning with generalized estimating equations to address these limitations and apply it to the M-bridge trial, which evaluates adaptive interventions to prevent problematic drinking among college freshmen. Simulation studies demonstrate our proposed method improves efficiency and robustness.</p>","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":"72 4","pages":"976-991"},"PeriodicalIF":1.6,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10474873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10163294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identifying irregular activity sequences: an application to passive household monitoring 识别不规则活动序列:在被动家庭监测中的应用
IF 1.6 4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-05-17 DOI: 10.1093/jrsssc/qlad005
Jess Gillam, R. Killick, Simon Taylor, Jack Heal, Ben Norwood
{"title":"Identifying irregular activity sequences: an application to passive household monitoring","authors":"Jess Gillam, R. Killick, Simon Taylor, Jack Heal, Ben Norwood","doi":"10.1093/jrsssc/qlad005","DOIUrl":"https://doi.org/10.1093/jrsssc/qlad005","url":null,"abstract":"\u0000 Approximately one in five people will live to see their 100th birthday due to advancements in modern medicine and other factors. Over 65’s constitute 42% of elective admissions and 43% of emergency admissions to hospitals. Increasingly, people are turning to technology to help improve health and care of the elderly. There is mixed evidence of the success of wearables in older populations with a key barrier being adoption. In contrast, passive sensors such as infra-red motion and plug sensors have had more success. These passive sensors give us a sequence of categorical “trigger” events throughout the day. This paper proposes a method for detecting subtle changes in sequences while taking account of the natural day-to-day variability and differing numbers of “trigger” events per day.","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":"7 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2023-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84226559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Bayesian feature allocation model for identifying cell subpopulations using CyTOF data. 使用CyTOF数据识别细胞亚群的贝叶斯特征分配模型。
IF 1.6 4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-04-25 eCollection Date: 2023-06-01 DOI: 10.1093/jrsssc/qlad029
Arthur Lui, Juhee Lee, Peter F Thall, May Daher, Katy Rezvani, Rafet Basar
{"title":"A Bayesian feature allocation model for identifying cell subpopulations using CyTOF data.","authors":"Arthur Lui, Juhee Lee, Peter F Thall, May Daher, Katy Rezvani, Rafet Basar","doi":"10.1093/jrsssc/qlad029","DOIUrl":"10.1093/jrsssc/qlad029","url":null,"abstract":"<p><p>A Bayesian feature allocation model (FAM) is presented for identifying cell subpopulations based on multiple samples of cell surface or intracellular marker expression level data obtained by cytometry by time of flight (CyTOF). Cell subpopulations are characterized by differences in marker expression patterns, and cells are clustered into subpopulations based on their observed expression levels. A model-based method is used to construct cell clusters within each sample by modeling subpopulations as latent features, using a finite Indian buffet process. Non-ignorable missing data due to technical artifacts in mass cytometry instruments are accounted for by defining a static missingship mechanism. In contrast with conventional cell clustering methods, which cluster observed marker expression levels separately for each sample, the FAM-based method can be applied simultaneously to multiple samples, and also identify important cell subpopulations likely to be otherwise missed. The proposed FAM-based method is applied to jointly analyse three CyTOF datasets to study natural killer (NK) cells. Because the subpopulations identified by the FAM may define novel NK cell subsets, this statistical analysis may provide useful information about the biology of NK cells and their potential role in cancer immunotherapy which may lead, in turn, to development of improved NK cell therapies.</p>","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":"72 3","pages":"718-738"},"PeriodicalIF":1.6,"publicationDate":"2023-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10264057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9752620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The impact of directly observed therapy on the efficacy of Tuberculosis treatment: a Bayesian multilevel approach 直接观察治疗对结核病治疗效果的影响:贝叶斯多水平方法
IF 1.6 4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-04-25 DOI: 10.1093/jrsssc/qlad034
Widemberg S. Nobre, A. M. Schmidt, E. Moodie, D. Stephens
{"title":"The impact of directly observed therapy on the efficacy of Tuberculosis treatment: a Bayesian multilevel approach","authors":"Widemberg S. Nobre, A. M. Schmidt, E. Moodie, D. Stephens","doi":"10.1093/jrsssc/qlad034","DOIUrl":"https://doi.org/10.1093/jrsssc/qlad034","url":null,"abstract":"\u0000 We propose and discuss a Bayesian procedure to estimate causal effects for multilevel observations in the presence of confounding. This work is motivated by an interest in determining the causal impact of directly observed therapy on the successful treatment of Tuberculosis. We focus on propensity score regression and covariate adjustment to balance the treatment allocation. We discuss the need to include latent local-level random effects in the propensity score model to reduce bias in the estimation of causal effects. A simulation study suggests that accounting for the multilevel nature of the data with latent structures in both the outcome and propensity score models has the potential to reduce bias in the estimation of causal effects.","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":"40 6 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2023-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88071403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Estimating subject-specific hazard functions 估计特定主题的危害函数
IF 1.6 4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-04-24 DOI: 10.1093/jrsssc/qlad030
Moumita Chatterjee, B. Ganguli, Sugata Sen Roy
{"title":"Estimating subject-specific hazard functions","authors":"Moumita Chatterjee, B. Ganguli, Sugata Sen Roy","doi":"10.1093/jrsssc/qlad030","DOIUrl":"https://doi.org/10.1093/jrsssc/qlad030","url":null,"abstract":"\u0000 The central idea of this paper is to compare mean responses of several subjects in the presence of censoring and subject-specific variation. We develop a semiparametric mixed model for fitting subject-specific hazard curves to a set of censored failure times. A spline-based model and a mixed effects framework for smoothing are used. Efficient estimators of fixed parameters and predictors of the random components are derived and their asymptotic properties studied. This is a generalization of the method proposed by [Cai, T., Hyndman, R. J., & Wand, M. P. (2002). Mixed model-based hazard estimation. Journal of Computational and Graphical Statistics, 11(4), 784–798. https://doi.org/10.1198/106186002862] to incorporate additional subject-specific variation of the hazard function. The results are illustrated using two motivating examples.","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":"11 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2023-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88976374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Penalized weighted least-squares estimate for variable selection on correlated multiply imputed data 在相关多重输入数据上进行变量选择的惩罚加权最小二乘估计
IF 1.6 4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-04-24 DOI: 10.1093/jrsssc/qlad028
Yang Li, Haoyu Yang, Haochen Yu, Hanwen Huang, Ye Shen
{"title":"Penalized weighted least-squares estimate for variable selection on correlated multiply imputed data","authors":"Yang Li, Haoyu Yang, Haochen Yu, Hanwen Huang, Ye Shen","doi":"10.1093/jrsssc/qlad028","DOIUrl":"https://doi.org/10.1093/jrsssc/qlad028","url":null,"abstract":"\u0000 Considering the inevitable correlation among different datasets within the same subject, we propose a framework of variable selection on multiply imputed data with penalized weighted least squares (PWLS–MI). The methodological development is motivated by an epidemiological study of A/H7N9 patients from Zhejiang province in China, where nearly half of the variables are not fully observed. Multiple imputation is commonly adopted as a missing data processing method. However, it generates correlations among imputed values within the same subject across datasets. Recent work on variable selection for multiply imputed data does not fully address such similarities. We propose PWLS–MI to incorporate the correlation when performing the variable selection. PWLS–MI can be considered as a framework for variable selection on multiply imputed data since it allows various penalties. We use adaptive LASSO as an illustrating example. Extensive simulation studies are conducted to compare PWLS–MI with recently developed methods and the results suggest that the proposed approach outperforms in terms of both selection accuracy and deletion accuracy. PWLS–MI is shown to select variables with clinical relevance when applied to the A/H7N9 database.","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":"1 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2023-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91394783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A spline-based time-varying reproduction number for modelling epidemiological outbreaks 基于样条的时变繁殖数，用于模拟流行病学暴发
IF 1.6 4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-04-05 DOI: 10.1093/jrsssc/qlad027
Eugen Pircalabelu
{"title":"A spline-based time-varying reproduction number for modelling epidemiological outbreaks","authors":"Eugen Pircalabelu","doi":"10.1093/jrsssc/qlad027","DOIUrl":"https://doi.org/10.1093/jrsssc/qlad027","url":null,"abstract":"\u0000 We develop in this manuscript a method for performing estimation and inference for the reproduction number of an epidemiological outbreak, focusing on the COVID-19 epidemic. The estimator is time-dependent and uses spline modelling to adapt to changes in the outbreak. This is accomplished by directly modelling the series of new infections as a function of time and subsequently using the derivative of the function to define a time-varying reproduction number, which is then used to assess the evolution of the epidemic for several countries.","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":"26 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2023-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74294069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
A Bayesian two-stage group sequential scheme for ordinal endpoints 有序端点的贝叶斯两阶段群序列格式
IF 1.6 4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-04-01 DOI: 10.1093/jrsssc/qlad026
Chengxue Zhong, Hongyu Miao, H. Pan
{"title":"A Bayesian two-stage group sequential scheme for ordinal endpoints","authors":"Chengxue Zhong, Hongyu Miao, H. Pan","doi":"10.1093/jrsssc/qlad026","DOIUrl":"https://doi.org/10.1093/jrsssc/qlad026","url":null,"abstract":"\u0000 Ordinal endpoints are common in clinical studies. For example, many clinical trials for evaluating COVID-19 infection therapies have adopted an ordinal scale as recommended by the World Health Organization. Despite their importance in clinical studies, design methods for ordinal endpoints are limited; in practice, a dichotomized approach is often used for simplicity. Here, we introduce a Bayesian group sequential scheme to assess ordinal endpoints, which considers a proportional-odds (PO) model, a nonproportional-odds (NPO) model, and a PO/NPO-switch model to handle various scenarios. Extensive simulations are conducted to demonstrate desirable performance, and the R package BayesOrdDesign has been made publicly available.","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":"1 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86828937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Learning torus PCA-based classification for multiscale RNA correction with application to SARS-CoV-2 基于学习环面pca的多尺度RNA校正分类及其在SARS-CoV-2中的应用
4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-03-24 DOI: 10.1093/jrsssc/qlad004
Henrik Wiechers, Benjamin Eltzner, Kanti V Mardia, Stephan F Huckemann
{"title":"Learning torus PCA-based classification for multiscale RNA correction with application to SARS-CoV-2","authors":"Henrik Wiechers, Benjamin Eltzner, Kanti V Mardia, Stephan F Huckemann","doi":"10.1093/jrsssc/qlad004","DOIUrl":"https://doi.org/10.1093/jrsssc/qlad004","url":null,"abstract":"Abstract Three-dimensional RNA structures frequently contain atomic clashes. Usually, corrections approximate the biophysical chemistry, which is computationally intensive and often does not correct all clashes. We propose fast, data-driven reconstructions from clash-free benchmark data with two-scale shape analysis: microscopic (suites) dihedral backbone angles, mesoscopic sugar ring centre landmarks. Our analysis relates concentrated mesoscopic scale neighbourhoods to microscopic scale clusters, correcting within-suite-backbone-to-backbone clashes exploiting angular shape and size-and-shape Fréchet means. Validation shows that learned classes highly correspond with literature clusters and reconstructions are well within physical resolution. We illustrate the power of our method using cutting-edge SARS-CoV-2 RNA.","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":"54 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136091430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bayesian model comparison for mortality forecasting 死亡率预测的贝叶斯模型比较
IF 1.6 4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-03-22 DOI: 10.1093/jrsssc/qlad021
Jackie S. T. Wong, J. Forster, Peter W. F. Smith
{"title":"Bayesian model comparison for mortality forecasting","authors":"Jackie S. T. Wong, J. Forster, Peter W. F. Smith","doi":"10.1093/jrsssc/qlad021","DOIUrl":"https://doi.org/10.1093/jrsssc/qlad021","url":null,"abstract":"\u0000 Stochastic models are appealing for mortality forecasting in their ability to generate intervals that quantify uncertainties underlying the forecasts. We present a fully Bayesian implementation of the age-period-cohort-improvement (APCI) model with overdispersion, which is compared with the Lee–Carter model with cohorts. We show that naive prior specification can yield misleading inferences, where we propose Laplace prior as an elegant solution. We also perform model averaging to incorporate model uncertainty. Our findings indicate that the APCI model offers better fit and forecast for England and Wales data spanning 1961–2002. Our approach also allows coherent inclusion of multiple sources of uncertainty, producing well-calibrated probabilistic intervals.","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":"46 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2023-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88234572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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