Journal of the Royal Statistical Society Series C-Applied Statistics最新文献

{"title":"Semi-parametric time-to-event modelling of lengths of hospital stays","authors":"Yang Li,&nbsp;Hao Liu,&nbsp;Xiaoshen Wang,&nbsp;Wanzhu Tu","doi":"10.1111/rssc.12593","DOIUrl":"10.1111/rssc.12593","url":null,"abstract":"<p>Length of stay (LOS) is an essential metric for the quality of hospital care. Published works on LOS analysis have primarily focused on skewed LOS distributions and the influences of patient diagnostic characteristics. Few authors have considered the events that terminate a hospital stay: Both successful discharge and death could end a hospital stay but with completely different implications. Modelling the time to the first occurrence of discharge or death obscures the true nature of LOS. In this research, we propose a structure that simultaneously models the probabilities of discharge and death. The model has a flexible formulation that accounts for both additive and multiplicative effects of factors influencing the occurrence of death and discharge. We present asymptotic properties of the parameter estimates so that valid inference can be performed for the parametric as well as nonparametric model components. Simulation studies confirmed the good finite-sample performance of the proposed method. As the research is motivated by practical issues encountered in LOS analysis, we analysed data from two real clinical studies to showcase the general applicability of the proposed model.</p>","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2022-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/e7/b9/RSSC-71-1623.PMC9826400.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10525190","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}

{"title":"Utility-based Bayesian personalized treatment selection for advanced breast cancer","authors":"Juhee Lee,&nbsp;Peter F. Thall,&nbsp;Bora Lim,&nbsp;Pavlos Msaouel","doi":"10.1111/rssc.12582","DOIUrl":"10.1111/rssc.12582","url":null,"abstract":"<p>A Bayesian method is proposed for personalized treatment selection in settings where data are available from a randomized clinical trial with two or more outcomes. The motivating application is a randomized trial that compared letrozole plus bevacizumab to letrozole alone as first-line therapy for hormone receptor-positive advanced breast cancer. The combination treatment arm had larger median progression-free survival time, but also a higher rate of severe toxicities. This suggests that the risk-benefit trade-off between these two outcomes should play a central role in selecting each patient's treatment, particularly since older patients are less likely to tolerate severe toxicities. To quantify the desirability of each possible outcome combination for an individual patient, we elicited from breast cancer oncologists a utility function that varied with age. The utility was used as an explicit criterion for quantifying risk-benefit trade-offs when making personalized treatment selections. A Bayesian nonparametric multivariate regression model with a dependent Dirichlet process prior was fit to the trial data. Under the fitted model, a new patient's treatment can be selected based on the posterior predictive utility distribution. For the breast cancer trial dataset, the optimal treatment depends on the patient's age, with the combination preferable for patients 70 years or younger and the single agent preferable for patients older than 70.</p>","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2022-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10116488","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}

{"title":"Measuring diachronic sense change: New models and Monte Carlo methods for Bayesian inference","authors":"Schyan Zafar,&nbsp;Geoff K. Nicholls","doi":"10.1111/rssc.12591","DOIUrl":"10.1111/rssc.12591","url":null,"abstract":"<p>In a bag-of-words model, the <i>senses</i> of a word with multiple meanings, for example ‘bank’ (used either in a river-bank or an institution sense), are represented as probability distributions over context words, and sense prevalence is represented as a probability distribution over senses. Both of these may change with time. Modelling and measuring this kind of sense change are challenging due to the typically high-dimensional parameter space and sparse datasets. A recently published corpus of ancient Greek texts contains expert-annotated sense labels for selected target words. Automatic sense-annotation for the word ‘kosmos’ (meaning decoration, order or world) has been used as a test case in recent work with related generative models and Monte Carlo methods. We adapt an existing generative sense change model to develop a simpler model for the main effects of sense and time, and give Markov Chain Monte Carlo methods for Bayesian inference on all these models that are more efficient than existing methods. We carry out automatic sense-annotation of snippets containing ‘kosmos’ using our model, and measure the time-evolution of its three senses and their prevalence. As far as we are aware, ours is the first analysis of this data, within the class of generative models we consider, that quantifies uncertainty and returns credible sets for evolving sense prevalence in good agreement with those given by expert annotation.</p>","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2022-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://rss.onlinelibrary.wiley.com/doi/epdf/10.1111/rssc.12591","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82774142","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}

{"title":"Environmental Engel curves: A neural network approach","authors":"Tullio Mancini,&nbsp;Hector Calvo-Pardo,&nbsp;Jose Olmo","doi":"10.1111/rssc.12588","DOIUrl":"10.1111/rssc.12588","url":null,"abstract":"<p>Environmental Engel curves describe how households' income relates to the pollution associated with the services and goods consumed. This paper estimates these curves with neural networks using the novel dataset constructed in Levinson and O'Brien. We provide further statistical rigor to the empirical analysis by constructing prediction intervals obtained from novel neural network methods such as extra-neural nets and MC dropout. The application of these techniques for five different pollutants allow us to confirm statistically that Environmental Engel curves are upward sloping, have income elasticities smaller than one and shift down, becoming more concave, over time. Importantly, for the last year of the sample, we find an inverted U shape that suggests the existence of a maximum in pollution for medium-to-high levels of household income beyond which pollution flattens or decreases for top income earners.</p>","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://rss.onlinelibrary.wiley.com/doi/epdf/10.1111/rssc.12588","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77934299","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}

{"title":"Non-parametric Bayesian covariate-dependent multivariate functional clustering: An application to time-series data for multiple air pollutants","authors":"Daewon Yang,&nbsp;Taeryon Choi,&nbsp;Eric Lavigne,&nbsp;Yeonseung Chung","doi":"10.1111/rssc.12589","DOIUrl":"10.1111/rssc.12589","url":null,"abstract":"<p>Air pollution is a major threat to public health. Understanding the spatial distribution of air pollution concentration is of great interest to government or local authorities, as it informs about target areas for implementing policies for air quality management. Cluster analysis has been popularly used to identify groups of locations with similar profiles of average levels of multiple air pollutants, efficiently summarising the spatial pattern. This study aimed to cluster locations based on the seasonal patterns of multiple air pollutants incorporating the location-specific characteristics such as socio-economic indicators. For this purpose, we proposed a novel non-parametric Bayesian sparse latent factor model for covariate-dependent multivariate functional clustering. Furthermore, we extend this model to conduct clustering with temporal dependency. The proposed methods are illustrated through a simulation study and applied to time-series data for daily mean concentrations of ozone (<math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mrow>\u0000 <mi>O</mi>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>3</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ {mathrm{O}}_3 $$</annotation>\u0000 </semantics></math>), nitrogen dioxide (<math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>N</mi>\u0000 <msub>\u0000 <mrow>\u0000 <mi>O</mi>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ mathrm{N}{mathrm{O}}_2 $$</annotation>\u0000 </semantics></math>), and fine particulate matter (<math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>P</mi>\u0000 <msub>\u0000 <mrow>\u0000 <mi>M</mi>\u0000 </mrow>\u0000 <mrow>\u0000 <mn>2</mn>\u0000 <mo>.</mo>\u0000 <mn>5</mn>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$$ mathrm{P}{mathrm{M}}_{2.5} $$</annotation>\u0000 </semantics></math>) collected for 25 cities in Canada in 1986–2015.</p>","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2022-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89028372","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}

{"title":"A model-based approach to predict employee compensation components","authors":"Andreea L. Erciulescu,&nbsp;Jean D. Opsomer","doi":"10.1111/rssc.12587","DOIUrl":"10.1111/rssc.12587","url":null,"abstract":"<p>The demand for official statistics at fine levels is motivating researchers to explore estimation methods that extend beyond the traditional survey-based estimation. For this work, the challenge originated with the US Bureau of Labor Statistics, who conducts the National Compensation Survey to collect compensation data from a nationwide sample of establishments. The objective is to obtain predictions of the wage and non-wage components of compensation for a large number of employment domains defined by detailed job characteristics. Survey estimates are only available for a small subset of these domains. To address the objective, we developed a bivariate hierarchical Bayes model that jointly predicts the wage and non-wage compensation components for a large number of employment domains defined by detailed job characteristics. We also discuss solutions to some practical challenges encountered in implementing small area estimation methods in large-scale settings, including methods for defining the prediction space, for constructing and selecting the information that serves as model input, and for obtaining stable survey variance and covariance estimates.</p>","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2022-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88880927","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}

{"title":"Inference on extended-spectrum beta-lactamase Escherichia coli and Klebsiella pneumoniae data through SMC2","authors":"L. Rimella, S. Alderton, M. Sammarro, B. Rowlingson, D. Cocker, N. Feasey, P. Fearnhead, C. Jewell","doi":"10.1093/jrsssc/qlad055","DOIUrl":"https://doi.org/10.1093/jrsssc/qlad055","url":null,"abstract":"\u0000 We propose a novel stochastic model for the spread of antimicrobial-resistant bacteria in a population, together with an efficient algorithm for fitting such a model to sample data. We introduce an individual-based model for the epidemic, with the state of the model determining which individuals are colonised by the bacteria. The transmission rate of the epidemic takes into account both individuals’ locations, individuals’ covariates, seasonality, and environmental effects. The state of our model is only partially observed, with data consisting of test results from individuals from a sample of households. Fitting our model to data is challenging due to the large state space of our model. We develop an efficient SMC2 algorithm to estimate parameters and compare models for the transmission rate. We implement this algorithm in a computationally efficient manner by using the scale invariance properties of the underlying epidemic model. Our motivating application focuses on the dynamics of community-acquired extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae, using data collected as part of the Drivers of Resistance in Uganda and Malawi project. We infer the parameters of the model and learn key epidemic quantities such as the effective reproduction number, spatial distribution of prevalence, household cluster dynamics, and seasonality.","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2022-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86122983","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}

{"title":"Investigating the association of a sensitive attribute with a random variable using the Christofides generalised randomised response design and Bayesian methods","authors":"Shen-Ming Lee,&nbsp;Truong-Nhat Le,&nbsp;Phuoc-Loc Tran,&nbsp;Chin-Shang Li","doi":"10.1111/rssc.12585","DOIUrl":"10.1111/rssc.12585","url":null,"abstract":"<p>In empirical studies involving sensitive topics, in addition to the problem of estimating the population proportion with a sensitive characteristic, a question arises as to whether or not there is heterogeneity in the distribution of an auxiliary random variable representing the information of subjects collected from a sensitive group and a non-sensitive group. That is, it is of interest to investigate the influence of sensitive attribute on the auxiliary random variable of interest. Finite mixture models are utilised to evaluate the association. A proposed Bayesian method through data augmentation and Markov chain Monte Carlo is applied to estimate unknown parameters of interest. Deviance information criterion and marginal likelihood are employed to select a suitable model to describe the association of the sensitive characteristic with the auxiliary random variable. Simulation and real data studies are conducted to assess the performance of and illustrate applications of the proposed methodology.</p>","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2022-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88884368","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}

{"title":"Statistical integration of heterogeneous omics data: Probabilistic two-way partial least squares (PO2PLS)","authors":"Said el Bouhaddani,&nbsp;Hae-Won Uh,&nbsp;Geurt Jongbloed,&nbsp;Jeanine Houwing-Duistermaat","doi":"10.1111/rssc.12583","DOIUrl":"10.1111/rssc.12583","url":null,"abstract":"<p>The availability of multi-omics data has revolutionized the life sciences by creating avenues for integrated system-level approaches. Data integration links the information across datasets to better understand the underlying biological processes. However, high dimensionality, correlations and heterogeneity pose statistical and computational challenges. We propose a general framework, probabilistic two-way partial least squares (PO2PLS), that addresses these challenges. PO2PLS models the relationship between two datasets using joint and data-specific latent variables. For maximum likelihood estimation of the parameters, we propose a novel fast EM algorithm and show that the estimator is asymptotically normally distributed. A global test for the relationship between two datasets is proposed, specifically addressing the high dimensionality, and its asymptotic distribution is derived. Notably, several existing data integration methods are special cases of PO2PLS. Via extensive simulations, we show that PO2PLS performs better than alternatives in feature selection and prediction performance. In addition, the asymptotic distribution appears to hold when the sample size is sufficiently large. We illustrate PO2PLS with two examples from commonly used study designs: a large population cohort and a small case–control study. Besides recovering known relationships, PO2PLS also identified novel findings. The methods are implemented in our R-package <i>PO2PLS</i>.</p>","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2022-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://rss.onlinelibrary.wiley.com/doi/epdf/10.1111/rssc.12583","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74773208","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}

{"title":"Modelling time-varying rankings with autoregressive and score-driven dynamics","authors":"Vladimír Holý,&nbsp;Jan Zouhar","doi":"10.1111/rssc.12584","DOIUrl":"10.1111/rssc.12584","url":null,"abstract":"<p>We develop a new statistical model to analyse time-varying ranking data. The model can be used with a large number of ranked items, accommodates exogenous time-varying covariates and partial rankings, and is estimated via the maximum likelihood in a straightforward manner. Rankings are modelled using the Plackett–Luce distribution with time-varying worth parameters that follow a mean-reverting time series process. To capture the dependence of the worth parameters on past rankings, we utilise the conditional score in the fashion of the generalised autoregressive score models. Simulation experiments show that the small-sample properties of the maximum-likelihood estimator improve rapidly with the length of the time series and suggest that statistical inference relying on conventional Hessian-based standard errors is usable even for medium-sized samples. In an empirical study, we apply the model to the results of the Ice Hockey World Championships. We also discuss applications to rankings based on underlying indices, repeated surveys and non-parametric efficiency analysis.</p>","PeriodicalId":49981,"journal":{"name":"Journal of the Royal Statistical Society Series C-Applied Statistics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2022-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83166449","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}