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posted to data time_series
by e2holmes
on 2011-03-02 03:25:01
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posted to data time_series
by e2holmes
on 2011-03-02 03:23:33
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Abstract
We consider a range of models that may be used to predict the future persistence of populations, particularly those based on discrete-state Markov processes. While the mathematical theory of such processes is very well-developed, they may be difficult to work with when attempting to estimate parameters or expected times to extinction. Hence, we focus on diffusion and other approximations to these models, presenting new and recent developments in parameter estimation for density dependent processes, and the calculation of extinction times for ...
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Abstract
For many populations and species, population viability analysis (PVA) plays a critical role in developing defensible conservation strategies and recovery plans. Although technical aspects of PVA have been well scrutinized, misapplication of PVA and misinterpretation of its results have received less attention. To illustrate potential hazards of improper use of PVA we reanalyzed data from a recent study on viability of wolves in Algonquin Provincial Park (APP), Ontario, Canada. The original PVA predicted extirpation of wolves from APP and prompted both ...
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Abstract
Conventional population viability analysis (PVA) is often impractical because data are scarce for many threatened species. For this reason, simple count-based models are being advocated. The simplest of these models requires nothing more than a time series of abundance estimates, from which variance and autocorrelation in growth rate are estimated and predictions of population persistence are generated. What remains unclear, however, is how many years of data are needed to generate reliable estimates of these parameters and hence reliable predictions of ...
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Abstract
We describe risk-based viable population monitoring, in which the monitoring indicator is a yearly prediction of the probability that, within a given timeframe, the population abundance will decline below a prespecified level. Common abundance-based monitoring strategies usually have low power to detect declines in threatened and endangered species and are largely reactive to declines. Comparisons of the population's estimated risk of decline over time will help determine status in a more defensible manner than current monitoring methods. Monitoring risk is a ...
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Abstract
A major debate in ecology concerns the relative importance of intrinsic factors and extrinsic environmental variations in determining population size fluctuations1, 2, 3, 4, 5, 6. Spatial correlation of fluctuations in different populations caused by synchronous environmental shocks2,7,8 is a powerful tool for quantifying the impact of environmental variations on population dynamics8,9. However, interpretation of synchrony is often complicated by migration between populations8,10. Here we address this issue by using time series from sheep populations on two islands in the St ...
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Abstract
Many species exhibit widespread spatial synchrony in population fluctuations. This pattern is of great ecological interest and can be a source of concern when the species is rare or endangered. Both dispersal and spatial correlations in the environment have been implicated as possible causes of this pattern, but these two factors have rarely been studied in combination. We develop a spatially structured population model, simple enough to obtain analytic solutions for the population correlation, that incorporates both dispersal and environmental correlation. ...
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Abstract
▪ Abstract Spatial synchrony refers to coincident changes in the abundance or other time-varying characteristics of geographically disjunct populations. This phenomenon has been documented in the dynamics of species representing a variety of taxa and ecological roles. Synchrony may arise from three primary mechanisms:(a) dispersal among populations, reducing the size of relatively large populations and increasing relatively small ones; (b) congruent dependence of population dynamics on a synchronous exogenous random factor such as temperature or rainfall, a phenomenon known as the ...
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Abstract
Autocorrelation is a very general statistical property of ecological variables observed across geographic space; it most common forms are patches and gradients. Spatial autocorrelation, which comes either from the physical forcing of environmental variables or from community processes, presents a problem for statistical testing because autocorrelated data violate the assumption of independence of most standard statistical procedures. The paper discusses first how autocorrelation in ecological variables can be described and measured, with emphasis on mapping techniques. Then, proper statistical testing in ...
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Abstract
Within the paradigm of population dynamics a central task is to identify environmental factors affecting population change and to estimate the strength of these effects. We here investigate the impact of observation errors in measurements of population densities on estimates of environmental effects. Adding observation errors may change the autocorrelation of a population time series with potential consequences for estimates of effects of autocorrelated environmental covariates. Using Monte Carlo simulations, we compare the performance of maximum likelihood estimates from three stochastic ...
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by Bernt-Erik Saether, Steinar Engen, Vidar Grotan, et al.Wolfgang Fiedler, Erik Matthysen, Marcel E. Visser, Jonathan Wright, Anders P. A. P. E. Moller, Frank Adriaensen, V. A. N. Balen, S. Han, Dawn Balmer, Mark C. Mainwaring, Robin H. Mccleery, Miriam Pampus, Wolfgang Winkel
posted to spatial_synchrony time_series
by e2holmes
on 2009-01-29 21:46:16
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Journal of Animal Ecology, Vol. 77, pp. 612-617
posted to data time_series
by e2holmes
on 2009-01-29 21:43:06
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BioScience, Vol. 55 (2005), pp. 501-510
posted to correlated_noise
by e2holmes
on 2009-01-29 21:23:56
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posted to spatial_synchrony
by e2holmes
on 2009-01-29 21:13:58
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Abstract
Abstract Many species exhibit widespread spatial synchrony in population fluctuations. This pattern is of great ecological interest and can be a source of concern when a species is rare or endangered. Moran’s theorem suggests that if two (or more) populations sharing a common linear density-dependence in the renewal process are disturbed with correlated noise, they will become synchronized with correlation matching the noise correlation. In this report, correlation of nonidentical populations that are described by linear and stationary autoregressive processes is analyzed. ...
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Abstract
Tracking marine animals with electronic tags has become an indispensable tool in understanding biology in relation to movement. Combining light based geolocation estimates with an underlying movement model has proved helpful in reconstructing the most probable track of tagged animals. These tracks can be further improved by including the tag measured sea-surface temperature and matching it to external sea-surface temperature (SST) data. The current methodology for doing this in a state-space model requires that external sea-surface temperature be smoothed before it ...
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Abstract
The importance of considering spatially-correlated extinction in metapopulation viability analyses was investigated using a model of the population dynamics of Gymnobelideus leadbeateri McCoy (Leadbeater's Possum). Fire caused local extinction of G. leadbeateri and induced changes in the suitability of the habitat over a period of decades and centuries. Spatially-correlated fires, in which the correlation between the incidence of fire declines with distance, and uniformly-correlated fires were simulated. The predicted risk of metapopulation extinction increased: (i) as the variance in the number ...
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Abstract
We use simple models to compare extinction risk among basic life history types when environmental noise is either uncorrelated ("white") or positively autocorrelated ("red"). The metric of extinction is probability of extinction in 50 years; variability of noise is scaled such that its expected variance is independent of colour at this time scale. We compare annual, semelparous biennial, iteroparous biennial and perennial life histories. Given an identical equilibrium population size and basic reproductive number, annual life history confers much higher extinction ...
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Canadian Journal of Zoology, Vol. 85, No. 10. (1 October 2007), pp. 1031-1048
Note (first note only)
this reviews methods for analyzing spatial data in order to discern metapopulation structure.
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Abstract
Population viability analysis (PVA) and metapopulation theory are valuable tools to model the dynamics of spatially structured populations. In this article we used a spatially realistic population dynamic model to simulate the trajectory of a Proclossiana eunomia metapopulation in a network of habitat patches located in the Belgian Ardenne. Sensitivity analysis was used to evaluate the relative influence of the different parameters on the model output. We simulated habitat loss by removing a percentage of the original habitat, proportionally in each ...
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Ecological Applications, Vol. 12, No. 2. (2002), pp. 335-345
Abstract
Ecologists have used a variety of comparative mensurative and manipulative experimental approaches to study the biological consequences of habitat fragmentation. In this paper, we evaluate the merits of the two major approaches and offer guidelines for selecting a design. Manipulative experiments rigorously assess fragmentation effects by comparing pre- and post-treatment conditions. Yet they are often constrained by a number of practical limitations, such as the difficulty in implementing large-scale treatments and the impracticality of measuring the long-term (decades to centuries) responses ...
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Ecological Applications, Vol. 12, No. 2. (2002), pp. 346-353
Abstract
I reviewed and reconciled predictions of four models on the effect of habitat fragmentation on the population extinction threshold, and I compared these predictions to results from empirical studies. All four models predict that habitat fragmentation can, under some conditions, increase the extinction threshold such that, in more fragmented landscapes, more habitat is required for population persistence. However, empirical studies have shown both positive and negative effects of habitat fragmentation on population abundance and distribution with about equal frequency, suggesting that ...
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Ecological Applications, Vol. 10, No. 3. (2000), pp. 639-670
Abstract
The many ways that people have used and managed land throughout history has emerged as a primary cause of land-cover change around the world. Thus, land use and land management increasingly represent a fundamental source of change in the global environment. Despite their global importance, however, many decisions about the management and use of land are made with scant attention to ecological impacts. Thus, ecologists' knowledge of the functioning of Earth's ecosystems is needed to broaden the scientific basis of decisions ...
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Ecology Letters, Vol. 2, No. 2., pp. 121-127
Abstract
Habitat fragmentation is a potentially critical factor in determining population persistence. In this paper, we explore the effect of fragmentation when the fragmentation follows a fractal pattern. The habitat is divided into patches, each of which is suitable or unsuitable. Suitable patches are either occupied or unoccupied, and change state depending on rates of colonization and local extinction. We compare the behaviour of two models: a spatially implicit patch-occupancy (PO) model and a spatially explicit cellular automaton (CA) model. The PO ...
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Ecology, Vol. 83, No. 12. (2002), pp. 3243-3249
posted to extinction metapopulation spatial
by e2holmes
on 2008-03-19 03:18:51
Abstract
Neither linear nor two-dimensional frameworks may be the most appropriate for fish and other species constrained to disperse within river-creek systems. In particular, the hierarchical, dendritic structures of riverine networks are not well captured by existing spatial models. Here I use a simple geometric model and metapopulation modeling to make three points concerning the ecological consequences of dendritic landscapes. First, connectivity patterns of river-creek networks differ from linear landscapes, and these differences in connectivity can either enhance or reduce metapopulation persistence ...
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Journal of the American Statistical Association, Vol. 86, No. 416. (1991), pp. 1024-1033
Abstract
The bootstrap is proposed as a method for assessing the precision of Gaussian maximum likelihood estimates of the parameters of linear state-space models. Our results also apply to autoregressive moving average models, since they are a special case of state-space models. It is shown that for a time-invariant, stable system, the bootstrap applied to the innovations yields asymptotically consistent standard errors. To investigate the performance of the bootstrap for finite sample lengths, simulation results are presented for a two-state model with ...
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Journal of the Royal Statistical Society: Series B (Statistical Methodology), Vol. 64, No. 4. (October 2002), pp. 583-639, doi:10.1111/1467-9868.00353
Abstract
Summary. We consider the problem of comparing complex hierarchical models in which the number of parameters is not clearly defined. Using an information theoretic argument we derive a measure pD for the effective number of parameters in a model as the difference between the posterior mean of the deviance and the deviance at the posterior means of the parameters of interest. In general pD approximately corresponds to the trace of the product of Fisher's information and the posterior covariance, which in ...
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(1998)
Abstract
Connects many different aspects of the growing model selection field by examining the different lines of reasoning that have motivated the derivation of both classical & modern criteria, & then examines their application to see how well it matches the intent of their creators. ...
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(12 July 2002)
Abstract
The second edition of this book is unique in that it focuses on methods for making formal statistical inference from all the models in an a priori set (Multi-Model Inference). A philosophy is presented for model-based data analysis and a general strategy outlined for the analysis of empirical data. The book invites increased attention on a priori science hypotheses and modeling. Kullback-Leibler Information represents a fundamental quantity in science and is Hirotugu Akaike's basis for model selection. The maximized log-likelihood function ...
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Abstract
Recently, researchers in several areas of ecology and evolution have begun to change the way in which they analyze data and make biological inferences. Rather than the traditional null hypothesis testing approach, they have adopted an approach called model selection, in which several competing hypotheses are simultaneously confronted with data. Model selection can be used to identify a single best model, thus lending support to one particular hypothesis, or it can be used to make inferences based on weighted support from ...
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Abstract
A bias correction to the Akaike information criterion, AIC, is derived for regression and autoregressive time series models. The correction is of particular use when the sample size is small, or when the number of fitted parameters is a moderate to large fraction of the sample size. The corrected method, called AICC, is asymptotically efficient if the true model is infinite dimensional. Furthermore, when the true model is of finite dimension, AICC is found to provide better model order choices than ...
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Ecological Applications, Vol. 17, pp. 1771-1782
Abstract
Spatially explicit population models (SEPMs) are often considered the best way to predict and manage species distributions in spatially heterogeneous landscapes. However, they are computationally intensive and require extensive knowledge of species' biology and behavior, limiting their application in many cases. An alternative to SEPMs is graph theory, which has minimal data requirements and efficient algorithms. Although only recently introduced to landscape ecology, graph theory is well suited to ecological applications concerned with connectivity or movement. This paper compares the performance ...
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Science of the Total Environment, Vol. 349 (2005), pp. 106-119
Abstract
Research initiated in 1970 has identified a long-term, year-round resident community of about 140 bottlenose dolphins (Tursiops truncatus) in Sarasota Bay, Florida, providing unparalleled opportunities to investigate relationships between organochlorine contaminant residues and life-history and reproductive parameters. Many individual dolphins are identifiable and of known age, sex, and maternal lineage (V4 generations). Observational monitoring provides data on dolphin spatial and temporal occurrence, births and fates of calves, and birth-order. Capture–release operations conducted for veterinary examinations provide biological data and samples for life-history and contaminant residue measurement. ...
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Environmental Toxicology and Chemistry, Vol. 18, pp. 452-458
Abstract
Organochlorine pesticides, polychlorinated biphenyls (PCBs) including non–ortho PCBs, polychlorinated dibenzo-p-dioxins (PCDDs), and polychlorinated dibenzofurans (PCDFs) were measured in sea otter liver tissue from California, southeast Alaska, and the western Aleutian archipelago collected between 1988 and 1992. Average total dichlorodiphenyltrichloroethane concentrations for California otters (850 μg/kg wet weight) were over 20 times higher than in Aleutian otters (40 μg/kg) and over 800 times higher than otters from southeast Alaska (1 μg/kg). Levels for total PCBs in Aleutian otters (310 μg/kg) were 1.7 ...
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Abstract
After nearly 3 decades of decline, the western stock of Steller sea lions (SSL; Eumetopias jubatus) was listed as an endangered species in 1997. While the cause of the decline in the 1970s and 1980s has been attributed to nutritional stress, recent declines are unexplained and may result from other factors including the presence of environmental contaminants. SSL tissues show accumulation of butyltins, mercury, PCBs, DDTs, chlordanes and hexachlorobenzene. SSL habitats and prey are contaminated with additional chemicals including mirex, endrin, ...
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Rev Environ Contam Toxicol, Vol. 136 (1994), pp. 123-167
Abstract
Organochlorines, such as PCBs and DDT, are ubiquitous contaminants. Most studies reporting concentrations of organochlorines in pinnipeds have investigated ringed, grey, and harbour seals. Very few studies have been carried out on pinnipeds from the southern hemisphere. Pre-1980, the highest mean wet-weight blubber concentrations of DDT and related metabolites (911 +/- 582 micrograms g-1) were recorded in sea lions from California. The highest pre-1980 blubber concentrations of PCBs (1470 +/- 922 micrograms g-1) were recorded in harbour seals from the Netherlands. ...
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Abstract
A review of the published literature indicates that marine mammal neoplasia includes the types and distributions of tumors seen in domestic species. A routine collection of samples from marine mammal species is hampered, and, hence, the literature is principally composed of reports from early whaling expeditions, captive zoo mammals, and epizootics that affect larger numbers of animals from a specific geographic location. The latter instances are most important, because many of these long-lived, free-ranging marine mammals may act as environmental sentinels ...
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J Wildl Dis, Vol. 12, No. 1. (1 January 1976), pp. 104-115
Abstract
Twenty percent of the California sea lion pups born on San Miguel Island die due to premature parturition. Specimens collected from premature-partus animals resulted in recovery of a virus, San Miguel Sea Lion Virus, indistinguishable from Vesicular Exanthema of Swine Virus, and Leptospira pomona from some of the premature cows and pups. The age range of 10 females delivering healthy pups in June was 10-14 years. With one exception, the ages in 10 aborting females was 6-8 years. The p,p'-DDE levels ...
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Vet Pathol, Vol. 40, No. 2. (1 March 2003), pp. 175-180
Abstract
A high prevalence of uterine leiomyoma has been reported in Baltic gray seals aged 15 years and above. Studies on Baltic seals during the 1970s revealed high tissue concentrations of the organochlorines bis(chlorophenyl)-1,1,1-trichloroethane (DDT) and polychlorinated biphenyls (PCBs), lowered reproduction rate, and pathologic changes. In the second half of the 1970s, decreases of PCB and DDT in Baltic biota occurred, and the prevalence of pregnancies in Baltic seals increased. Between 1975 and 1997, 53 Baltic gray seal females of age 15-40 ...
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Antarctic Science, Vol. 15, No. 3. (01 January 2006), pp. 249-256
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Oikos, Vol. 84, No. 1., pp. 153-159
Abstract
Population ecologists continue to debate population regulation. If anything, the controversy intensified during the last decade. Does it mean that our field has not progressed very far since the days of the "great debate" between Nicholson and Andrewartha? Three years ago I suggested that in actuality the broad outlines of a consensus were emerging. What I have read in the literature since then has only confirmed me in the opinion that most population ecologists are in agreement on the major, strategic ...
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Ecology, Vol. 71, No. 6., pp. 2044-2052
Abstract
Some practical techniques are discussed for analyzing time series whose statistical properties are changing with time. We first consider how principal component analysis can reduce the multidimensional nature of certain series and, in particular, apply this technique to the analysis of changing seasonal patterns. Discussions of trend, changes in oscillatory behavior, and unusual events follow. The problem of making inferences regarding causation is briefly considered. We conclude with a call for flexibility in approach. ...
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Marine Mammal Science, Vol. 18 (2002), pp. 746-764
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Ecological Applications, Vol. 16 (2006), pp. 704-717
Abstract
The Steller sea lion (SSL) population in Alaska was listed as threatened under the Endangered Species Act in 1990. At that time, several procedural restrictions were placed on the commercial fisheries of the region in an effort to reduce the potential for human-induced mortality on sea lions. Several years have elapsed since these restrictions were put into place, and questions about their efficacy remain. In an effort to determine whether or not fisheries management measures have helped the SSL population to ...
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Mathematical Psychology (2005)
Abstract
This article examines a Bayesian nonparametric approach to model selection and model testing, which is based on concepts from Bayesian decision theory and information theory. The approach can be used to evaluate the predictive-utility of any model that is either probabilistic or deterministic, with that model analyzed under either the Bayesian or classical-frequentist approach to statistical inference. Conditional on an observed set of data, generated from some unknown true sampling density, the approach identifies the ‘‘best’’ model as the one that predicts a sampling density ...
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