The use of auxiliary variables in capture-recapture modelling: An overview

I review the use of auxiliary variables in capture-recapture models for estimation of demographic parameters (e.g. capture probability, population size, survival probability, and recruitment, emigration and immigration numbers). I focus on what has been done in current research and what still needs to be done. Typically in the literature, covariate modelling has made capture and survival probabilities functions of covariates, but there are good reasons also to make other parameters functions of covariates as well. The types of covariates considered include environmental covariates that may vary by occasion but are constant over animals, and individual animal covariates that are usually assumed constant over time. I also discuss the difficulties of using time-dependent individual animal covariates and some possible solutions. Covariates are usually assumed to be measured without error, and that may not be realistic. For closed populations, one approach to modelling heterogeneity in capture probabilities uses observable individual covariates and is thus related to the primary purpose of this paper. The now standard Huggins-Alho approach conditions on the captured animals and then uses a generalized Horvitz-Thompson estimator to estimate population size. This approach has the advantage of simplicity in that one does not have to specify a distribution for the covariates, and the disadvantage is that it does not use the full likelihood to estimate population size. Alternately one could specify a distribution for the covariates and implement a full likelihood approach to inference to estimate the capture function, the covariate probability distribution, and the population size. The general Jolly-Seber open model enables one to estimate capture probability, population sizes, survival rates, and birth numbers. Much of the focus on modelling covariates in program MARK has been for survival and capture probability in the Cormack-Jolly-Seber model and its generalizations (including tag-return models). These models condition on the number of animals marked and released. A related, but distinct, topic is radio telemetry survival modelling that typically uses a modified Kaplan-Meier method and Cox proportional hazards model for auxiliary variables. Recently there has been an emphasis on integration of recruitment in the likelihood, and research on how to implement covariate modelling for recruitment and perhaps population size is needed. The combined open and closed 'robust' design model can also benefit from covariate modelling and some important options have already been implemented into MARK. Many models are usually fitted to one data set. This has necessitated development of model selection criteria based on the AIC (Akaike Information Criteria) and the alternative of averaging over reasonable models. The special problems of estimating over-dispersion when covariates are included in the model and then adjusting for over-dispersion in model selection could benefit from further research.     

The use of auxiliary variables in capture-recapture modelling: an overview

I review the use of auxiliary variables in capture-recapture models for estimation of demographic parameters (e.g. capture probability, population size, survival probability, and recruitment, emigration and immigration numbers). I focus on what has been done in current research and what still needs to be done. Typically in the literature, covariate modelling has made capture and survival probabilities functions of covariates, but there are good reasons also to make other parameters functions of covariates as well. The types of covariates considered include environmental covariates that may vary by occasion but are constant over animals, and individual animal covariates that are usually assumed constant over time. I also discuss the difficulties of using time-dependent individual animal covariates and some possible solutions. Covariates are usually assumed to be measured without error, and that may not be realistic. For closed populations, one approach to modelling heterogeneity in capture probabilities uses observable individual covariates and is thus related to the primary purpose of this paper. The now standard Huggins-Alho approach conditions on the captured animals and then uses a generalized Horvitz-Thompson estimator to estimate population size. This approach has the advantage of simplicity in that one does not have to specify a distribution for the covariates, and the disadvantage is that it does not use the full likelihood to estimate population size. Alternately one could specify a distribution for the covariates and implement a full likelihood approach to inference to estimate the capture function, the covariate probability distribution, and the population size. The general Jolly-Seber open model enables one to estimate capture probability, population sizes, survival rates, and birth numbers. Much of the focus on modelling covariates in program MARK has been for survival and capture probability in the Cormack-Jolly-Seber model and its generalizations (including tag-return models). These models condition on the number of animals marked and released. A related, but distinct, topic is radio telemetry survival modelling that typically uses a modified Kaplan-Meier method and Cox proportional hazards model for auxiliary variables. Recently there has been an emphasis on integration of recruitment in the likelihood, and research on how to implement covariate modelling for recruitment and perhaps population size is needed. The combined open and closed 'robust' design model can also benefit from covariate modelling and some important options have already been implemented into MARK. Many models are usually fitted to one data set. This has necessitated development of model selection criteria based on the AIC (Akaike Information Criteria) and the alternative of averaging over reasonable models. The special problems of estimating over-dispersion when covariates are included in the model and then adjusting for over-dispersion in model selection could benefit from further research.     

Embedding latent class regression and latent class distal outcome models into cluster-weighted latent class analysis: a detailed simulation experiment

Usually in latent class (LC) analysis, external predictors are taken to be cluster conditional probability predictors (LC models with external predictors), and/or score conditional probability predictors (LC regression models). In such cases, their distribution is not of interest. Class-specific distribution is of interest in the distal outcome model, when the distribution of the external variables is assumed to depend on LC membership. In this paper, we consider a more general formulation, that embeds both the LC regression and the distal outcome models, as is typically done in cluster-weighted modelling. This allows us to investigate (1) whether the distribution of the external variables differs across classes, (2) whether there are significant direct effects of the external variables on the indicators, by modelling jointly the relationship between the external and the latent variables. We show the advantages of the proposed modelling approach through a set of artificial examples, an extensive simulation study and an empirical application about psychological contracts among employees and employers in Belgium and the Netherlands.     

Non-parametric procedure for knockout tournaments

In a seeded knockout tournament, where teams have some preassigned strength, do we have any assurances that the best team in fact has won? Is there some insight to be gained by considering which teams beat which other teams solely examining the seeds? We pose an answer to these questions by using the difference in the seeds of the two players as the basis for a test statistic. We offer several models for the underlying probability structure to examine the null distribution and power functions and determine these for small tournaments (less than five teams). One structure each for 8 teams and 16 teams is examined, and we conjecture an asymptotic normal distribution for the test statistic.     

On a mixture autoregressive model

We generalize the Gaussian mixture transition distribution (GMTD) model introduced by Le and co-workers to the mixture autoregressive (MAR) model for the modelling of non-linear time series. The models consist of a mixture of K stationary or non-stationary AR components. The advantages of the MAR model over the GMTD model include a more full range of shape changing predictive distributions and the ability to handle cycles and conditional heteroscedasticity in the time series. The stationarity conditions and autocorrelation function are derived. The estimation is easily done via a simple EM algorithm and the model selection problem is addressed. The shape changing feature of the conditional distributions makes these models capable of modelling time series with multimodal conditional distributions and with heteroscedasticity. The models are applied to two real data sets and compared with other competing models. The MAR models appear to capture features of the data better than other competing models do.     

The McDonald arcsine distribution: a new model to proportional data

We propose a new three-parameter continuous model called the McDonald arcsine distribution, which is a very competitive model to the beta, beta type I and Kumaraswamy distributions for modelling rates and proportions. We provide a mathematical treatment of the new distribution including explicit expressions for the density function, moments, generating and quantile functions, mean deviations, two probability measures based on the Bonferroni and Lorenz curves, Shannon entropy, Rényi entropy and cumulative residual entropy. Maximum likelihood is used to estimate the model parameters and the expected information matrix is determined. An application of the proposed model to real data shows that it can give consistently a better fit than other important statistical models.     

Test for age-specificity in survival of the common tern

Much effort in life-history theory has been addressed to the dependence of life-history traits on age, especially the phenomenon of senescence and its evolution. Although senescent declines in survival are well documented in humans and in domestic and laboratory animals, evidence for their occurrence and importance in wild animal species remains limited and equivocal. Several recent papers have suggested that methodological issues may contribute to this problem, and have encouraged investigators to improve sampling designs and to analyse their data using recently developed approaches to modelling of capture-mark-recapture data. Here we report on a three-year, two-site, mark-recapture study of known-aged common terns (Sterna hirundo) in the north-eastern USA. The study was nested within a long-term ecological study in which large numbers of chicks had been banded in each year for > 25 years. We used a range of models to test the hypothesis of an influence of age on survival probability. We also tested for a possible influence of sex on survival. The cross-sectional design of the study (one year's parameter estimates) avoided the possible confounding of effects of age and time. The study was conducted at a time when one of the study sites was being colonized and numbers were increasing rapidly. We detected two-way movements between the sites and estimated movement probabilities in the year for which they could be modelled. We also obtained limited data on emigration from our study area to more distant sites. We found no evidence that survival depended on either sex or age, except that survival was lower among the youngest birds (ages 2-3 years). Despite the large number of birds included in the study (1599 known-aged birds, 2367 total), confidence limits on estimates of survival probability were wide, especially for the oldest age-classes, so that a slight decline in survival late in life could not have been detected. In addition, the cross-sectional design of this study meant that a decline in survival probability within individuals (actuarial senescence) could have been masked by heterogeneity in survival probability among individuals (mortality selection). This emphasizes the need for the development of modelling tools permitting separation of these two phenomena, valid under field conditions in which the recapture probabilities are less than one.     

Generalized Additive Modelling of Mixed Distribution Markov Models with Application to Melbourne's Rainfall

The paper considers the modelling of time series using a generalized additive model with first-order Markov structure and mixed transition density having a discrete component at zero and a continuous component with positive sample space. Such models have application, for example, in modelling daily occurrence and intensity of rainfall, and in modelling numbers and sizes of insurance claims. The paper shows how these methods extend the usual sinusoidal seasonal assumption in standard chain-dependent models by assuming a general smooth pattern of occurrence and intensity over time. These models can be fitted using standard statistical software. The methods of Grunwald & Jones (2000) can be used to combine these separate occurrence and intensity models into a single model for amount. The models are used to investigate the relationship between the Southern Oscillation Index and Melbourne's rainfall, illustrated with 36 years of rainfall data from Melbourne, Australia.     

Estimation of parameterized spatio-temporal dynamic models

Spatio-temporal processes are often high-dimensional, exhibiting complicated variability across space and time. Traditional state-space model approaches to such processes in the presence of uncertain data have been shown to be useful. However, estimation of state-space models in this context is often problematic since parameter vectors and matrices are of high dimension and can have complicated dependence structures. We propose a spatio-temporal dynamic model formulation with parameter matrices restricted based on prior scientific knowledge and/or common spatial models. Estimation is carried out via the expectation–maximization (EM) algorithm or general EM algorithm. Several parameterization strategies are proposed and analytical or computational closed form EM update equations are derived for each. We apply the methodology to a model based on an advection–diffusion partial differential equation in a simulation study and also to a dimension-reduced model for a Palmer Drought Severity Index (PDSI) data set.     

Mixture modelling as an exploratory framework for genotype-trait associations

We propose a mixture modelling framework for both identifying and exploring the nature of genotype-trait associations. This framework extends the classical mixed effects modelling approach for this setting by incorporating a Gaussian mixture distribution for random genotype effects. The primary advantages of this paradigm over existing approaches include that the mixture modelling framework addresses the degrees-of-freedom challenge that is inherent in application of the usual fixed effects analysis of covariance, relaxes the restrictive single normal distribution assumption of the classical mixed effects models and offers an exploratory framework for discovery of underlying structure across multiple genetic loci. An application to data arising from a study of antiretroviral-associated dyslipidaemia in human immunodeficiency virus infection is presented. Extensive simulations studies are also implemented to investigate the performance of this approach.     

Specification and testing of multiplicative time-varying GARCH models with applications

In this article, we develop a specification technique for building multiplicative time-varying GARCH models of Amado and Teräsvirta (2008, 2013). The variance is decomposed into an unconditional and a conditional component such that the unconditional variance component is allowed to evolve smoothly over time. This nonstationary component is defined as a linear combination of logistic transition functions with time as the transition variable. The appropriate number of transition functions is determined by a sequence of specification tests. For that purpose, a coherent modelling strategy based on statistical inference is presented. It is heavily dependent on Lagrange multiplier type misspecification tests. The tests are easily implemented as they are entirely based on auxiliary regressions. Finite-sample properties of the strategy and tests are examined by simulation. The modelling strategy is illustrated in practice with two real examples: an empirical application to daily exchange rate returns and another one to daily coffee futures returns.     

Scalable spatio‐temporal Bayesian analysis of high‐dimensional electroencephalography data

We present a scalable Bayesian modelling approach for identifying brain regions that respond to a certain stimulus and use them to classify subjects. More specifically, we deal with multi‐subject electroencephalography (EEG) data with a binary response distinguishing between alcoholic and control groups. The covariates are matrix‐variate with measurements taken from each subject at different locations across multiple time points. EEG data have a complex structure with both spatial and temporal attributes. We use a divide‐and‐conquer strategy and build separate local models, that is, one model at each time point. We employ Bayesian variable selection approaches using a structured continuous spike‐and‐slab prior to identify the locations that respond to a certain stimulus. We incorporate the spatio‐temporal structure through a Kronecker product of the spatial and temporal correlation matrices. We develop a highly scalable estimation algorithm, using likelihood approximation, to deal with large number of parameters in the model. Variable selection is done via clustering of the locations based on their duration of activation. We use scoring rules to evaluate the prediction performance. Simulation studies demonstrate the efficiency of our scalable algorithm in terms of estimation and fast computation. We present results using our scalable approach on a case study of multi‐subject EEG data.     

Reliabilities of a single-unit system with multi-phased missions

ABSTRACT

Phased-mission systems (PMS) can be widely found in a lot of practical application areas. Reliability evaluations and analysis for this kind of systems become important issues. The reliability of PMS is typically defined as the probability that the system successfully accomplishes the missions of all phases. However, the k-out-of-n system success criterion for PMS has not been investigated. In this paper, according to this criterion, we develop two new models, which are static and dynamic, respectively. The assumptions for these two models are described in detail as well. The system reliabilities for both models are presented for the first time by employing finite Markov chain imbedding approach (FMCIA). In terms of FMCIA, we define different state spaces for the two models, and transition probability matrices are obtained. Then some numerical examples are given to illustrate the application of FMCIA. Finally, some discussions are made and conclusions are summarized.     

Efficient estimation of auto-regression parameters and innovation distributions for semiparametric integer-valued AR(p) models

Summary.  Integer-valued auto-regressive (INAR) processes have been introduced to model non-negative integer-valued phenomena that evolve over time. The distribution of an INAR( p ) process is essentially described by two parameters: a vector of auto-regression coefficients and a probability distribution on the non-negative integers, called an immigration or innovation distribution. Traditionally, parametric models are considered where the innovation distribution is assumed to belong to a parametric family. The paper instead considers a more realistic semiparametric INAR( p ) model where there are essentially no restrictions on the innovation distribution. We provide an (semiparametrically) efficient estimator of both the auto-regression parameters and the innovation distribution.     

Analysing Financial Returns by Using Regression Models Based on Non-Symmetric Stable Distributions

The daily evolution of the price of Abbey National shares over a 10-week period is analysed by using regression models based on possibly non-symmetric stable distributions. These distributions, which are only known through their characteristic function, can be used in practice for interactive modelling of heavy-tailed processes. A regression model for the location parameter is proposed and shown to induce a similar model for the mode. Finally, regression models for the other three parameters of the stable distribution are introduced. The model found to fit best allows the skewness of the distribution, rather than the location or scale parameters, to vary over time. The most likely share return is thus changing over time although the region where most returns are observed is stationary.     

The Distribution of Family Sizes Under a Time-Homogeneous Birth and Death Process

The number of extant individuals within a lineage, as exemplified by counts of species numbers across genera in a higher taxonomic category, is known to be a highly skewed distribution. Because the sublineages (such as genera in a clade) themselves follow a random birth process, deriving the distribution of lineage sizes involves averaging the solutions to a birth and death process over the distribution of time intervals separating the origin of the lineages. In this article, we show that the resulting distributions can be represented by hypergeometric functions of the second kind. We also provide approximations of these distributions up to the second order, and compare these results to the asymptotic distributions and numerical approximations used in previous studies. For two limiting cases, one with a relatively high rate of lineage origin, one with a low rate, the cumulative probability densities and percentiles are compared to show that the approximations are robust over a wide range of parameters. It is proposed that the probability distributions of lineage size may have a number of relevant applications to biological problems such as the coalescence of genetic lineages and in predicting the number of species in living and extinct higher taxa, as these systems are special instances of the underlying process analyzed in this article.     

Sparse Markov Chains for Sequence Data

Finite memory sources and variable‐length Markov chains have recently gained popularity in data compression and mining, in particular, for applications in bioinformatics and language modelling. Here, we consider denser data compression and prediction with a family of sparse Bayesian predictive models for Markov chains in finite state spaces. Our approach lumps transition probabilities into classes composed of invariant probabilities, such that the resulting models need not have a hierarchical structure as in context tree‐based approaches. This can lead to a substantially higher rate of data compression, and such non‐hierarchical sparse models can be motivated for instance by data dependence structures existing in the bioinformatics context. We describe a Bayesian inference algorithm for learning sparse Markov models through clustering of transition probabilities. Experiments with DNA sequence and protein data show that our approach is competitive in both prediction and classification when compared with several alternative methods on the basis of variable memory length.     

Soccer matches as experiments: how often does the ‘best’ team win?

Models in which the number of goals scored by a team in a soccer match follow a Poisson distribution, or a closely related one, have been widely discussed. We here consider a soccer match as an experiment to assess which of two teams is superior and examine the probability that the outcome of the experiment (match) truly represents the relative abilities of the two teams. Given a final score, it is possible by using a Bayesian approach to quantify the probability that it was or was not the case that ‘the best team won’. For typical scores, the probability of a misleading result is significant. Modifying the rules of the game to increase the typical number of goals scored would improve the situation, but a level of confidence that would normally be regarded as satisfactory could not be obtained unless the character of the game was radically changed.     

A litter-based approach to risk assessment in developmental toxicity studies via a power family of completely monotone functions

Summary.  A new class of distributions for exchangeable binary data is proposed that originates from modelling the joint success probabilities of all orders by a power family of completely monotone functions. The distribution proposed allows flexible modelling of the dose–response relationship for both the marginal response probability and the pairwise odds ratio and is especially well suited for a litter-based approach to risk assessment. Specifically, the risk of at least one adverse response within a litter takes on a simple form under the distribution proposed and can be reduced further to a generalized linear model if a complementary log–log-link function is used. Existing distributions such as the beta–binomial or folded logistic functions have a tendency to assign too much probability to zero, leading to an underestimation of the risk that at least one foetus is affected and an overestimation of the safe dose. The distribution proposed does not suffer from this problem. With the aid of symbolic differentiation, the distribution proposed can be fitted easily and quickly via the method of scoring. The usefulness of the class of distributions proposed and its superiority over existing distributions are demonstrated in a series of examples involving developmental toxicology and teratology data.     

Time-Varying Systemic Risk: Evidence From a Dynamic Copula Model of CDS Spreads

This article proposes a new class of copula-based dynamic models for high-dimensional conditional distributions, facilitating the estimation of a wide variety of measures of systemic risk. Our proposed models draw on successful ideas from the literature on modeling high-dimensional covariance matrices and on recent work on models for general time-varying distributions. Our use of copula-based models enables the estimation of the joint model in stages, greatly reducing the computational burden. We use the proposed new models to study a collection of daily credit default swap (CDS) spreads on 100 U.S. firms over the period 2006 to 2012. We find that while the probability of distress for individual firms has greatly reduced since the financial crisis of 2008–2009, the joint probability of distress (a measure of systemic risk) is substantially higher now than in the precrisis period. Supplementary materials for this article are available online.