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N-mixture models for estimating population size from spatially replicated counts

Spatial replication is a common theme in count surveys of animals. Such surveys often generate sparse count data from which it is difficult to estimate population size while formally accounting for detection probability. In this article, I describe a class of models (n-mixture models) which allow for estimation of population size from such data. The key idea is to view site-specific population sizes, n, as independent random variables distributed according to some mixing distribution (e.g., Poisson). Prior parameters are estimated from the marginal likelihood of the data, having integrated over the prior distribution for n. Carroll and Lombard (1985, Journal of American Statistical Association 80, 423-426) proposed a class of estimators based on mixing over a prior distribution for detection probability. Their estimator can be applied in limited settings, but is sensitive to prior parameter values that are fixed a priori. Spatial replication provides additional information regarding the parameters of the prior distribution on n that is exploited by the n-mixture models and which leads to reasonable estimates of abundance from sparse data. A simulation study demonstrates superior operating characteristics (bias, confidence interval coverage) of the n-mixture estimator compared to the Caroll and Lombard estimator. Both estimators are applied to point count data on six species of birds illustrating the sensitivity to choice of prior on p and substantially different estimates of abundance as a consequence.

Biometrics

Estimation and confidence intervals for empirical mixing distributions

Questions regarding collections of parameter estimates can frequently be expressed in terms of an empirical mixing distribution (EMD). This report discusses empirical Bayes estimation of an EMD, with emphasis on the construction of interval estimates. Estimation of the EMD is accomplished by substitution of estimates of prior parameters in the posterior mean of the EMD. This procedure is examined in a parametric model (the normal-normal mixture) and in a semi-parametric model. In both cases, the empirical Bayes bootstrap of Laird and Louis (1987, Journal of the American Statistical Association 82, 739-757) is used to assess the variability of the estimated EMD arising from the estimation of prior parameters. The proposed methods are applied to a meta-analysis of population trend estimates for groups of birds.

Biometrics

Basis function models for animal movement

Advances in satellite-based data collection techniques have served as a catalyst for new statistical methodology to analyze these data. In wildlife ecological studies, satellite-based data and methodology have provided a wealth of information about animal space use and the investigation of individual-based animal–environment relationships. With the technology for data collection improving dramatically over time, we are left with massive archives of historical animal telemetry data of varying quality. While many contemporary statistical approaches for inferring movement behavior are specified in discrete time, we develop a flexible continuous-time stochastic integral equation framework that is amenable to reduced-rank second-order covariance parameterizations. We demonstrate how the associated first-order basis functions can be constructed to mimic behavioral characteristics in realistic trajectory processes using telemetry data from mule deer and mountain lion individuals in western North America. Our approach is parallelizable and provides inference for heterogenous trajectories using nonstationary spatial modeling techniques that are feasible for large telemetry datasets. Supplementary materials for this article are available online.

Journal of the American Statistical Association

Circuit theory and model-based inference for landscape connectivity

Circuit theory has seen extensive recent use in the field of ecology, where it is often applied to study functional connectivity. The landscape is typically represented by a network of nodes and resistors, with the resistance between nodes a function of landscape characteristics. The effective distance between two locations on a landscape is represented by the resistance distance between the nodes in the network. Circuit theory has been applied to many other scientific fields for exploratory analyses, but parametric models for circuits are not common in the scientific literature. To model circuits explicitly, we demonstrate a link between Gaussian Markov random fields and contemporary circuit theory using a covariance structure that induces the necessary resistance distance. This provides a parametric model for second-order observations from such a system. In the landscape ecology setting, the proposed model provides a simple framework where inference can be obtained for effects that landscape features have on functional connectivity. We illustrate the approach through a landscape genetics study linking gene flow in alpine chamois (Rupicapra rupicapra) to the underlying landscape.

Journal of the American Statistical Association

Estimating size and composition of biological communities by modeling the occurrence of species

We develop a model that uses repeated observations of a biological community to estimate the number and composition of species in the community. Estimators of community-level attributes are constructed from model-based estimators of occurrence of individual species that incorporate imperfect detection of individuals. Data from the North American Breeding Bird Survey are analyzed to illustrate the variety of ecologically important quantities that are easily constructed and estimated using our model-based estimators of species occurrence. In particular, we compute site-specific estimates of species richness that honor classical notions of species-area relationships. We suggest extensions of our model to estimate maps of occurrence of individual species and to compute inferences related to the temporal and spatial dynamics of biological communities.

Journal of the American Statistical Association

Estimation of long-term discharge statistics by regional adjustment

A regional adjustment relationship was developed to estimate long-term (30-year) monthly median discharges from short term (three-year) records. This method differs from traditional approaches in that it is based on site-specific discharge data but does not require correlation of these data with discharges from a single hydrologically similar long-term gage. The method is shown to be statistically robust, and applicable to statistics other than the median.A regional adjustment relationship was developed to estimate long-term (30-year) monthly discharges from short term (three-year) records. This method differs from traditional approaches in that it is based on site-specific discharge data but does not require correlation of these data with discharges from a single hydrologically similar long-term gage. The method is shown to be statistically robust, and applicable to statistics other than the median.

Journal of the American Water Resources Associatio

Hydrologic landscapes on the Delmarva Peninsula - Part 2: Estimates of base-flow nitrogen load to Chesapeake Bay

ABSTRACT: The relation between landscape characteristics and water chemistry on the Delmarva Peninsula can be determined through a principal-component analysis of basin characteristics. Two basin types were defined by factor scores: (1) well-drained basins, characterized by combinations of a low percentage of forest cover, a low percentage of poorly drained soil, and elevated channel slope; and (2) poorly drained basins, characterized by a combinations of an elevated percentage of forest cover, an elevated percentage of poorly drained soil, and low channel slopes. Results from base-flow sampling of 29 basins during spring 1991 indicate that water chemistry of the two basin types differ significantly. Concentrations of calcium, magnesium, potassium, alkalinity, chloride, and nitrate are elevated in well-drained basins, and specific conductance is elevated. Concentrations of aluminum, dissolved organic carbon, sodium, and silica are elevated in poorly drained basins whereas specific conductance is low. The chemical patterns found in well-drained basins can be attributed to the application of agricultural chemicals, and those in poorly drained basins can be attributed to ground-water flowpaths. These results indicate that basin types determined by a quantitative analysis of basin characteristics can be related statistically to differences in base-flow chemistry, and that the observed statistical differences can be related to major processes that affect water chemistry.

Journal of the American Water Resources Associatio

Use of a portable electric barrier to estimate Chinook salmon escapement in a turbid Alaskan river

We developed a portable electric barrier to aid in the capture of adult chinook salmon Oncorhynchus tshawytscha undergoing spawning migrations up a turbid stream in south-central Alaska. In 1981, we tagged and released 157 chinook salmon after diverting them from the main-stem Killey River into a conventional trap with the aid of the electric barrier. On the basis of returns of tagged salmon to Benjamin Creek, a clear-water tributary of the upper Killey River, we estimated spawners in the drainage to number 8,000 fish. Two different statistical approaches to the mark–recapture data yielded similar estimates. Through several modifications of the electric barrier, we were able to reduce mortality associated with the barrier's use.

Alaska

The consequences of neglecting reservoir storage in national-scale hydrologic models: An appraisal of key streamflow statistics

A better understanding of modeled streamflow errors related to basin reservoir storage is needed for large regions, which normally have many ungaged basins with reservoirs. We quantified the difference between modeled and observed streamflows for one process-based and three statistical-transfer hydrologic models, none of which explicitly accounted for reservoir storage. Streamflow statistics representing low to high flows, seasonality, annual variability, and daily autocorrelation were examined at 1082 study basins across the conterminous USA. All models increasingly overpredict (or decreasingly underpredict) observed annual maximum flows with increasing storage. Correlations between absolute values of errors for low-flow statistics and storage are often larger in magnitude than those for signed errors—additional storage is associated with increases in model errors in both directions even when its overall effect in one direction is weak. The rate of increase in absolute values of model errors was nonlinear for most statistics. For low flows, model errors had a change point to larger errors at 48 days of reservoir storage (relative to long-term mean daily flow); mean and high flows had change points at 147 to 176 days. We present predicted-to-observed errors for nine streamflow statistics over a large range of reservoir storage to help modelers and users of modeled streamflow understand the amount of storage for which explicit reservoir modeling is needed.

Journal of the American Water Resources Associatio

Using a Geographic Information System to determine the relation between stream quality and geology in the Roberts Creek watershed, Clayton County, Iowa

A geographic information system (GIS) was used to determine the relation between the stream-water quality and underlying geology in Roberts Creek watershed, Clayton County, Iowa, for base-flow conditions during the spring and summer of 1988–90. Geologic, stream, basin and subbasin boundaries, and water-quality sampling-site coverages were created by digitizing available maps. A contour coverage was created from digital line-graph data. The areal extent of geologic units subcropping in each subbasin was quantified with GIS, and the results then were output and joined with the discharge and water-quality data for statistical analyses. Illustrations showing the geology of the study area and the results of the study were prepared using GIS. By using GIS and a statistical software package, a weak but statistically significant relation was found between the water temperature, pH, and nitrogen concentrations in Roberts Creek and the underlying geology during base-flow conditions.

Iowa

Disruptions of stream sediment size and stability by lakes in mountain watersheds: Potential effects on periphyton biomass

The location of a stream reach relative to other landforms in a watershed is an important attribute. We hypothesized that lakes disrupt the frequency of finer, more mobile sediments and thereby change sediment transport processes such that benthic substrates are more stable (i.e., less mobile) below lakes than above lakes. In turn, we hypothesized that this reduced mobility would lead to greater periphyton biomass below lakes. We tested these hypotheses in study reaches above and below lakes in 3 mountain watersheds. To expand this comparison, we analyzed the relationship between sediment attributes and periphyton biomass in one watershed with and one watershed without a lake. We hypothesized that no clear pattern or change in sediment size or chlorophyll a (chl a) would be observed over a 3-km-long study reach without a lake. In contrast, we expected a clear discontinuity in both sediment size and chl a in a 7-km-long study reach interrupted by a lake. Average median sediment size (D50) was significantly larger (p < 0.01) in lake-outlet than lake-inlet reaches (41 mm vs 10 mm). Bed sediments in lake-outlet reaches were immobile during bankfull flows, whereas sediments at lake-inlet reaches were mobile during bankfull flows. Chlorophyll a was ???10x greater in lake-outlet reaches than in lake-inlet reaches, although this difference was not statistically significant (p = 0.17). The longitudinal analysis clearly showed geomorphic transitions in sediment size and mobility downstream of mountain lakes, and these geomorphic transitions might be associated with changes in periphyton biomass. Geomorphic transitions can alter sediment transport and should be considered in concert with other factors that are considered more commonly in benthic ecology, such as light, nutrients, and temperature. ?? 2007 by The North American Benthological Society.

Journal of the North American Benthological Societ

Stationarity: Wanted dead or alive?

Aligning engineering practice with natural process behavior would appear, on its face, to be a prudent and reasonable course of action. However, if we do not understand the long-term characteristics of hydroclimatic processes, how does one find the prudent and reasonable course needed for water management? We consider this question in light of three aspects of existing and unresolved issues affecting hydroclimatic variability and statistical inference: Hurst-Kolmogorov phenomena; the complications long-term persistence introduces with respect to statistical understanding; and the dependence of process understanding on arbitrary sampling choices. These problems are not easily addressed. In such circumstances, humility may be more important than physics; a simple model with well-understood flaws may be preferable to a sophisticated model whose correspondence to reality is uncertain.

Journal of the American Water Resources Associatio

Problems and methods involved in relating land use to ground-water quality

Efforts to relate shallow ground-water quality to the land use near a well lead to several statistical difficulties. These include potential uncertainty in land-use categorical data due to misclassification, data closure, distributional skewing, and spatial autocorrelation. Methods of addressing these problems are, respectively, the establishment of limits on minimum buffer radius, the estimation of contrasts, rank-based tests of association, and sub-sampling to prevent buffer overlap. Relations between the presence of purgeable organic compounds in ground water and land use are used to illustrate these problems and methods.

Journal of the American Water Resources Associatio

Assessment of endocrine-disrupting chemicals attenuation in a coastal plain stream prior to wastewater treatment plant closure

The U.S. Geological Survey is conducting a combined pre/post-closure assessment at a long-term wastewater treatment plant (WWTP) site at Fort Gordon near Augusta, Georgia. Here, we assess select endocrine-active chemicals and benthic macroinvertebrate community structure prior to closure of the WWTP. Substantial downstream transport and limited instream attenuation of endocrine-disrupting chemicals (EDCs) was observed in Spirit Creek over a 2.2-km stream segment downstream of the WWTP outfall. A modest decline (less than 20% in all cases) in surface water detections was observed with increasing distance downstream of the WWTP and attributed to partitioning to the sediment. Estrogens detected in surface water in this study included estrone (E1), 17β-estradiol (E2), and estriol (E3). The 5 ng/l and higher mean estrogen concentrations observed in downstream locations indicated that the potential for endocrine disruption was substantial. Concentrations of alkylphenol ethoxylate (APE) metabolite EDCs also remained statistically elevated above levels observed at the upstream control site. Wastewater-derived pharmaceutical and APE metabolites were detected in the outflow of Spirit Lake, indicating the potential for EDC transport to aquatic ecosystems downstream of Fort Gordon. The results indicate substantial EDC occurrence, downstream transport, and persistence under continuous supply conditions and provide a baseline for a rare evaluation of ecosystem response to WWTP closure.

Georgia

The new GFDL global atmosphere and land model AM2-LM2: Evaluation with prescribed SST simulations

The configuration and performance of a new global atmosphere and land model for climate research developed at the Geophysical Fluid Dynamics Laboratory (GFDL) are presented. The atmosphere model, known as AM2, includes a new gridpoint dynamical core, a prognostic cloud scheme, and a multispecies aerosol climatology, as well as components from previous models used at GFDL. The land model, known as LM2, includes soil sensible and latent heat storage, groundwater storage, and stomatal resistance. The performance of the coupled model AM2-LM2 is evaluated with a series of prescribed sea surface temperature (SST) simulations. Particular focus is given to the model's climatology and the characteristics of interannual variability related to El Nin??o-Southern Oscillation (ENSO). One AM2-LM2 integration was perfor med according to the prescriptions of the second Atmospheric Model Intercomparison Project (AMIP II) and data were submitted to the Program for Climate Model Diagnosis and Intercomparison (PCMDI). Particular strengths of AM2-LM2, as judged by comparison to other models participating in AMIP II, include its circulation and distributions of precipitation. Prominent problems of AM2-LM2 include a cold bias to surface and tropospheric temperatures, weak tropical cyclone activity, and weak tropical intraseasonal activity associated with the Madden-Julian oscillation. An ensemble of 10 AM2-LM 2 integrations with observed SSTs for the second half of the twentieth century permits a statistically reliable assessment of the model's response to ENSO. In general, AM2-LM2 produces a realistic simulation of the anomalies in tropical precipitation and extratropical circulation that are associated with ENSO. ?? 2004 American Meteorological Society.

Journal of Climate

Response of seismicity to Coulomb stress triggers and shadows of the 1999 Mw=7.6 Chi-Chi, Taiwan, earthquake

The correlation between static Coulomb stress increases and aftershocks has thus far provided the strongest evidence that stress changes promote seismicity, a correlation that the Chi-Chi earthquake well exhibits. Several studies have deepened the argument by resolving stress changes on aftershock focal mechanisms, which removes the assumption that the aftershocks are optimally oriented for failure. Here one compares the percentage of planes on which failure is promoted after the main shock relative to the percentage beforehand. For Chi-Chi we find a 28% increase for thrust and an 18% increase for strike-slip mechanisms, commensurate with increases reported for other large main shocks. However, perhaps the chief criticism of static stress triggering is the difficulty in observing predicted seismicity rate decreases in the stress shadows, or sites of Coulomb stress decrease. Detection of sustained drops in seismicity rate demands a long catalog with a low magnitude of completeness and a high seismicity rate, conditions that are met at Chi-Chi. We find four lobes with statistically significant seismicity rate declines of 40-90% for 50 months, and they coincide with the stress shadows calculated for strike-slip faults, the dominant faulting mechanism. The rate drops are evident in uniform cell calculations, 100-month time series, and by visual inspection of the M ??? 3 seismicity. An additional reason why detection of such declines has proven so rare emerges from this study: there is a widespread increase in seismicity rate during the first 3 months after Chi-Chi, and perhaps many other main shocks, that might be associated with a different mechanism. Copyright 2005 by the American Geophysical Union.

Journal of Geophysical Research B: Solid Earth

Spatiotemporal variability of modeled watershed scale surface-depression storage and runoff for the conterminous United States

This study uses the explores the viability of a proxy model calibration strategy through assessment of the spatiotemporal variability of surface-depression storage and runoff generated with the U.S. Geological Survey’s National Hydrologic Model (NHM) infrastructure for hydrologic response units (HRUs; n=109,951) across the conterminous United States (CONUS). Simulated values for each HRU of daily surface-depression storage (treated as a decimal fraction of total possible volume) and monthly normalized runoff (0 to 1) values were calculated using Spearman’s rho at monthly and annual aggregations. Locations where values are correlated show where previously-developed proxy calibration strategies are likely to be effective. In addition, differences in the correlation for monthly and annual time scale aggregations show which time scale drives surface-depression storage processes in the NHM. Results show overall long-term (annual) correlation is more common than short-term (monthly) correlation over the CONUS; however, summary statistics for eighty-six ecoregions show five with higher ranges of monthly relative to annual Spearman’s rank coefficient values. This landscape-scale analysis shows simulations aggregated to an annual time scale are generally more dominant for the CONUS; however, simulations aggregated to monthly, short-term time scales are more dominant in focused areas where surface-depression storage processes are investigated.

Journal of the American Water Resources Associatio