Analysis of population pharmacokinetic data using NONMEM and WinBUGS

The aim of this report is to describe the use of WinBUGS for two datasets that arise from typical population pharmacokinetic studies. The first dataset relates to gentamicin concentration-time data that arose as part of routine clinical care of 55 neonates. The second dataset incorporated data from 96 patients receiving enoxaparin. Both datasets were originally analyzed by using NONMEM. In the first instance, although NONMEM provided reasonable estimates of the fixed effects parameters it was unable to provide satisfactory estimates of the between-subject variance. In the second instance, the use of NONMEM resulted in the development of a successful model, albeit with limited available information on the between-subject variability of the pharmacokinetic parameters. WinBUGS was used to develop a model for both of these datasets. Model comparison for the enoxaparin dataset was performed by using the posterior distribution of the log-likelihood and a posterior predictive check. The use of WinBUGS supported the same structural models tried in NONMEM. For the gentamicin dataset a one-compartment model with intravenous infusion was developed, and the population parameters including the full between-subject variance-covariance matrix were available. Analysis of the enoxaparin dataset supported a two compartment model as superior to the one-compartment model, based on the posterior predictive check. Again, the full between-subject variance-covariance matrix parameters were available. Fully Bayesian approaches using MCMC methods, via WinBUGS, can offer added value for analysis of population pharmacokinetic data.

Modelos de volatilidade estocástica em séries financeiras: uma aplicação para o IBOVESPA

Neste artigo apresentamos uma análise Bayesiana para o modelo de volatilidade estocástica (SV) e uma forma generalizada deste, cujo objetivo é estimar a volatilidade de séries temporais financeiras. Considerando alguns casos especiais dos modelos SV usamos algoritmos de Monte Carlo em Cadeias de Markov e o software WinBugs para obter sumários a posteriori para as diferentes formas de modelos SV. Introduzimos algumas técnicas Bayesianas de discriminação para a escolha do melhor modelo a ser usado para estimar as volatilidades e fazer previsões de séries financeiras. Um exemplo empírico de aplicação da metodologia é introduzido com a série financeira do IBOVESPA.

Determinação da prevalência de fibrilhação auricular na população portuguesa ao nível da NUTS III usando modelos hierárquicos bayesianos

A Fibrilhação Auricular é uma alteração do ritmo cardíaco designada por arritmia. Esta patologia é considerada a forma de arritmia mais frequentemente observada na prática clínica e que constitui uma importante causa de morbilidade pelo risco inerente de desenvolvimento de AVC. Em 2010 foi realizado um estudo epidemiológico na população Portuguesa com o objectivo determinar a prevalência de Fibrilhação Auricular na população portuguesa com idade igual ou superior a 40 anos, sob o acrónimo de FAMA. Os dados publicados indicaram uma estimativa de prevalência de 2,5%, com um aumento da prevalência em função da classe etária. A nível regional não foram observadas diferenças na taxa de prevalência. Estudos de mapeamento de doenças mostraram que a determinação de taxas de prevalência por região, quando o número de casos observados é relativamente baixo, apresentam sobredispersão e, consequentemente, uma falta de precisão nas estimativas obtidas através um método frequencista clássico. A utilização de modelos Bayesianos hierárquicos no mapeamento de doenças tem apresentado vantagem na estimação de valores de risco da doença comparativamente à abordagem clássica. Assim, é objectivo deste trabalho determinar a prevalência de Fibrilhação Auricular na população Portuguesa por região, ao nível da NUTS III, usando modelos hierárquicos Bayesianos. Os dados utilizados neste estudo são os dados referentes ao estudo FAMA, pós-estratificados para correcção dos ponderadores. O modelo Bayesiano proposto por Besag, York e Mollié (1991) foi usado para modelar os dados, covariando para a idade e índice de massa corporal. A revisão do desenho do estudo e o recálculo dos ponderadores foi realizado com recurso ao software R, survey, e a análise Bayesiana efectuada através do WinBugs. iii Os resultados deste estudo demonstram que o uso de modelos Bayesianos são uma melhor opção para a estimação de valores risco relativo e prevalência da doença. Contudo, a utilização de covariáveis não resultou numa melhoria considerável ao contrário do que seria esperado. Conclui-se que a Fibrilhação Auricular apresenta variações regionais significativas, a nível de NUTS III, que não devem ser desvalorizadas na determinação de políticas de saúde pública para controle da doença.

The Effect of Four-Lane to Three-Lane Conversion on the Number of Crashes and Crash Rates in Iowa Roads, June 2005

We analyze crash data collected by the Iowa Department of Transportation using Bayesian methods. The data set includes monthly crash numbers, estimated monthly traffic volumes, site length and other information collected at 30 paired sites in Iowa over more than 20 years during which an intervention experiment was set up. The intervention consisted in transforming 15 undivided road segments from four-lane to three lanes, while an additional 15 segments, thought to be comparable in terms of traffic safety-related characteristics were not converted. The main objective of this work is to find out whether the intervention reduces the number of crashes and the crash rates at the treated sites. We fitted a hierarchical Poisson regression model with a change-point to the number of monthly crashes per mile at each of the sites. Explanatory variables in the model included estimated monthly traffic volume, time, an indicator for intervention reflecting whether the site was a “treatment” or a “control” site, and various interactions. We accounted for seasonal effects in the number of crashes at a site by including smooth trigonometric functions with three different periods to reflect the four seasons of the year. A change-point at the month and year in which the intervention was completed for treated sites was also included. The number of crashes at a site can be thought to follow a Poisson distribution. To estimate the association between crashes and the explanatory variables, we used a log link function and added a random effect to account for overdispersion and for autocorrelation among observations obtained at the same site. We used proper but non-informative priors for all parameters in the model, and carried out all calculations using Markov chain Monte Carlo methods implemented in WinBUGS. We evaluated the effect of the four to three-lane conversion by comparing the expected number of crashes per year per mile during the years preceding the conversion and following the conversion for treatment and control sites. We estimated this difference using the observed traffic volumes at each site and also on a per 100,000,000 vehicles. We also conducted a prospective analysis to forecast the expected number of crashes per mile at each site in the study one year, three years and five years following the four to three-lane conversion. Posterior predictive distributions of the number of crashes, the crash rate and the percent reduction in crashes per mile were obtained for each site for the months of January and June one, three and five years after completion of the intervention. The model appears to fit the data well. We found that in most sites, the intervention was effective and reduced the number of crashes. Overall, and for the observed traffic volumes, the reduction in the expected number of crashes per year and mile at converted sites was 32.3% (31.4% to 33.5% with 95% probability) while at the control sites, the reduction was estimated to be 7.1% (5.7% to 8.2% with 95% probability). When the reduction in the expected number of crashes per year, mile and 100,000,000 AADT was computed, the estimates were 44.3% (43.9% to 44.6%) and 25.5% (24.6% to 26.0%) for converted and control sites, respectively. In both cases, the difference in the percent reduction in the expected number of crashes during the years following the conversion was significantly larger at converted sites than at control sites, even though the number of crashes appears to decline over time at all sites. Results indicate that the reduction in the expected number of sites per mile has a steeper negative slope at converted than at control sites. Consistent with this, the forecasted reduction in the number of crashes per year and mile during the years after completion of the conversion at converted sites is more pronounced than at control sites. Seasonal effects on the number of crashes have been well-documented. In this dataset, we found that, as expected, the expected number of monthly crashes per mile tends to be higher during winter months than during the rest of the year. Perhaps more interestingly, we found that there is an interaction between the four to three-lane conversion and season; the reduction in the number of crashes appears to be more pronounced during months, when the weather is nice than during other times of the year, even though a reduction was estimated for the entire year. Thus, it appears that the four to three-lane conversion, while effective year-round, is particularly effective in reducing the expected number of crashes in nice weather.

Longitudinal Poisson modeling: an application for CD4 counting in HIV-infected patients

In this paper, we present different ofrailtyo models to analyze longitudinal data in the presence of covariates. These models incorporate the extra-Poisson variability and the possible correlation among the repeated counting data for each individual. Assuming a CD4 counting data set in HIV-infected patients, we develop a hierarchical Bayesian analysis considering the different proposed models and using Markov Chain Monte Carlo methods. We also discuss some Bayesian discrimination aspects for the choice of the best model.

Estimação clássica e Bayesiana em modelos de sobrevida com fração de cura

In Survival Analysis, long duration models allow for the estimation of the healing fraction, which represents a portion of the population immune to the event of interest. Here we address classical and Bayesian estimation based on mixture models and promotion time models, using different distributions (exponential, Weibull and Pareto) to model failure time. The database used to illustrate the implementations is described in Kersey et al. (1987) and it consists of a group of leukemia patients who underwent a certain type of transplant. The specific implementations used were numeric optimization by BFGS as implemented in R (base::optim), Laplace approximation (own implementation) and Gibbs sampling as implemented in Winbugs. We describe the main features of the models used, the estimation methods and the computational aspects. We also discuss how different prior information can affect the Bayesian estimates

Clinical judgment to estimate pretest probability in the diagnosis of Cushing's syndrome under a Bayesian perspective

OBJECTIVE: To estimate the pretest probability of Cushing's syndrome (CS) diagnosis by a Bayesian approach using intuitive clinical judgment. MATERIALS AND METHODS: Physicians were requested, in seven endocrinology meetings, to answer three questions: "Based on your personal expertise, after obtaining clinical history and physical examination, without using laboratorial tests, what is your probability of diagnosing Cushing's Syndrome?"; "For how long have you been practicing Endocrinology?"; and "Where do you work?". A Bayesian beta regression, using the WinBugs software was employed. RESULTS: We obtained 294 questionnaires. The mean pretest probability of CS diagnosis was 51.6% (95%CI: 48.7-54.3). The probability was directly related to experience in endocrinology, but not with the place of work. CONCLUSION: Pretest probability of CS diagnosis was estimated using a Bayesian methodology. Although pretest likelihood can be context-dependent, experience based on years of practice may help the practitioner to diagnosis CS. Arq Bras Endocrinol Metab. 2012;56(9):633-7

Validation of candidate smear microscopy quality indicators, extracted from tuberculosis laboratory registers

SETTING: Kinshasa Province, Democratic Republic of Congo. OBJECTIVE: To identify and validate register-based indicators of acid-fast bacilli (AFB) microscopy quality. DESIGN: Selection of laboratories based on reliability and variation in routine smear rechecking results. Calculation of relative sensitivity (RS) compared to recheckers and its correlation coefficient (R) with candidate indicators based on a fully probabilistic analysis incorporating vague prior information using WinBUGS. RESULTS: The proportion of positive follow-up smears correlated well (median R 0.81, 95% credibility interval [CI] 0.58-0.93), and the proportion of first smear-positive cases fairly (median R 0.70, 95% CI 0.38-0.89) with RS. The proportions of both positive suspect and low positive case smears showed poor correlations (median R 0.27 and -0.22, respectively, with ranges including zero). CONCLUSIONS: The proportion of positives in follow-up smears is the most promising indicator of AFB smear sensitivity, while the proportion of positive suspects may be more indicative of accessibility and suspect selection. Both can be obtained from simple reports, and should be used for internal and external monitoring and as guidance for supervision. As proportion of low positive suspect smears and consistency within case series are more difficult to interpret, they should be used only on-site by laboratory professionals. All indicators require more research to define their optimal range in various settings.

Extracting more out of relocation data: building movement models as mixtures of random walks

We present a framework for fitting multiple random walks to animal movement paths consisting of ordered sets of step lengths and turning angles. Each step and turn is assigned to one of a number of random walks, each characteristic of a different behavioral state. Behavioral state assignments may be inferred purely from movement data or may include the habitat type in which the animals are located. Switching between different behavioral states may be modeled explicitly using a state transition matrix estimated directly from data, or switching probabilities may take into account the proximity of animals to landscape features. Model fitting is undertaken within a Bayesian framework using the WinBUGS software. These methods allow for identification of different movement states using several properties of observed paths and lead naturally to the formulation of movement models. Analysis of relocation data from elk released in east-central Ontario, Canada, suggests a biphasic movement behavior: elk are either in an "encamped" state in which step lengths are small and turning angles are high, or in an "exploratory" state, in which daily step lengths are several kilometers and turning angles are small. Animals encamp in open habitat (agricultural fields and opened forest), but the exploratory state is not associated with any particular habitat type.

Modelos Estadísticos Dinámicos para Análisis de Evolución de Tasas de Accidentes: Metodología y Herramientas Computacionales

Los accidentes del tráfico son un fenómeno social muy relevantes y una de las principales causas de mortalidad en los países desarrollados. Para entender este fenómeno complejo se aplican modelos econométricos sofisticados tanto en la literatura académica como por las administraciones públicas. Esta tesis está dedicada al análisis de modelos macroscópicos para los accidentes del tráfico en España. El objetivo de esta tesis se puede dividir en dos bloques: a. Obtener una mejor comprensión del fenómeno de accidentes de trafico mediante la aplicación y comparación de dos modelos macroscópicos utilizados frecuentemente en este área: DRAG y UCM, con la aplicación a los accidentes con implicación de furgonetas en España durante el período 2000-2009. Los análisis se llevaron a cabo con enfoque frecuencista y mediante los programas TRIO, SAS y TRAMO/SEATS. b. La aplicación de modelos y la selección de las variables más relevantes, son temas actuales de investigación y en esta tesis se ha desarrollado y aplicado una metodología que pretende mejorar, mediante herramientas teóricas y prácticas, el entendimiento de selección y comparación de los modelos macroscópicos. Se han desarrollado metodologías tanto para selección como para comparación de modelos. La metodología de selección de modelos se ha aplicado a los accidentes mortales ocurridos en la red viaria en el período 2000-2011, y la propuesta metodológica de comparación de modelos macroscópicos se ha aplicado a la frecuencia y la severidad de los accidentes con implicación de furgonetas en el período 2000-2009. Como resultado de los desarrollos anteriores se resaltan las siguientes contribuciones: a. Profundización de los modelos a través de interpretación de las variables respuesta y poder de predicción de los modelos. El conocimiento sobre el comportamiento de los accidentes con implicación de furgonetas se ha ampliado en este proceso. bl. Desarrollo de una metodología para selección de variables relevantes para la explicación de la ocurrencia de accidentes de tráfico. Teniendo en cuenta los resultados de a) la propuesta metodológica se basa en los modelos DRAG, cuyos parámetros se han estimado con enfoque bayesiano y se han aplicado a los datos de accidentes mortales entre los años 2000-2011 en España. Esta metodología novedosa y original se ha comparado con modelos de regresión dinámica (DR), que son los modelos más comunes para el trabajo con procesos estocásticos. Los resultados son comparables, y con la nueva propuesta se realiza una aportación metodológica que optimiza el proceso de selección de modelos, con escaso coste computacional. b2. En la tesis se ha diseñado una metodología de comparación teórica entre los modelos competidores mediante la aplicación conjunta de simulación Monte Cario, diseño de experimentos y análisis de la varianza ANOVA. Los modelos competidores tienen diferentes estructuras, que afectan a la estimación de efectos de las variables explicativas. Teniendo en cuenta el estudio desarrollado en bl) este desarrollo tiene el propósito de determinar como interpretar la componente de tendencia estocástica que un modelo UCM modela explícitamente, a través de un modelo DRAG, que no tiene un método específico para modelar este elemento. Los resultados de este estudio son importantes para ver si la serie necesita ser diferenciada antes de modelar. b3. Se han desarrollado nuevos algoritmos para realizar los ejercicios metodológicos, implementados en diferentes programas como R, WinBUGS, y MATLAB. El cumplimiento de los objetivos de la tesis a través de los desarrollos antes enunciados se remarcan en las siguientes conclusiones: 1. El fenómeno de accidentes del tráfico se ha analizado mediante dos modelos macroscópicos. Los efectos de los factores de influencia son diferentes dependiendo de la metodología aplicada. Los resultados de predicción son similares aunque con ligera superioridad de la metodología DRAG. 2. La metodología para selección de variables y modelos proporciona resultados prácticos en cuanto a la explicación de los accidentes de tráfico. La predicción y la interpretación también se han mejorado mediante esta nueva metodología. 3. Se ha implementado una metodología para profundizar en el conocimiento de la relación entre las estimaciones de los efectos de dos modelos competidores como DRAG y UCM. Un aspecto muy importante en este tema es la interpretación de la tendencia mediante dos modelos diferentes de la que se ha obtenido información muy útil para los investigadores en el campo del modelado. Los resultados han proporcionado una ampliación satisfactoria del conocimiento en torno al proceso de modelado y comprensión de los accidentes con implicación de furgonetas y accidentes mortales totales en España. ABSTRACT Road accidents are a very relevant social phenomenon and one of the main causes of death in industrialized countries. Sophisticated econometric models are applied in academic work and by the administrations for a better understanding of this very complex phenomenon. This thesis is thus devoted to the analysis of macro models for road accidents with application to the Spanish case. The objectives of the thesis may be divided in two blocks: a. To achieve a better understanding of the road accident phenomenon by means of the application and comparison of two of the most frequently used macro modelings: DRAG (demand for road use, accidents and their gravity) and UCM (unobserved components model); the application was made to van involved accident data in Spain in the period 2000-2009. The analysis has been carried out within the frequentist framework and using available state of the art software, TRIO, SAS and TRAMO/SEATS. b. Concern on the application of the models and on the relevant input variables to be included in the model has driven the research to try to improve, by theoretical and practical means, the understanding on methodological choice and model selection procedures. The theoretical developments have been applied to fatal accidents during the period 2000-2011 and van-involved road accidents in 2000-2009. This has resulted in the following contributions: a. Insight on the models has been gained through interpretation of the effect of the input variables on the response and prediction accuracy of both models. The behavior of van-involved road accidents has been explained during this process. b1. Development of an input variable selection procedure, which is crucial for an efficient choice of the inputs. Following the results of a) the procedure uses the DRAG-like model. The estimation is carried out within the Bayesian framework. The procedure has been applied for the total road accident data in Spain in the period 2000-2011. The results of the model selection procedure are compared and validated through a dynamic regression model given that the original data has a stochastic trend. b2. A methodology for theoretical comparison between the two models through Monte Carlo simulation, computer experiment design and ANOVA. The models have a different structure and this affects the estimation of the effects of the input variables. The comparison is thus carried out in terms of the effect of the input variables on the response, which is in general different, and should be related. Considering the results of the study carried out in b1) this study tries to find out how a stochastic time trend will be captured in DRAG model, since there is no specific trend component in DRAG. Given the results of b1) the findings of this study are crucial in order to see if the estimation of data with stochastic component through DRAG will be valid or whether the data need a certain adjustment (typically differencing) prior to the estimation. The model comparison methodology was applied to the UCM and DRAG models, considering that, as mentioned above, the UCM has a specific trend term while DRAG does not. b3. New algorithms were developed for carrying out the methodological exercises. For this purpose different softwares, R, WinBUGs and MATLAB were used. These objectives and contributions have been resulted in the following findings: 1. The road accident phenomenon has been analyzed by means of two macro models: The effects of the influential input variables may be estimated through the models, but it has been observed that the estimates vary from one model to the other, although prediction accuracy is similar, with a slight superiority of the DRAG methodology. 2. The variable selection methodology provides very practical results, as far as the explanation of road accidents is concerned. Prediction accuracy and interpretability have been improved by means of a more efficient input variable and model selection procedure. 3. Insight has been gained on the relationship between the estimates of the effects using the two models. A very relevant issue here is the role of trend in both models, relevant recommendations for the analyst have resulted from here. The results have provided a very satisfactory insight into both modeling aspects and the understanding of both van-involved and total fatal accidents behavior in Spain.

Assessing the impacts of grazing levels on bird density in woodland habitat: a Bayesian approach using expert opinion

Many studies on birds focus on the collection of data through an experimental design, suitable for investigation in a classical analysis of variance (ANOVA) framework. Although many findings are confirmed by one or more experts, expert information is rarely used in conjunction with the survey data to enhance the explanatory and predictive power of the model. We explore this neglected aspect of ecological modelling through a study on Australian woodland birds, focusing on the potential impact of different intensities of commercial cattle grazing on bird density in woodland habitat. We examine a number of Bayesian hierarchical random effects models, which cater for overdispersion and a high frequency of zeros in the data using WinBUGS and explore the variation between and within different grazing regimes and species. The impact and value of expert information is investigated through the inclusion of priors that reflect the experience of 20 experts in the field of bird responses to disturbance. Results indicate that expert information moderates the survey data, especially in situations where there are little or no data. When experts agreed, credible intervals for predictions were tightened considerably. When experts failed to agree, results were similar to those evaluated in the absence of expert information. Overall, we found that without expert opinion our knowledge was quite weak. The fact that the survey data is quite consistent, in general, with expert opinion shows that we do know something about birds and grazing and we could learn a lot faster if we used this approach more in ecology, where data are scarce. Copyright (c) 2005 John Wiley & Sons, Ltd.

Pharmacokinetic-pharmacodynamic modelling of QT interval prolongation following citalopram overdoses

Aims To develop a pharmacokinetic-pharmacodynamic model describing the time-course of QT interval prolongation after citalopram overdose and to evaluate the effect of charcoal on the relative risk of developing abnormal QT and heart-rate combinations. Methods Plasma concentrations and electrocardiograph (ECG) data from 52 patients after 62 citalopram overdose events were analysed in WinBUGS using a Bayesian approach. The reported doses ranged from 20 to 1700 mg and on 17 of the events a single dose of activated charcoal was administered. The developed pharmacokinetic-pharmacodynamic model was used for predicting the probability of having abnormal combinations of QT-RR, which was assumed to be related to an increased risk for torsade de pointes (TdP). Results The absolute QT interval was related to the observed heart rate with an estimated individual heart-rate correction factor [alpha = 0.36, between-subject coefficient of variation (CV) = 29%]. The heart-rate corrected QT interval was linearly dependent on the predicted citalopram concentration (slope = 40 ms l mg(-1), between-subject CV = 70%) in a hypothetical effect-compartment (half-life of effect-delay = 1.4 h). The heart-rate corrected QT was predicted to be higher in women than in men and to increase with age. Administration of activated charcoal resulted in a pronounced reduction of the QT prolongation and was shown to reduce the risk of having abnormal combinations of QT-RR by approximately 60% for citalopram doses above 600 mg. Conclusion Citalopram caused a delayed lengthening of the QT interval. Administration of activated charcoal was shown to reduce the risk that the QT interval exceeds a previously defined threshold and therefore is expected to reduce the risk of TdP.

Bayesian population pharmacokinetic analysis of sirolimus

Objective: It is usual that data collected from routine clinical care is sparse and unable to support the more complex pharmacokinetic (PK) models that may have been reported in previous rich data studies. Informative priors may be a pre-requisite for model development. The aim of this study was to estimate the population PK parameters of sirolimus using a fully Bayesian approach with informative priors. Methods: Informative priors including prior mean and precision of the prior mean were elicited from previous published studies using a meta-analytic technique. Precision of between-subject variability was determined by simulations from a Wishart distribution using MATLAB (version 6.5). Concentration-time data of sirolimus retrospectively collected from kidney transplant patients were analysed using WinBUGS (version 1.3). The candidate models were either one- or two-compartment with first order absorption and first order elimination. Model discrimination was based on computation of the posterior odds supporting the model. Results: A total of 315 concentration-time points were obtained from 25 patients. Most data were clustered at trough concentrations with range of 1.6 to 77 hours post-dose. Using informative priors, either a one- or two-compartment model could be used to describe the data. When a one-compartment model was applied, information was gained from the data for the value of apparent clearance (CL/F = 18.5 L/h), and apparent volume of distribution (V/F = 1406 L) but no information was gained about the absorption rate constant (ka). When a two-compartment model was fitted to the data, the data were informative about CL/F, apparent inter-compartmental clearance, and apparent volume of distribution of the peripheral compartment (13.2 L/h, 20.8 L/h, and 579 L, respectively). The posterior distribution of the volume distribution of central compartment and ka were the same as priors. The posterior odds for the two-compartment model was 8.1, indicating the data supported the two-compartment model. Conclusion: The use of informative priors supported the choice of a more complex and informative model that would otherwise have not been supported by the sparse data.