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1.
A model-based clustering method for cross-sectional time series data is proposed and applied to crop insurance programs. To design an effective grouprisk plan, an important step is to group together the farms that resemble each other and decide the number of clusters, both of which can be achieved via the model-based clustering. The mixture maximum likelihood is employed for inferences. However, with the presence of correlation and missing values, the exact maximum likelihood estimators (MLEs) are difficult to obtain. An approach for obtaining approximate MLEs is proposed and evaluated through simulation studies. A bootstrapping method is used to choose the number of components in the mixture model.  相似文献   

2.
The uncertainty in estimation of spatial animal density from line transect surveys depends on the degree of spatial clustering in the animal population. To quantify the clustering we model line transect data as independent thinnings of spatial shot-noise Cox processes. Likelihood-based inference is implemented using Markov chain Monte Carlo (MCMC) methods to obtain efficient estimates of spatial clustering parameters. Uncertainty is addressed using parametric bootstrap or by consideration of posterior distributions in a Bayesian setting. Maximum likelihood estimation and Bayesian inference are compared in an example concerning minke whales in the northeast Atlantic.  相似文献   

3.
This article introduces a hierarchical model for compositional analysis. Our approach models both source and mixture data simultaneously, and accounts for several different types of variation: these include measurement error on both the mixture and source data; variability in the sample from the source distributions; and variability in the mixing proportions themselves, generally of main interest. The method is an improvement on some existing methods in that estimates of mixing proportions (including their interval estimates) are sure to lie in the range [0, 1]; in addition, it is shown that our model can help in situations where identification of appropriate source data is difficult, especially when we extend our model to include a covariate. We first study the likelihood surface of a base model for a simple example, and then include prior distributions to create a Bayesian model that allows analysis of more complex situations via Markov chain Monte Carlo sampling from the likelihood. Application of the model is illustrated with two examples using real data: one concerning chemical markers in plants, and another on water chemistry.  相似文献   

4.
The few distance sampling studies that use Bayesian methods typically consider only line transect sampling with a half-normal detection function. We present a Bayesian approach to analyse distance sampling data applicable to line and point transects, exact and interval distance data and any detection function possibly including covariates affecting detection probabilities. We use an integrated likelihood which combines the detection and density models. For the latter, densities are related to covariates in a log-linear mixed effect Poisson model which accommodates correlated counts. We use a Metropolis-Hastings algorithm for updating parameters and a reversible jump algorithm to include model selection for both the detection function and density models. The approach is applied to a large-scale experimental design study of northern bobwhite coveys where the interest was to assess the effect of establishing herbaceous buffers around agricultural fields in several states in the US on bird densities. Results were compared with those from an existing maximum likelihood approach that analyses the detection and density models in two stages. Both methods revealed an increase of covey densities on buffered fields. Our approach gave estimates with higher precision even though it does not condition on a known detection function for the density model.  相似文献   

5.
A Bayesian approach to covariance estimation and spatial prediction based on flexible variogram models is introduced. In particular, we consider black-box kriging models. These variogram models do not require restrictive assumptions on the functional shape of the variogram; furthermore, they can handle quite naturally non isotropic random fields. The proposed Bayesian approach does not require the computation of an empirical variogram estimator, thus avoiding the arbitrariness implied in the construction of the empirical variogram itself. Moreover, it provides a complete assessment of the uncertainty in the variogram estimation. The advantages of this approach are illustrated via simulation studies and by application to a well known benchmark dataset.  相似文献   

6.
Much of animal ecology is devoted to studies of abundance and occurrence of species, based on surveys of spatially referenced sample units. These surveys frequently yield sparse counts that are contaminated by imperfect detection, making direct inference about abundance or occurrence based on observational data infeasible. This article describes a flexible hierarchical modeling framework for estimation and inference about animal abundance and occurrence from survey data that are subject to imperfect detection. Within this framework, we specify models of abundance and detectability of animals at the level of the local populations defined by the sample units. Information at the level of the local population is aggregated by specifying models that describe variation in abundance and detection among sites. We describe likelihood-based and Bayesian methods for estimation and inference under the resulting hierarchical model. We provide two examples of the application of hierarchical models to animal survey data, the first based on removal counts of stream fish and the second based on avian quadrat counts. For both examples, we provide a Bayesian analysis of the models using the software WinBUGS.  相似文献   

7.
When stones prevent the measurement of cone resistance, and missing values below the stones are ignored, then averages can be seriously underestimated. Methods are considered for correcting this bias and an algorithm is proposed in which missing observations are replaced by their expected values. A numerical example gives results in close agreement with those obtained using the optimal, but computationally expensive, method of maximum likelihood estimation. It is recommended that data from incomplete penetrations should not be discarded but should be used, preferably with the proposed algorithm, to reduce the bias in estimates of mean values.  相似文献   

8.
This article suggests a linear functional relationship model for comparing two sets of circular data subject to unobservable errors. Unlike the corresponding and relatively well-studied model for linear data, maximum likelihood estimation for this model is very complicated and no explicit solutions are possible. Using a numerical approximation, we are able to solve the likelihood equations approximately, and to obtain good approximations to the likelihood estimates of the parameters. The quality of our estimates and the feasibility of the estimation method are illustrated via simulation. By establishing a parallel with the model for linear data, we are able to explain the various problems occurring in the process of estimation and to substantiate our numerical results. The interest in the model arose in connection with the study of ocean wave data; an application to such data is also given.  相似文献   

9.
The study of individual animal movement in relation to objects in a landscape is important in many areas of ecology and conservation biology. Yet, many of the models used by ecologists do not account for landscape features and thus may not be conducive to analysis of animal movement data. This article develops a set of nonlinear regression models for both move angles and move distances in relation to a single object in the landscape. Our models incorporate the concept of perceptual range from theories of animal movement behavior. We describe numerical methods for obtaining the maximum likelihood estimates of the model parameters. For illustration, we show results from both computer simulated data and real movement data collected for a red diamond rattlesnake (Crotalus ruber) via radio telemetry field techniques.  相似文献   

10.
When predicting scores in the Draize eye irritation test based on measurements of in vitro alternative tests, we are often faced with estimating parameters in a linear measurement error model with heterogeneous error variances. This article proposes a new statistical method for parameter estimation to address this issue. The proposed method is an extension of an earlier proposal that applied a linear measurement error model with homogeneous error variances, to cases with heterogeneous error variances. A simulation study to examine the performance of the proposed method was conducted in a framework that was adaptable to the data, which was obtained in a validation study of alternative methods to animal experiments conducted in Japan. The proposed method reduced the biases of estimates in comparison with an ordinary regression analysis method and three other methods under the assumption of homogeneous error variances. Although the proposed method did not fit the real data well, the resulting prediction formula was far better than those obtained by other methods.  相似文献   

11.
Insects are among the most significant indicators of a changing climate. Here we evaluate the impact of temperature, precipitation, and elevation on the tree-killing ability of an eruptive species of bark beetle in pine forests of British Columbia, Canada. We consider a spatial-temporal linear regression model and in particular, a new statistical method that simultaneously performs model selection and parameter estimation. This approach is penalized maximum likelihood estimation under a spatial-temporal adaptive Lasso penalty, paired with a computationally efficient algorithm to obtain approximate penalized maximum likelihood estimates. A simulation study shows that finite-sample properties of these estimates are sound. In a case study, we apply this approach to identify the appropriate components of a general class of landscape models which features the factors that propagate an outbreak. We interpret the results from ecological perspectives and compare our method with alternative model selection procedures.  相似文献   

12.
Traditional analyses of capture–recapture data are based on likelihood functions that explicitly integrate out all missing data. We use a complete data likelihood (CDL) to show how a wide range of capture–recapture models can be easily fitted using readily available software JAGS/BUGS even when there are individual-specific time-varying covariates. The models we describe extend those that condition on first capture to include abundance parameters, or parameters related to abundance, such as population size, birth rates or lifetime. The use of a CDL means that any missing data, including uncertain individual covariates, can be included in models without the need for customized likelihood functions. This approach also facilitates modeling processes of demographic interest rather than the complexities caused by non-ignorable missing data. We illustrate using two examples, (i) open population modeling in the presence of a censored time-varying individual covariate in a full robust design, and (ii) full open population multi-state modeling in the presence of a partially observed categorical variable. Supplemental materials for this article are available online.  相似文献   

13.
A statistically efficient approach is adopted for modeling spatial time-series of large data sets. The estimation of the main diagnostic tool such as the likelihood function in Gaussian spatiotemporal models is a cumbersome task when using extended spatial time-series such as air pollution. Here, using the Innovation Algorithm, we manage to compute it for many spatiotemporal specifications. These specifications refer to the spatial periodic-trend, the spatial autoregressive moving average, the spatial autoregressive integrated and fractionally integrated moving average Gaussian models. Our method is applied to daily pollutants over a large metropolitan area like Athens. In the applied part of our paper, we first diagnose temporal and spatial structures of data using non-likelihood based criteria, such as the empirical autocorrelation and covariance functions. Second, we use likelihood and non-likelihood based criteria to select a spatiotemporal model among various specifications. Finally, using kriging we regionalize the resulting parameter estimates of the best-fitted model in space at any unmonitored location in the Athens region. The results show that a specific autoregressive integrated moving average spatiotemporal model can optimally perform in within and out of spatial sample estimation. Supplemental materials for this article are available from the journal website.  相似文献   

14.
B.P. Marchant  R.M. Lark   《Geoderma》2007,140(4):337-345
The Matérn variogram model has been advocated because it is flexible and can represent varied behaviour at small lags. We show how the constraints on the spherical and exponential variogram at short lags ignore a possible source of uncertainty in the variogram and so in kriging surveys, that the Matérn model can describe. Matérn, spherical and exponential variogram models were fitted by maximum likelihood to a set of log10(K) observations made on a regular grid at Broom's Barn Farm, Suffolk, England. The likelihood profiles of the Matérn parameter estimates were asymmetric. Thus the uncertainty of these estimates could only be adequately assessed by a Bayesian approach. The uncertainty of estimated parameters of the Matérn variogram was larger than for the exponential variogram. This is an indication that the assumption of an exponential model limits the behaviour that may be described by the variogram. Thus uncertainty analyses where an exponential variogram is assumed may underestimate the uncertainty of kriged estimates. Bayesian analysis of the kriged estimates of log10(K) at Broom's Barn Farm using the Matérn variogram revealed an observable component of uncertainty due to variogram uncertainty. When an exponential variogram model was used, the estimate of this component of uncertainty was negligible. The Matérn variogram should therefore be used rather than the exponential model when assessing the adequacy of a variogram estimate. A method of designing sample schemes which is suitable for both estimating a Matérn variogram and interpolation is suggested.  相似文献   

15.
This paper develops a Bayesian approach for spatial inference on animal density from line transect survey data. We model the spatial distribution of animals within a geographical area of interest by an inhomogeneous Poisson process whose intensity function incorporates both covariate effects and spatial smoothing of residual variation. Independently thinning the animal locations according to their estimated detection probabilities results into another spatial Poisson process for the sightings (the observations). Prior distributions are elicited for all unknown model parameters. Due to the sparsity of data in the application we consider, eliciting sensible prior distributions is important in order to get meaningful estimation results. A reversible jump Markov Chain Monte Carlo (MCMC) algorithm for simulation of the posterior distribution is developed. We present results for simulated data and a real data set of minke whale pods from Antarctic waters. The main advantages of our method compared to design-based analyses are that it can use data arising from sources other than specifically designed surveys and its ability to link covariate effects to variation of animal density. The Bayesian paradigm provides a coherent framework for quantifying uncertainty in estimation results.  相似文献   

16.
Multivariate hierarchical Bayesian models provide a flexible framework for comprehensive study of biological systems with more than one outcome. Recent methodological developments facilitate modeling of heterogeneous associations between outcomes by specifying a linear mixed model on (co)variances at different levels of the data structure. Motivated by previous evidence for heterogeneous correlations in animal agriculture, we apply the proposed hierarchical Bayesian models to study the nature of the correlations between key performance outcomes in dairy cattle production systems, namely milk yield and reproduction. That is, the association between these outcomes might depend upon various fixed and random effect sources of heterogeneity both at the individual cow (residual) level as well as the herd (cluster) level. We thus propose a sequential modeling approach based on the deviance information criterion to select relevant explanatory variables on both types of associations. Furthermore, we extend the proposed methodology to accommodate right-censored outcomes, as common for dairy reproduction data, and use it to analyze field data from the Michigan dairy industry. The nature of the associations between milk production and reproduction in dairy cattle was inferred to be strongly heterogeneous and driven by multiple farm management practices and herd attributes, as well as by random clustering effects, at both cow and herd levels, thereby suggesting potential between-herd and within-herd intervention strategies to optimize performance of dairy production systems. Supplementary materials are available online.  相似文献   

17.
Seabirds such as albatrosses and petrels are frequently caught in longline and trawl fisheries, but limited demographic data for many species creates management challenges. A method for estimating the potential biological removal (the PBR method) for birds requires knowledge of adult survival, age at first breeding, a conservation goal, and the lower limit of a 60% confidence interval for the population size. For seabirds, usually only the number of breeding pairs is known, rather than the actual population size. This requires estimating the population size from the number of breeding pairs when important demographic variables, such as breeding success, juvenile survival, and the proportion of the adult population that engages in breeding, are unknown. In order to do this, a simple population model was built where some demographic parameters were known while others were constrained by considering plausible asymptotic estimates of the growth rate. While the median posterior population estimates are sensitive to the assumed population growth rate, the 20th percentile estimates are not. This allows the calculation of a modified PBR value that is based on the number of breeding pairs instead of the population size. For threatened albatross species, this suggests that human-caused mortalities should not exceed 1.5% of the number of breeding pairs, while for threatened petrel species, mortalities should be kept below 1.2% of the number of breeding pairs. The method is applied to 22 species and sub-species of albatrosses and petrels in New Zealand that are of management concern, of which at least 10 have suffered mortalities near or above these levels.  相似文献   

18.
Abundance estimates from animal point-count surveys require accurate estimates of detection probabilities. The standard model for estimating detection from removal-sampled point-count surveys assumes that organisms at a survey site are detected at a constant rate; however, this assumption can often lead to biased estimates. We consider a class of N-mixture models that allows for detection heterogeneity over time through a flexibly defined time-to-detection distribution (TTDD) and allows for fixed and random effects for both abundance and detection. Our model is thus a combination of survival time-to-event analysis with unknown-N, unknown-p abundance estimation. We specifically explore two-parameter families of TTDDs, e.g., gamma, that can additionally include a mixture component to model increased probability of detection in the initial observation period. Based on simulation analyses, we find that modeling a TTDD by using a two-parameter family is necessary when data have a chance of arising from a distribution of this nature. In addition, models with a mixture component can outperform non-mixture models even when the truth is non-mixture. Finally, we analyze an Ovenbird data set from the Chippewa National Forest using mixed effect models for both abundance and detection. We demonstrate that the effects of explanatory variables on abundance and detection are consistent across mixture TTDDs but that flexible TTDDs result in lower estimated probabilities of detection and therefore higher estimates of abundance.Supplementary materials accompanying this paper appear on-line.  相似文献   

19.
In this paper, we estimate the distribution of population by exposure to multiple airborne pollutants, taking into account the spatio-temporal variability of daily air quality and the high-resolution spatial spread of human population around Europe. In particular, we consider monitoring network data for five pollutants, namely carbon monoxide, nitrogen dioxide, ozone, coarse and fine particulate matters. The spatial information contained in the large dataset of daily continental air quality is exploited using a multivariate spatio-temporal model capable to cover cross correlation among pollutants, covariates, and missing data as well as spatial and temporal variability and correlation. At the same time, the model is simple enough to be feasible for the large dataset of daily continental air quality over three years. Maximum likelihood estimation is performed using the EM algorithm, and kriging-like spatial estimates are used to compute high-resolution exposure distribution. Moreover, a novel semi-parametric bootstrap technique is used to assess the exposure distribution uncertainty. In this way, we compare the daily population exposure of 33 European countries and three important metropolitan areas in years 2009–2011 using a single flexible model. Extensive tabulations and graphs are reported in the supplementary material.  相似文献   

20.
In this paper we consider generalized linear latent variable models that can handle overdispersed counts and continuous but non-negative data. Such data are common in ecological studies when modelling multivariate abundances or biomass. By extending the standard generalized linear modelling framework to include latent variables, we can account for any covariation between species not accounted for by the predictors, notably species interactions and correlations driven by missing covariates. We show how estimation and inference for the considered models can be performed efficiently using the Laplace approximation method and use simulations to study the finite-sample properties of the resulting estimates. In the overdispersed count data case, the Laplace-approximated estimates perform similarly to the estimates based on variational approximation method, which is another method that provides a closed form approximation of the likelihood. In the biomass data case, we show that ignoring the correlation between taxa affects the regression estimates unfavourably. To illustrate how our methods can be used in unconstrained ordination and in making inference on environmental variables, we apply them to two ecological datasets: abundances of bacterial species in three arctic locations in Europe and abundances of coral reef species in Indonesia.Supplementary materials accompanying this paper appear on-line.  相似文献   

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