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Sensitivity of ecological models to their climate drivers: statistical ensembles for forcing.

Global and regional numerical models for terrestrial ecosystem dynamics require fine spatial resolution and temporally complete historical climate fields as input variables. However, because climate observations are unevenly spaced and have incomplete records, such fields need to be estimated. In addition, uncertainty in these fields associated with their estimation are rarely assessed. Ecological models are usually driven with a geostatistical model's mean estimate (kriging) of these fields without accounting for this uncertainty, much less evaluating such errors in terms of their propagation in ecological simulations. We introduce a Bayesian statistical framework to model climate observations to create spatially uniform and temporally complete fields, taking into account correlation in time and space, spatial heterogeneity, lack of normality, and uncertainty about all these factors. A key benefit of the Bayesian model is that it generates uncertainty measures for the generated fields. To demonstrate this method, we reconstruct historical monthly precipitation fields (a driver for ecological models) on a fine resolution grid for a climatically heterogeneous region in the western United States. The main goal of this work is to evaluate the sensitivity of ecological models to the uncertainty associated with prediction of their climate drivers. To assess their numerical sensitivity to predicted input variables, we generate a set of ecological model simulations run using an ensemble of different versions of the reconstructed fields. We construct such an ensemble by sampling from the posterior predictive distribution of the climate field. We demonstrate that the estimated prediction error of the climate field can be very high. We evaluate the importance of such errors in ecological model experiments using an ensemble of historical precipitation time series in simulations of grassland biogeochemical dynamics with an ecological numerical model, Century. We show how uncertainty in predicted precipitation fields is propagated into ecological model results and that this propagation had different modes. Depending on output variable, the response of model dynamics to uncertainty in inputs ranged from uncertainty in outputs that matched that of inputs to those that were muted or that were biased, as well as uncertainty that was persistent in time after input errors dropped.

Animals↗

On some applications of Bayesian methods in cancer clinical trials.

The NCCTG randomized controlled clinical trial for the treatment of advanced colorectal carcinoma is a wonderful case study of the dynamic interplay between scientific learning and statistical inference. Ethical concerns for minimizing the number of patients assigned to an inferior treatment and interest in identifying subsets of patients for whom a treatment is most likely efficacious pose challenging problems for the practice of statistics. In the first part of this paper, I comment on the applications of Bayesian methods to these problems in the NCCTG trial as presented by Freedman and Spieglehalter and Dixon and Simon, respectively. In the second part of this paper, I discuss and illustrate a Bayesian approach to model sensitivity analysis with a particular focus on model specification and criticism. The Bayesian approach provides a formal methodology to assess the sensitivity of inferences to the inputs into an analysis so that it is possible to investigate the consequences of the specification of the model. I apply these methods to the specification and criticism of a class of survival models for the analysis of survival times in the NCCTG trial.

Antineoplastic Combined Chemotherapy Protocols↗

Bayesian inferences in the Cox model for order-restricted hypotheses.

In studying the relationship between an ordered categorical predictor and an event time, it is standard practice to include dichotomous indicators of the different levels of the predictor in a Cox model. One can then use a multiple degree-of-freedom score or partial likelihood ratio test for hypothesis testing. Often, interest focuses on comparing the null hypothesis of no difference to an order-restricted alternative, such as a monotone increase across levels of a predictor. This article proposes a Bayesian approach for addressing hypotheses of this type. We reparameterize the Cox model in terms of a cumulative product of parameters having conjugate prior densities, consisting of mixtures of point masses at one, and truncated gamma densities. Due to the structure of the model, posterior computation can proceed via a simple and efficient Gibbs sampling algorithm. Posterior probabilities for the global null hypothesis and subhypotheses, comparing the hazards for specific groups, can be calculated directly from the output of a single Gibbs chain. The approach allows for level sets across which a predictor has no effect. Generalizations to multiple predictors are described, and the method is applied to a study of emergency medical treatment for stroke.

Bayes Theorem↗

An expert judgment model applied to estimating the safety effect of a bicycle facility.

This paper presents a risk index model that can be used for assessing the safety effect of countermeasures. The model estimates risk in a multiplicative way, which makes it possible to analyze the impact of different factors separately. Expert judgments are incorporated through a Bayesian error model. The variance of the risk estimate is determined by Monte-Carlo simulation. The model was applied to assess the safety effect of a new design of a bicycle crossing. The intent was to gain safety by raising the crossings to reduce vehicle speeds and by making the crossings more visible by painting them in a bright color. Before the implementations, bicyclists were riding on bicycle crossings of conventional Swedish type, i.e. similar to crosswalks but delineated by white squares rather than solid lines or zebra markings. Automobile speeds were reduced as anticipated. However, it seems as if the positive effect of this was more or less canceled out by increased bicycle speeds. The safety per bicyclist was still improved by approximately 20%. This improvement was primarily caused by an increase in bicycle flow, since the data show that more bicyclists at a given location seem to benefit their safety. The increase in bicycle flow was probably caused by the new layout of the crossings since bicyclists perceived them as safer and causing less delay. Some future development work is suggested. Pros and cons with the used methodology are discussed. The most crucial parameter to be added is probably a model describing the interaction between motorists and bicyclists, for example, how risk is influenced by the lateral position of the bicyclist in relation to the motorist. It is concluded that the interaction seems to be optimal when both groups share the roadway.

Acceleration↗

An evaluation of factors influencing Bayesian learning systems.

OBJECTIVES: To examine the influences of situational and model factors on the accuracy of Bayesian learning systems. DESIGN: This study examines the impacts of variations in two situational factors, training sample size and number of attributes, and in two model factors, choice of Bayesian model and criteria for excluding model attributes, on the overall accuracy of Bayesian learning systems. MEASUREMENTS: The test data were derived from myocardial infarction patients who were admitted to eight hospitals in New Orleans during 1985. The test sample consisted of 339 cases; the training samples included 100, 400, and 800 cases. APACHE II variables were used for the model attributes and patient discharge status as the outcome predicted. Attribute sets were selected in sizes of 4, 8, and 12. The authors varied the Bayesian models (proper and simple) and the attribute exclusion criteria (optimism and pessimism). RESULTS: The simple Bayes model, which assumes conditional independence, consistently equalled or outperformed the proper (maximally dependent) Bayes model, which assumes conditional dependence, across all training sample and attribute set sizes. Not excluding model attributes was found to be preferable to using sample theory as an attribute exclusion criterion in both the simple and the proper models. CONCLUSION: In the domain tested, the simple Bayes model with optimistic exclusion is more robust than previously assumed and increasing the number of attributes in a model had a greater relative impact on model accuracy than did increasing the number of training sample cases. Assessment of applicability of these findings to other domains will require further study. In addition, other models that are between these two extremes must be investigated. These include models that approximate proper Bayes' conditional dependence computations while requiring fewer training sample cases, attribute exclusion criteria between optimism and pessimism that improve accuracy, and ordering techniques for introducing attributes into Bayes models that optimize the information value associated with the attributes in test-sample cases.

APACHE↗

Bayesian analysis of logistic regression with an unknown change point and covariate measurement error.

We discuss Bayesian estimation of a logistic regression model with an unknown threshold limiting value (TLV). In these models it is assumed that there is no effect of a covariate on the response under a certain unknown TLV. The estimation of these models in a Bayesian context by Markov chain Monte Carlo (MCMC) methods is considered with focus on the TLV. We extend the model by accounting for measurement error in the covariate. The Bayesian solution is compared with the likelihood solution proposed by Küchenhoff and Carroll using a data set concerning the relationship between dust concentration in the working place and the occurrence of chronic bronchitis.

Bayes Theorem↗

A Bayesian A-optimal and model robust design criterion.

Suppose that the true model underlying a set of data is one of a finite set of candidate models, and that parameter estimation for this model is of primary interest. With this goal, optimal design must depend on a loss function across all possible models. A common method that accounts for model uncertainty is to average the loss over all models; this is the basis of what is known as Läuter's criterion. We generalize Läuter's criterion and show that it can be placed in a Bayesian decision theoretic framework, by extending the definition of Bayesian A-optimality. We use this generalized A-optimality to find optimal design points in an environmental safety setting. In estimating the smallest detectable trace limit in a water contamination problem, we obtain optimal designs that are quite different from those suggested by standard A-optimality.

Bayes Theorem↗

Ideal observer approximation using Bayesian classification neural networks.

It is well understood that the optimal classification decision variable is the likelihood ratio or any monotonic transformation of the likelihood ratio. An automated classifier which maps from an input space to one of the likelihood ratio family of decision variables is an optimal classifier or "ideal observer." Artificial neural networks (ANNs) are frequently used as classifiers for many problems. In the limit of large training sample sizes, an ANN approximates a mapping function which is a monotonic transformation of the likelihood ratio, i.e., it estimates an ideal observer decision variable. A principal disadvantage of conventional ANNs is the potential over-parameterization of the mapping function which results in a poor approximation of an optimal mapping function for smaller training samples. Recently, Bayesian methods have been applied to ANNs in order to regularize training to improve the robustness of the classifier. The goal of training a Bayesian ANN with finite sample sizes is, as with unlimited data, to approximate the ideal observer. We have evaluated the accuracy of Bayesian ANN models of ideal observer decision variables as a function of the number of hidden units used, the signal-to-noise ratio of the data and the number of features or dimensionality of the data. We show that when enough training data are present, excess hidden units do not substantially degrade the accuracy of Bayesian ANNs. However, the minimum number of hidden units required to best model the optimal mapping function varies with the complexity of the data.

Bayes Theorem↗

Predicting postoperative nausea and vomiting with the application of an artificial neural network.

BACKGROUND: Several medications have proved to be useful in preventing postoperative nausea and vomiting (PONV). However, routine antiemetic prophylaxis is not cost-effective. We evaluated the accuracy and discriminating power of an artificial neural network (ANN) to predict PONV. METHODS: We analysed data from 1086 in-patients who underwent various surgical procedures under general anaesthesia without antiemetic prophylaxis. Predictors used for ANN training were selected by computing the value of chi(2) statistic and information gain with respect to PONV. The configuration of the ANN was chosen by using a software tool. Then the training of the ANN was performed based on data from a training set (n=656). Testing validation was performed with the remaining patients (n=430) whose outcome regarding PONV was unknown to the ANN. Area under the receiver operating characteristic (ROC) curves were used to quantify predictive performance. ANN performance was compared with those of the Naïve Bayesian classifier model, logistic regression model, simplified Apfel score and Koivuranta score. RESULTS: ANN accuracy was 83.3%, sensitivity 77.9% and specificity 85.0% in predicting PONV. The areas under the ROC curve follow: ANN, 0.814 (0.774-0.850); Naïve Bayesian classifier, 0.570 (0.522-0.617); logistic regression, 0.669 (0.623-0.714); Koivuranta score, 0.626 (0.578-0.672); simplified Apfel score, 0.624 (0.576-0.670). ANN discriminatory power was superior to those of the other predicting models (P<0.05). CONCLUSIONS: The ANN provided the best predictive performance among all tested models.

Adult↗

Meta-analysis: apolipoprotein E genotypes and risk for coronary heart disease.

BACKGROUND: Apolipoprotein E (apoE) genotypes play critical roles in lipid metabolism and are believed to influence risk for coronary heart disease (CHD). Despite many population studies, however, the impact of apoE polymorphism on risk for CHD remains uncertain. PURPOSE: To qualitatively and quantitatively assess the evidence regarding the relation of apoE polymorphism to CHD risk. DATA SOURCES: All relevant reports and references from original and review papers published from 1966 to January 2004. STUDY SELECTION: Predefined criteria were used to identify 48 relevant studies. DATA EXTRACTION: A summary database that contained variables of study design, study sample and ethnicity, sex, apoE genotypes, CHD end points, plasma lipid levels, and other CHD risk factors was developed. DATA SYNTHESIS: The authors qualitatively evaluated many potential sources of heterogeneity. To quantify the extent of heterogeneity and assess the consistency of apoE-CHD associations, stratified analyses were conducted using the classic random-effects model. To further incorporate uncertainty due to between-study variation, the pooled odds ratios (ORs) and 95% credible intervals (CrIs) were estimated by using a Bayesian hierarchical model. Finally, the robustness of the pooled estimates was tested in multiple sensitivity analyses. Compared with individuals with the epsilon3/3 genotype, carriers of the apoE epsilon4 allele had a 42% higher risk for CHD (OR, 1.42 [95% CrI, 1.26 to 1.61]). The epsilon2 allele had no significant association with CHD risk (OR, 0.98 [CrI, 0.66 to 1.46]). LIMITATIONS: This meta-analysis did not include unpublished data or studies published in languages other than English. CONCLUSIONS: Inadequate statistical power, differences in geographic and ethnic background, allele frequency, sex, CHD phenotypes, study design, and potential gene-environment interactions may have contributed to the conflicting results of previous studies. The apoE epsilon4 allele is a significant risk factor for CHD.

Apolipoproteins E↗

Municipal pleural cancer mortality in Spain.

BACKGROUND: Pleural cancer is a recognised indicator of exposure to asbestos and mesothelioma mortality. AIMS: To investigate the distribution of municipal mortality due to this tumour, using the autoregressive spatial model proposed by Besag, York, and Mollie. METHODS: It was possible to compile and ascertain the posterior distribution of relative risk on the basis of a single Bayesian spatial model covering all of Spain's 8077 municipal areas. Maps were plotted depicting standardised mortality ratios, smoothed relative risk (RR) estimates, and the distribution of the posterior probability that RR >1. RESULTS: There was a higher risk of death due to pleural cancer in well defined towns and areas, many of which correspond to municipalities where asbestos using industries once existed for many years, the prime example being the municipal pattern registered for Barcelona Province. The quality of mortality data, the suitability of the model used, and the usefulness of municipal atlases for environmental surveillance are discussed.

Asbestos↗

Municipal mortality due to thyroid cancer in Spain.

BACKGROUND: Thyroid cancer is a tumor with a low but growing incidence in Spain. This study sought to depict its spatial municipal mortality pattern, using the classic model proposed by Besag, York and Mollié. METHODS: It was possible to compile and ascertain the posterior distribution of relative risk on the basis of a single Bayesian spatial model covering all of Spain's 8077 municipal areas. Maps were plotted depicting standardized mortality ratios, smoothed relative risk (RR) estimates, and the posterior probability that RR > 1. RESULTS: From 1989 to 1998 a total of 2,538 thyroid cancer deaths were registered in 1,041 municipalities. The highest relative risks were mostly situated in the Canary Islands, the province of Lugo, the east of La Coruña (Corunna) and western areas of Asturias and Orense. CONCLUSION: The observed mortality pattern coincides with areas in Spain where goiter has been declared endemic. The higher frequency in these same areas of undifferentiated, more aggressive carcinomas could be reflected in the mortality figures. Other unknown genetic or environmental factors could also play a role in the etiology of this tumor.

Bayes Theorem↗

A Bayesian approach to finite mixture models in bioassay via data augmentation and Gibbs sampling and its application to-insecticide resistance.

After continued treatment with an insecticide, within the population of the susceptible insects, resistant strains will occur. It is important to know whether there are any resistant strains, what the proportions are, and what the median lethal doses are for the insecticide. Lwin and Martin (1989, Biometrics 45, 721-732) propose a probit mixture model and use the EM algorithm to obtain the maximum likelihood estimates for the parameters. This approach has difficulties in estimating the confidence intervals and in testing the number of components. We propose a Bayesian approach to obtaining the credible intervals for the location and scale of the tolerances in each component and for the mixture proportions by using data augmentation and Gibbs sampler. We use Bayes factor for model selection and determining the number of components. We illustrate the method with data published in Lwin and Martin (1989).

Algorithms↗

Hierarchical Bayes estimation of hunting success rates with spatial correlations.

A Bayesian hierarchical generalized linear model is used to estimate hunting success rates at the subarea level for postseason harvest surveys. The model includes fixed week effects, random geographic effects, and spatial correlations between neighboring subareas. The computation is done by Gibbs sampling and adaptive rejection sampling techniques. The method is illustrated using data from the Missouri Turkey Hunting Survey in the spring of 1996. Bayesian model selection methods are used to demonstrate that there are significant week differences and spatial correlations of hunting success rates among counties. The Bayesian estimates are also shown to be quite robust in terms of changes of hyperparameters.

Animals↗

A Bayesian hierarchical non-linear regression model in receiver operating characteristic analysis of clustered continuous diagnostic data.

Receiver operating characteristic (ROC) analysis is a useful evaluative method of diagnostic accuracy. A Bayesian hierarchical nonlinear regression model for ROC analysis was developed. A validation analysis of diagnostic accuracy was conducted using prospective multi-center clinical trial prostate cancer biopsy data collected from three participating centers. The gold standard was based on radical prostatectomy to determine local and advanced disease. To evaluate the diagnostic performance of PSA level at fixed levels of Gleason score, a normality transformation was applied to the outcome data. A hierarchical regression analysis incorporating the effects of cluster (clinical center) and cancer risk (low, intermediate, and high) was performed, and the area under the ROC curve (AUC) was estimated.

Bayes Theorem↗

Forecasting clinical disease in pigs: comparing a naive and a Bayesian approach.

In veterinary practice the clinician often evaluates and predicts herd health status over time according to clinical criteria. In this paper, we modeled three different clinical signs among pigs based on longitudinal clinical observations in 15 pig herds. We compared and discussed the outputs from two different approaches for making clinical forecasts in a herd: a naive approach using a simple time series model with previous disease observations as predictors and a Bayesian state space models approach, in which the time lag variable entered into the random component of the model. We used the Markov chain Monte Carlo technique to calculate posterior distributions of the forecasts. For the herd specific forecasts the results showed that there were only minor differences between the forecasts from the simple time series model and the median forecasts from the Bayesian model. However, the credibility intervals from the Bayesian model were wider than the forecasts from the simple model and, therefore the Bayesian model encompassed the variability in the forecasts better. Compared to the statistical model, the simple time series would be easier to implement in a practical setting. However, the latter lacks the inherent "generality" from the statistical model that allows the user to make statements about the distribution of the herds and to predict disease status based on the "average" correlation among the herds. The applicability of the Bayesian approach within a clinical decision-making framework was discussed, with special emphasis on the use of prior information and clinical forecasting.

Animals↗

Effect of lot variability on ultraviolet radiation inactivation kinetics of Cryptosporidium parvum oocysts.

Numerous studies have demonstrated the efficiency of ultraviolet (UV) radiation for the inactivation of oocysts of Cryptosporidium parvum. In these studies inactivation is measured as reduction in oocysts. A primary goal is to estimate the UV radiation required to achieve a high degree of inactivation. Different lots of Cryptosporidium parvum oocysts are used in these studies, and the inactivation rate may vary depending on the lot of oocysts used. The goal of this paper is to account for the error in estimating the amount of inactivation after exposure to UV radiation, and for the effect of lot variability in determining the required UV radiation. A Bayesian approach is used to simultaneously model the logistic dose-response model and the UV inactivation kinetic model. The oocysts lot variability is incorporated using a hierarchical Bayesian model. Posterior distributions using Markov Chain Monte Carlo method is used to obtain estimates and Bayesian credible interval for the required UV radiation to achieve a given inactivation level of Cryptosporidium parvum oocysts.

Animals↗

Technical note: how to use Winbugs to draw inferences in animal models.

This paper deals with Bayesian inferences of animal models using Gibbs sampling. First, we suggest a general and efficient method for updating additive genetic effects, in which the computational cost is independent of the pedigree depth and increases linearly only with the size of the pedigree. Second, we show how this approach can be used to draw inferences from a wide range of animal models using the computer package Winbugs. Finally, we illustrate the approach in a simulation study, in which the data are generated and analyzed using Winbugs according to a linear model with i.i.d errors having Student's t distributions. In conclusion, Winbugs can be used to make inferences in small-sized, quantitative, genetic data sets applying a wide range of animal models that are not yet standard in the animal breeding literature.

Animals↗