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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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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
Modelling intra-annual tree stem growth with a distributional regression approach for Gaussian process responses 用高斯过程响应的分布回归方法模拟年际树茎生长
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/qlad015
Hannes Riebl, N. Klein, T. Kneib
{"title":"Modelling intra-annual tree stem growth with a distributional regression approach for Gaussian process responses","authors":"Hannes Riebl, N. Klein, T. Kneib","doi":"10.1093/jrsssc/qlad015","DOIUrl":"https://doi.org/10.1093/jrsssc/qlad015","url":null,"abstract":"\u0000 High-resolution circumference dendrometers measure the irreversible growth and the reversible shrinking and swelling due to the water content of a tree stem. We propose a novel statistical method to decompose these measurements into a permanent and a temporary component, while explaining differences between the trees and years by covariates. Our model embeds Gaussian processes with parametric mean and covariance functions as response structures in a distributional regression framework with structured additive predictors. We discuss different mean and covariance functions, connections with other model classes, Markov chain Monte Carlo inference, and the efficiency of our sampling scheme.","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84823517","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
Approximately linear INGARCH models for spatio-temporal counts 时空计数的近似线性INGARCH模型
IF 1.6 4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-03-16 DOI: 10.1093/jrsssc/qlad018
Malte Jahn, C. Weiß, Hee-Young Kim
{"title":"Approximately linear INGARCH models for spatio-temporal counts","authors":"Malte Jahn, C. Weiß, Hee-Young Kim","doi":"10.1093/jrsssc/qlad018","DOIUrl":"https://doi.org/10.1093/jrsssc/qlad018","url":null,"abstract":"\u0000 Existing integer-valued generalised autoregressive conditional heteroskedasticity (INGARCH) models for spatio-temporal counts do not allow for negative parameter and autocorrelation values. Using approximately linear INGARCH models, the unified and flexible spatio-temporal (B)INGARCH framework for modelling unbounded (bounded) counts is proposed. These models combine negative dependencies with kinds of a long memory. They are easily adapted to special marginal features or cross-dependencies: When modelling precipitation data (counts of rainy hours), we account for zero-inflation, while for cloud-coverage data (counts of okta), we deal with missing data and additional cross-correlation. A copula related to the spatial error model shows an appealing performance.","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80040119","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: 3
Bayesian matrix completion for hypothesis testing. 用于假设检验的贝叶斯矩阵补全。
IF 1.6 4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-03-15 eCollection Date: 2023-05-01 DOI: 10.1093/jrsssc/qlac005
Bora Jin, David B Dunson, Julia E Rager, David M Reif, Stephanie M Engel, Amy H Herring
{"title":"Bayesian matrix completion for hypothesis testing.","authors":"Bora Jin, David B Dunson, Julia E Rager, David M Reif, Stephanie M Engel, Amy H Herring","doi":"10.1093/jrsssc/qlac005","DOIUrl":"10.1093/jrsssc/qlac005","url":null,"abstract":"<p><p>We aim to infer bioactivity of each chemical by assay endpoint combination, addressing sparsity of toxicology data. We propose a Bayesian hierarchical framework which borrows information across different chemicals and assay endpoints, facilitates out-of-sample prediction of activity for chemicals not yet assayed, quantifies uncertainty of predicted activity, and adjusts for multiplicity in hypothesis testing. Furthermore, this paper makes a novel attempt in toxicology to simultaneously model heteroscedastic errors and a nonparametric mean function, leading to a broader definition of activity whose need has been suggested by toxicologists. Real application identifies chemicals most likely active for neurodevelopmental disorders and obesity.</p>","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10184491/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9480094","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
Enumeration of regular fractional factorial designs with four-level and two-level factors 列举具有四水平和二水平因子的规则分数因子设计
IF 1.6 4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-03-10 DOI: 10.1093/jrsssc/qlad031
Alexandre Bohyn, E. Schoen, P. Goos
{"title":"Enumeration of regular fractional factorial designs with four-level and two-level factors","authors":"Alexandre Bohyn, E. Schoen, P. Goos","doi":"10.1093/jrsssc/qlad031","DOIUrl":"https://doi.org/10.1093/jrsssc/qlad031","url":null,"abstract":"\u0000 Designs for screening experiments usually include factors with two levels only. Adding a few four-level factors allows for the inclusion of multi-level categorical factors or quantitative factors with possible quadratic or third-order effects. Three examples motivated us to generate a large catalogue of designs with two-level factors as well as four-level factors. To create the catalogue, we considered three methods. In the first method, we select designs using a search table, and in the second method, we use a procedure that selects candidate designs based on the properties of their projections into fewer factors. The third method is actually a benchmark method, in which we use a general orthogonal array enumeration algorithm. We compare the efficiencies of the new methods for generating complete sets of nonisomorphic designs. Finally, we use the most efficient method to generate a catalogue of designs with up to three four-level factors and up to 20 two-level factors for run sizes 16, 32, 64, and 128. In some cases, a complete enumeration was infeasible. For these cases, we used a bounded enumeration strategy instead. We demonstrate the usefulness of the catalogue by revisiting the motivating examples.","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90815208","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 spatial stochastic frontier model introducing inefficiency spillovers 引入无效率溢出的空间随机前沿模型
IF 1.6 4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-02-24 DOI: 10.1093/jrsssc/qlad012
Federica Galli
{"title":"A spatial stochastic frontier model introducing inefficiency spillovers","authors":"Federica Galli","doi":"10.1093/jrsssc/qlad012","DOIUrl":"https://doi.org/10.1093/jrsssc/qlad012","url":null,"abstract":"\u0000 This paper develops a spatial Durbin stochastic frontier model for panel data introducing spillover effects in the determinants of technical efficiency (SDF-STE). The model nests several existing spatial and non-spatial stochastic frontier specifications and is estimated using maximum-likelihood techniques. Estimates are shown to be unbiased even for small sample sizes and for alternative specifications of the spatial weight matrix implementing different Monte Carlo simulations. Finally, an application to the Italian accommodation sector is provided. Empirical findings suggest the relevance of the SDF-STE model in capturing labour productivity and knowledge spillover effects.","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81544168","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
Using natural strata when examining unmeasured biases in an observational study of neurological side effects of antibiotics 在抗生素神经系统副作用的观察性研究中，使用天然地层检查未测量偏差
IF 1.6 4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-02-23 DOI: 10.1093/jrsssc/qlad010
K. Brumberg, Darcy E. Ellis, D. Small, S. Hennessy, P. Rosenbaum
{"title":"Using natural strata when examining unmeasured biases in an observational study of neurological side effects of antibiotics","authors":"K. Brumberg, Darcy E. Ellis, D. Small, S. Hennessy, P. Rosenbaum","doi":"10.1093/jrsssc/qlad010","DOIUrl":"https://doi.org/10.1093/jrsssc/qlad010","url":null,"abstract":"\u0000 Fluoroquinolones are widely prescribed antibiotics that carry a US Food and Drug Administration warning about possible side-effects on the central and peripheral nervous system. We compare 436,891 patients with sinusitis treated with fluoroquinolones to two control groups treated with azithromycin or amoxicillin. In addition to looking for nervous system complications, we look for evidence of bias using outcomes for which an effect was not anticipated. The comparison uses ‘natural strata’ that form control groups proportional in size to the treated group and balance many covariates beyond those that define the strata. The main technical contribution is a new method for near-optimal construction of natural strata with multiple groups. The online supplement material contains proofs, details, and information about the R package natstrat and replication.","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84822538","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
The importance of context in extreme value analysis with application to extreme temperatures in the USA and Greenland 语境在极端值分析中的重要性，并应用于美国和格陵兰岛的极端温度
IF 1.6 4区 数学
Journal of the Royal Statistical Society Series C-Applied Statistics Pub Date : 2023-02-16 DOI: 10.1093/jrsssc/qlad020
D. Clarkson, E. Eastoe, A. Leeson
{"title":"The importance of context in extreme value analysis with application to extreme temperatures in the USA and Greenland","authors":"D. Clarkson, E. Eastoe, A. Leeson","doi":"10.1093/jrsssc/qlad020","DOIUrl":"https://doi.org/10.1093/jrsssc/qlad020","url":null,"abstract":"\u0000 Statistical extreme value models allow estimation of the frequency, magnitude and spatio-temporal extent of extreme temperature events in the presence of climate change. Unfortunately, the assumptions of many standard methods are not valid for complex environmental data sets, with a realistic statistical model requiring appropriate incorporation of scientific context. We examine two case studies in which the application of routine extreme value methods result in inappropriate models and inaccurate predictions. In the first scenario, record-breaking temperatures experienced in the US in the summer of 2021 are found to exceed the maximum feasible temperature predicted from a standard extreme value analysis of pre-2021 data. Incorporating random effects into the standard methods accounts for additional variability in the model parameters, reflecting shifts in unobserved climatic drivers and permitting greater accuracy in return period prediction. The second scenario examines ice surface temperatures in Greenland. The temperature distribution is found to have a poorly-defined upper tail, with a spike in observations just below 0◦C and an unexpectedly large number of measurements above this value. A Gaussian mixture model fit to the full range of measurements improves fit and predictive abilities in the upper tail when compared to traditional extreme value methods.","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87796961","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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