Optimizing Presence–Absence Surveys For Detecting Population Trends

Presence-absence surveys are a commonly used method for monitoring broad-scale changes in wildlife distributions. However, the lack of power of these surveys for detecting population trends is problematic for their application in wildlife management. Options for improving power include increasing the sampling effort or arbitrarily relaxing the type I error rate. We present an alternative, whereby targeted sampling of particular habitats in the landscape using information from a habitat model increases power. The advantage of this approach is that it does not require a trade-off with either cost or the Pr(type I error) to achieve greater power. We use a demographic model of koala (Phascolarctos cinereus) population dynamics and simulations of the monitoring process to estimate the power to detect a trend in occupancy for a range of strategies, thereby demonstrating that targeting particular habitat qualities can improve power substantially. If the objective is to detect a decline in occupancy, the optimal strategy is to sample high-quality habitats. Alternatively, if the objective is to detect an increase in occupancy, the optimal strategy is to sample intermediate-quality habitats. The strategies with the highest power remained the same under a range of parameter assumptions, although observation error had a strong influence on the optimal strategy. Our approach specifically applies to monitoring for detecting long-term trends in occupancy or abundance. This is a common and important monitoring objective for wildlife managers, and we provide guidelines for more effectively achieving it.

Towards user profiling for web recommendation

Collaborative recommendation is one of widely used recommendation systems, which recommend items to visitor on a basis of referring other's preference that is similar to current user. User profiling technique upon Web transaction data is able to capture such informative knowledge of user task or interest. With the discovered usage pattern information, it is likely to recommend Web users more preferred content or customize the Web presentation to visitors via collaborative recommendation. In addition, it is helpful to identify the underlying relationships among Web users, items as well as latent tasks during Web mining period. In this paper, we propose a Web recommendation framework based on user profiling technique. In this approach, we employ Probabilistic Latent Semantic Analysis (PLSA) to model the co-occurrence activities and develop a modified k-means clustering algorithm to build user profiles as the representatives of usage patterns. Moreover, the hidden task model is derived by characterizing the meaningful latent factor space. With the discovered user profiles, we then choose the most matched profile, which possesses the closely similar preference to current user and make collaborative recommendation based on the corresponding page weights appeared in the selected user profile. The preliminary experimental results performed on real world data sets show that the proposed approach is capable of making recommendation accurately and efficiently.

A Bayesian hierarchical model for categorical longitudinal data from a social survey of immigrants

The paper investigates a Bayesian hierarchical model for the analysis of categorical longitudinal data from a large social survey of immigrants to Australia. Data for each subject are observed on three separate occasions, or waves, of the survey. One of the features of the data set is that observations for some variables are missing for at least one wave. A model for the employment status of immigrants is developed by introducing, at the first stage of a hierarchical model, a multinomial model for the response and then subsequent terms are introduced to explain wave and subject effects. To estimate the model, we use the Gibbs sampler, which allows missing data for both the response and the explanatory variables to be imputed at each iteration of the algorithm, given some appropriate prior distributions. After accounting for significant covariate effects in the model, results show that the relative probability of remaining unemployed diminished with time following arrival in Australia.

Likelihood-based estimation of the regression model with scrambled responses

A significant problem in the collection of responses to potentially sensitive questions, such as relating to illegal, immoral or embarrassing activities, is non-sampling error due to refusal to respond or false responses. Eichhorn & Hayre (1983) suggested the use of scrambled responses to reduce this form of bias. This paper considers a linear regression model in which the dependent variable is unobserved but for which the sum or product with a scrambling random variable of known distribution, is known. The performance of two likelihood-based estimators is investigated, namely of a Bayesian estimator achieved through a Markov chain Monte Carlo (MCMC) sampling scheme, and a classical maximum-likelihood estimator. These two estimators and an estimator suggested by Singh, Joarder & King (1996) are compared. Monte Carlo results show that the Bayesian estimator outperforms the classical estimators in almost all cases, and the relative performance of the Bayesian estimator improves as the responses become more scrambled.

Adjustment of homeless adolescents to a crisis shelter: Application of a stress and coping model

The present study examined the utility of a stress and coping model of adaptation to a homeless shelter among homeless adolescents. Seventy-eight homeless adolescents were interviewed and completed self-administered scales at Time 1 (day of shelter entry) and Time 2 (day of discharge). The mean duration of stay at the shelter was 7.23 days (SD = 7.01). Predictors included appraisal (threat and self-efficacy), coping resources, and coping strategies (productive, nonproductive, and reference to others coping). Adjustment outcomes were Time I measures of global distress, physical health, clinician-and youthworker- rated social adjustment, and externalizing behavior and Time 2 youthworker-rated social adjustment and goal achievement. Results of hierarchical regression analyses indicated that after controlling for the effects of relevant background variables (number of other shelters visited, sexual, emotional, and physical abuse), measures of coping resources, appraisal, and coping strategies evidenced distinct relations with measures of adjustment in ways consistent with the model's predictions with few exceptions. In cross-sectional analyses better Time I adjustment was related to reports of higher levels of coping resources, self-efficacy beliefs, and productive coping strategies, and reports of lower levels of threat appraisal and nonproductive coping strategies. Prospective analyses showed a link between reports of higher levels of reference to others coping strategies and greater goal achievement and, unexpectedly, an association between lower self-efficacy beliefs and better Time 2 youthworker-rated social adjustment. Hence, whereas prospective analyses provide only limited support for the use of a stress and coping model in explaining the adjustment of homeless adolescents to a crisis shelter, cross-sectional findings provide stronger support.

Fitting genetic models to twin data with binary and ordered categorical responses: A comparison of structural equation modelling and Bayesian hierarchical models

We compare Bayesian methodology utilizing free-ware BUGS (Bayesian Inference Using Gibbs Sampling) with the traditional structural equation modelling approach based on another free-ware package, Mx. Dichotomous and ordinal (three category) twin data were simulated according to different additive genetic and common environment models for phenotypic variation. Practical issues are discussed in using Gibbs sampling as implemented by BUGS to fit subject-specific Bayesian generalized linear models, where the components of variation may be estimated directly. The simulation study (based on 2000 twin pairs) indicated that there is a consistent advantage in using the Bayesian method to detect a correct model under certain specifications of additive genetics and common environmental effects. For binary data, both methods had difficulty in detecting the correct model when the additive genetic effect was low (between 10 and 20%) or of moderate range (between 20 and 40%). Furthermore, neither method could adequately detect a correct model that included a modest common environmental effect (20%) even when the additive genetic effect was large (50%). Power was significantly improved with ordinal data for most scenarios, except for the case of low heritability under a true ACE model. We illustrate and compare both methods using data from 1239 twin pairs over the age of 50 years, who were registered with the Australian National Health and Medical Research Council Twin Registry (ATR) and presented symptoms associated with osteoarthritis occurring in joints of the hand.

Model-based clustering in gene expression microarrays: An application to breast cancer data

In microarray studies, the application of clustering techniques is often used to derive meaningful insights into the data. In the past, hierarchical methods have been the primary clustering tool employed to perform this task. The hierarchical algorithms have been mainly applied heuristically to these cluster analysis problems. Further, a major limitation of these methods is their inability to determine the number of clusters. Thus there is a need for a model-based approach to these. clustering problems. To this end, McLachlan et al. [7] developed a mixture model-based algorithm (EMMIX-GENE) for the clustering of tissue samples. To further investigate the EMMIX-GENE procedure as a model-based -approach, we present a case study involving the application of EMMIX-GENE to the breast cancer data as studied recently in van 't Veer et al. [10]. Our analysis considers the problem of clustering the tissue samples on the basis of the genes which is a non-standard problem because the number of genes greatly exceed the number of tissue samples. We demonstrate how EMMIX-GENE can be useful in reducing the initial set of genes down to a more computationally manageable size. The results from this analysis also emphasise the difficulty associated with the task of separating two tissue groups on the basis of a particular subset of genes. These results also shed light on why supervised methods have such a high misallocation error rate for the breast cancer data.

Modelling inpatient length of stay by a hierarchical mixture regression via the EM algorithm

The modelling of inpatient length of stay (LOS) has important implications in health care studies. Finite mixture distributions are usually used to model the heterogeneous LOS distribution, due to a certain proportion of patients sustaining-a longer stay. However, the morbidity data are collected from hospitals, observations clustered within the same hospital are often correlated. The generalized linear mixed model approach is adopted to accommodate the inherent correlation via unobservable random effects. An EM algorithm is developed to obtain residual maximum quasi-likelihood estimation. The proposed hierarchical mixture regression approach enables the identification and assessment of factors influencing the long-stay proportion and the LOS for the long-stay patient subgroup. A neonatal LOS data set is used for illustration, (C) 2003 Elsevier Science Ltd. All rights reserved.

A generalized Markov sampler

A recent development of the Markov chain Monte Carlo (MCMC) technique is the emergence of MCMC samplers that allow transitions between different models. Such samplers make possible a range of computational tasks involving models, including model selection, model evaluation, model averaging and hypothesis testing. An example of this type of sampler is the reversible jump MCMC sampler, which is a generalization of the Metropolis-Hastings algorithm. Here, we present a new MCMC sampler of this type. The new sampler is a generalization of the Gibbs sampler, but somewhat surprisingly, it also turns out to encompass as particular cases all of the well-known MCMC samplers, including those of Metropolis, Barker, and Hastings. Moreover, the new sampler generalizes the reversible jump MCMC. It therefore appears to be a very general framework for MCMC sampling. This paper describes the new sampler and illustrates its use in three applications in Computational Biology, specifically determination of consensus sequences, phylogenetic inference and delineation of isochores via multiple change-point analysis.

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.

Subgeometric rates of convergence for a class of continuous-time Markov process

Let (Phi(t))(t is an element of R+) be a Harris ergodic continuous-time Markov process on a general state space, with invariant probability measure pi. We investigate the rates of convergence of the transition function P-t(x, (.)) to pi; specifically, we find conditions under which r(t) vertical bar vertical bar P-t (x, (.)) - pi vertical bar vertical bar -> 0 as t -> infinity, for suitable subgeometric rate functions r(t), where vertical bar vertical bar - vertical bar vertical bar denotes the usual total variation norm for a signed measure. We derive sufficient conditions for the convergence to hold, in terms of the existence of suitable points on which the first hitting time moments are bounded. In particular, for stochastically ordered Markov processes, explicit bounds on subgeometric rates of convergence are obtained. These results are illustrated in several examples.

Adjustment in mothers of children with Asperger syndrome: An application of the double ABCX model of family adjustment

The present study examined the applicability of the double ABCX model of family adjustment in explaining maternal adjustment to caring for a child diagnosed with Asperger syndrome. Forty-seven mothers completed questionnaires at a university clinic while their children were participating in an anxiety intervention. The children were aged between 10 and 12 years. Results of correlations showed that each of the model components was related to one or more domains of maternal adjustment in the direction predicted, with the exception of problem-focused coping. Hierarchical regression analyses demonstrated that, after controlling for the effects of relevant demographics, stressor severity, pile-up of demands and coping were related to adjustment. Findings indicate the utility of the double ABCX model in guiding research into parental adjustment when caring for a child with Asperger syndrome. Limitations of the study and clinical implications are discussed.

A stochastic metapopulation model accounting for habitat dynamics

A stochastic metapopulation model accounting for habitat dynamics is presented. This is the stochastic SIS logistic model with the novel aspect that it incorporates varying carrying capacity. We present results of Kurtz and Barbour, that provide deterministic and diffusion approximations for a wide class of stochastic models, in a form that most easily allows their direct application to population models. These results are used to show that a suitably scaled version of the metapopulation model converges, uniformly in probability over finite time intervals, to a deterministic model previously studied in the ecological literature. Additionally, they allow us to establish a bivariate normal approximation to the quasi-stationary distribution of the process. This allows us to consider the effects of habitat dynamics on metapopulation modelling through a comparison with the stochastic SIS logistic model and provides an effective means for modelling metapopulations inhabiting dynamic landscapes.