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Matsena Zingoni Z, Chirwa TF, Todd J, Musenge E. A review of multistate modelling approaches in monitoring disease progression: Bayesian estimation using the Kolmogorov-Chapman forward equations. Stat Methods Med Res 2021; 30:1373-1392. [PMID: 33826459 PMCID: PMC7612622 DOI: 10.1177/0962280221997507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
There are numerous fields of science in which multistate models are used, including biomedical research and health economics. In biomedical studies, these stochastic continuous-time models are used to describe the time-to-event life history of an individual through a flexible framework for longitudinal data. The multistate framework can describe more than one possible time-to-event outcome for a single individual. The standard estimation quantities in multistate models are transition probabilities and transition rates which can be mapped through the Kolmogorov-Chapman forward equations from the Bayesian estimation perspective. Most multistate models assume the Markov property and time homogeneity; however, if these assumptions are violated, an extension to non-Markovian and time-varying transition rates is possible. This manuscript extends reviews in various types of multistate models, assumptions, methods of estimation and data features compatible with fitting multistate models. We highlight the contrast between the frequentist (maximum likelihood estimation) and the Bayesian estimation approaches in the multistate modeling framework and point out where the latter is advantageous. A partially observed and aggregated dataset from the Zimbabwe national ART program was used to illustrate the use of Kolmogorov-Chapman forward equations. The transition rates from a three-stage reversible multistate model based on viral load measurements in WinBUGS were reported.
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Affiliation(s)
- Zvifadzo Matsena Zingoni
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,National Institute of Health Research, Causeway, Harare, Zimbabwe
| | - Tobias F Chirwa
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jim Todd
- Department of Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Eustasius Musenge
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Hansen CH, Warner P, Walker A, Parker RA, Whitaker L, Critchley HOD, Weir CJ. A practical guide to pre-trial simulations for Bayesian adaptive trials using SAS and BUGS. Pharm Stat 2018; 17:854-865. [PMID: 30215881 PMCID: PMC6283249 DOI: 10.1002/pst.1897] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 05/03/2018] [Accepted: 07/12/2018] [Indexed: 01/09/2023]
Abstract
It is often unclear what specific adaptive trial design features lead to an efficient design which is also feasible to implement. Before deciding on a particular design, it is generally advisable to carry out a simulation study to characterise the properties of candidate designs under a range of plausible assumptions. The implementation of such pre‐trial simulation studies presents many challenges and requires considerable statistical programming effort and time. Despite the scale and complexity, there is little existing literature to guide the implementation of such projects using commonly available software. This Teacher's Corner article provides a practical step‐by‐step guide to implementing such simulation studies including how to specify and fit a Bayesian model in WinBUGS or OpenBUGS using SAS, and how results from the Bayesian analysis may be pulled back into SAS and used for adaptation of allocation probabilities before simulating subsequent stages of the trial. The interface between the two software platforms is described in detail along with useful tips and tricks. A key strength of our approach is that the entire exercise can be defined and controlled from within a single SAS program.
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Affiliation(s)
- Christian Holm Hansen
- MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
| | - Pamela Warner
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Allan Walker
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.,Edinburgh Clinical Trials Unit, University of Edinburgh, Edinburgh, UK
| | - Richard A Parker
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.,Edinburgh Clinical Trials Unit, University of Edinburgh, Edinburgh, UK
| | - Lucy Whitaker
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
| | | | - Christopher J Weir
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
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Liu Z, Rong T, Zeng D, Shen X, Ma X, Zeng Z. Bayesian population pharmacokinetic modeling of florfenicol in pigs after intravenous and intramuscular administration. J Vet Pharmacol Ther 2018; 41:719-725. [PMID: 29974964 DOI: 10.1111/jvp.12677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 05/11/2018] [Indexed: 12/11/2022]
Abstract
Bayesian population pharmacokinetic models of florfenicol in healthy pigs were developed based on retrospective data in pigs either via intravenous (i.v.) or intramuscular (i.m.) administration. Following i.v. administration, the disposition of florfenicol was best described by a two-compartment open model with the typical values of half-life at α phase (t1/2α ), half-life at β phase (t1/2β ), total body clearance (Cl), and volume of distribution (Vd ) were 0.132 ± 0.0289, 2.78 ± 0.166 hr, 0.215 ± 0.0102, and 0.841 ± 0.0289 L kg-1 , respectively. The disposition of florfenicol after i.m. administration was best described by a one-compartment open model. The typical values of maximum concentration of drug in serum (Cmax ), elimination half-life (t1/2Kel ), Cl, and Volume (V) were 5.52 ± 0.605 μg/ml, 9.96 ± 1.12 hr, 0.228 ± 0.0154 L hr-1 kg-1 , and 3.28 ± 0.402 L/kg, respectively. The between-subject variabilities of all the parameters after i.m. administration were between 25.1%-92.1%. Florfenicol was well absorbed (94.1%) after i.m. administration. According to Monte Carlo simulation, 8.5 and 6 mg/kg were adequate to exert 90% bactericidal effect against Actinobacillus pleuropneumoniae after i.v. and i.m. administration.
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Affiliation(s)
- Zhichang Liu
- Key Laboratory of Animal Nutrition and Feed Science (South China) of Ministry of Agriculture, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ting Rong
- Key Laboratory of Animal Nutrition and Feed Science (South China) of Ministry of Agriculture, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Dongping Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiangguang Shen
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xianyong Ma
- Key Laboratory of Animal Nutrition and Feed Science (South China) of Ministry of Agriculture, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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Ayala-Díaz M, Richardson JML, Anholt BR. Local site differences in survival and parasitism of periwinkles ( Littorina sitkana Philippi, 1846). Ecol Evol 2017; 7:1021-1029. [PMID: 28303174 PMCID: PMC5306019 DOI: 10.1002/ece3.2708] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 11/04/2016] [Accepted: 12/17/2016] [Indexed: 11/13/2022] Open
Abstract
The periwinkle, Littorina sitkana, is found throughout the intertidal zone, often in isolated subpopulations. The majority of trematode parasites use snails as intermediate hosts, and decreased survivorship is often observed in snails infected with trematodes. Sampling L. sitkana from four sites in Barkley Sound, British Columbia, Canada, we test the effects of parasitic infection on snail survival using maximum likelihood and Bayesian approaches using the software MARK and WinBUGS. We found that survival of periwinkles and trematode community composition differed among sites, but survival and trematode prevalence were uncorrelated. WinBUGS performed better than MARK in two ways: (1) by allowing the use of information on known mortality, thus preventing survival overestimation; and (2) by giving more stable estimates while testing the effect of body size on snail survival. Our results suggest that snail survival depends heavily on local environmental factors that may vary greatly within a small geographical region. These findings are important because the majority of experimental studies on survival are done on snails from a single location.
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Affiliation(s)
- Mónica Ayala-Díaz
- Bamfield Marine Sciences Centre Bamfield BC Canada; Department of Biology University of Victoria Victoria BC Canada
| | | | - Bradley R Anholt
- Bamfield Marine Sciences Centre Bamfield BC Canada; Department of Biology University of Victoria Victoria BC Canada
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Wiczling P, Bartkowska-Śniatkowska A, Szerkus O, Siluk D, Rosada-Kurasińska J, Warzybok J, Borsuk A, Kaliszan R, Grześkowiak E, Bienert A. The pharmacokinetics of dexmedetomidine during long-term infusion in critically ill pediatric patients. A Bayesian approach with informative priors. J Pharmacokinet Pharmacodyn 2016; 43:315-24. [PMID: 27221375 PMCID: PMC4886153 DOI: 10.1007/s10928-016-9474-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/06/2016] [Indexed: 12/11/2022]
Abstract
The purpose of this study was to assess the pharmacokinetics of dexmedetomidine in the ICU settings during the prolonged infusion and to compare it with the existing literature data using the Bayesian population modeling with literature-based informative priors. Thirty-eight patients were included in the analysis with concentration measurements obtained at two occasions: first from 0 to 24 h after infusion initiation and second from 0 to 8 h after infusion end. Data analysis was conducted using WinBUGS software. The prior information on dexmedetomidine pharmacokinetics was elicited from the literature study pooling results from a relatively large group of 95 children. A two compartment PK model, with allometrically scaled parameters, maturation of clearance and t-student residual distribution on a log-scale was used to describe the data. The incorporation of time-dependent (different between two occasions) PK parameters improved the model. It was observed that volume of distribution is 1.5-fold higher during the second occasion. There was also an evidence of increased (1.3-fold) clearance for the second occasion with posterior probability equal to 62 %. This work demonstrated the usefulness of Bayesian modeling with informative priors in analyzing pharmacokinetic data and comparing it with existing literature knowledge.
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Affiliation(s)
- Paweł Wiczling
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdansk, Gdansk, Poland.
| | - Alicja Bartkowska-Śniatkowska
- Department of Pediatric Anesthesiology and Intensive Therapy, Poznan University of Medical Sciences, Szpitalna Street 27/33, 60572, Poznan, Poland.
| | - Oliwia Szerkus
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdansk, Gdansk, Poland
| | - Danuta Siluk
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdansk, Gdansk, Poland
| | - Jowita Rosada-Kurasińska
- Department of Pediatric Anesthesiology and Intensive Therapy, Poznan University of Medical Sciences, Szpitalna Street 27/33, 60572, Poznan, Poland
| | - Justyna Warzybok
- Department of Clinical Pharmacy and Biopharmacy, Poznan University of Medical Sciences, Poznan, Poland
| | - Agnieszka Borsuk
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdansk, Gdansk, Poland
| | - Roman Kaliszan
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdansk, Gdansk, Poland
| | - Edmund Grześkowiak
- Department of Clinical Pharmacy and Biopharmacy, Poznan University of Medical Sciences, Poznan, Poland
| | - Agnieszka Bienert
- Department of Clinical Pharmacy and Biopharmacy, Poznan University of Medical Sciences, Poznan, Poland
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Law J. Exploring the Specifications of Spatial Adjacencies and Weights in Bayesian Spatial Modeling with Intrinsic Conditional Autoregressive Priors in a Small-area Study of Fall Injuries. AIMS Public Health 2016; 3:65-82. [PMID: 29546147 PMCID: PMC5690264 DOI: 10.3934/publichealth.2016.1.65] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 03/02/2016] [Indexed: 11/18/2022] Open
Abstract
Intrinsic conditional autoregressive modeling in a Bayeisan hierarchical framework has been increasingly applied in small-area ecological studies. This study explores the specifications of spatial structure in this Bayesian framework in two aspects: adjacency, i.e., the set of neighbor(s) for each area; and (spatial) weight for each pair of neighbors. Our analysis was based on a small-area study of falling injuries among people age 65 and older in Ontario, Canada, that was aimed to estimate risks and identify risk factors of such falls. In the case study, we observed incorrect adjacencies information caused by deficiencies in the digital map itself. Further, when equal weights was replaced by weights based on a variable of expected count, the range of estimated risks increased, the number of areas with probability of estimated risk greater than one at different probability thresholds increased, and model fit improved. More importantly, significance of a risk factor diminished. Further research to thoroughly investigate different methods of variable weights; quantify the influence of specifications of spatial weights; and develop strategies for better defining spatial structure of a map in small-area analysis in Bayesian hierarchical spatial modeling is recommended.
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Affiliation(s)
- Jane Law
- School of Public Health and Health Systems, University of Waterloo, ON, Canada
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Abstract
Recent studies of (cost-) effectiveness in cardiothoracic transplantation have required estimation of mean survival over the lifetime of the recipients. In order to calculate mean survival, the complete survivor curve is required but is often not fully observed, so that survival extrapolation is necessary. After transplantation, the hazard function is bathtub-shaped, reflecting latent competing risks which operate additively in overlapping time periods. The poly-Weibull distribution is a flexible parametric model that may be used to extrapolate survival and has a natural competing risks interpretation. In addition, treatment effects and subgroups can be modelled separately for each component of risk. We describe the model and develop inference procedures using freely available software. The methods are applied to two problems from cardiothoracic transplantation.
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Affiliation(s)
| | - David Lunn
- Medical Research Council Biostatistics Unit, Cambridge, UK
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Abstract
This study presents an overview of conceptual and practical issues of a network meta-analysis (NMA), particularly focusing on its application to randomised controlled trials with a binary outcome of interest. We start from general considerations on NMA to specifically appraise how to collect study data, structure the analytical network and specify the requirements for different models and parameter interpretations, with the ultimate goal of providing physicians and clinician-investigators a practical tool to understand pros and cons of NMA. Specifically, we outline the key steps, from the literature search to sensitivity analysis, necessary to perform a valid NMA of binomial data, exploiting Markov Chain Monte Carlo approaches. We also apply this analytical approach to a case study on the beneficial effects of volatile agents compared to total intravenous anaesthetics for surgery to further clarify the statistical details of the models, diagnostics and computations. Finally, datasets and models for the freeware WinBUGS package are presented for the anaesthetic agent example.
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Affiliation(s)
- Teresa Greco
- Anaesthesia and Intensive Care Department, San Raffaele Scientific Institute, Milan, Italy Section of Medical Statistics and Biometry Giulio A. Maccacaro, Department of Occupational and Environmental Health, University of Milan, Milan, Italy
| | - Giovanni Landoni
- Anaesthesia and Intensive Care Department, San Raffaele Scientific Institute, Milan, Italy
| | - Giuseppe Biondi-Zoccai
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Italy Meta-analysis and Evidence based medicine Training in Cardiology (METCARDIO), Italy
| | - Fabrizio D'Ascenzo
- Meta-analysis and Evidence based medicine Training in Cardiology (METCARDIO), Italy Division of Cardiology, Department of Internal Medicine, Città Della Salute e Della Scienza, Turin, Italy
| | - Alberto Zangrillo
- Anaesthesia and Intensive Care Department, San Raffaele Scientific Institute, Milan, Italy
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