Workshop 5: Uncertainty in Ecological Analysis

(April 3,2006 - April 6,2006 )

Organizers


Catherine Calder
Statistics, The Ohio State University
Jim Clark
Biology, Duke University
Noel Cressie
Statistics, The Ohio State University
Jay Ver Hoef
NOAA, National Oceanographic and Atmospheric Administration (NOAA)
Chris Wikle
Statistics, University of Missouri

The field of ecology is becoming increasingly aware of the importance of accurately accounting for multiple sources of uncertainty when modeling ecological phenomena and making forecasts. This development is motivated in part by the desire to provide an accurate picture of the state of knowledge of ecosystems and to be able to better assess the quality of predictions of local and global change. However, accounting for various sources of uncertainty is by no means a simple task. Ecological data are almost always observed incompletely with large and unknown amounts of measurement error or data uncertainty, and often the expense of data collection prohibits collecting as much data as might be desirable. In addition, most ecological phenomena of interest can only be studied by combining various sources of data; aligning these data properly presents interesting statistical challenges. While data plays a large role in most ecological analyses, incorporating scientific knowledge into the analyses through substantive modeling of ecological processes is essential. Often such theoretical contributions are based on competing scientific theories and simplifications of reality. This results in an additional source of uncertainty termed model or process uncertainty. Finally, substantive models must acknowledge parameter uncertainty. For example, more realistic descriptions of ecosystems might allow parameters to vary over space and time.

The aim of this workshop is to present a thorough investigation and discussion of these various sources of uncertainty that typically play a role in ecological analyses and of the statistical techniques that enable proper inferences and predictions to be made in light of these uncertainties. These concepts will be illustrated using new data sources and sophisticated modeling tools developed for studying a diverse collection of ecological phenomena. In addition, there will be a discussion of strategies for reducing some of the sources of uncertainty including improved design of monitoring networks. This discussion will promote increased communication between the theoretical and empirical communities as to prioritizing data collection efforts. One of the largest communities to use these methods for important decision-making is state and federal governments, and they will be involved in the workshop as well. In summary, this workshop will provide an opportunity for the ecological science community to interact with the statistical and abstract-modeling communities and will promote novel, interdisciplinary research developments on complex models, inference, and design in the face of various sources of uncertainty.

Monday, April 3, 2006
Time Session
09:00 AM
10:00 AM
Noel Cressie - Uncertainty in Ecological Analysis: Introduction

Ecological processes evolve dynamically and spatially. Uncertainties abound as science tries to describe, and then explain, these processes. Statistical modeling and analysis offers a framework within which scientists can work, but the spatio-temporal setting offers special challenges. This talk will address some of these and pay particular attention to one of the most fascinating: change of support.

10:30 AM
12:00 PM
Byron Morgan - Likelihood Methods in Ecology

Likelihood-based methods have been widely and successfully used for the estimation of wild animal abundance and survival. In this talk we review the many advantages of this classical approach, and also outline a number of recent developments.


We now have tools for choosing between models, for constructing confidence intervals, and for variable selection in appropriate regressions. We can evaluate methods through repeated simulations, and if necessary we can average predictions over models. In addition, we can combine likelihoods if we have relevant different samples of data, and a particular case of this arises when there are data that allow the estimation of demographic rates, as well as data providing appropriate census information.


We shall consider the possible advantages of reparameterisation, and the importance of testing for parameter redundancy, which arises when it is not possible to estimate all of the parameters in a model. An interesting application involves the use of covariates in survival, which may relate to climate and population density, or attributes of individuals, when the covariates may be constant or time-varying. We shall mention a new approach to modelling time-varying individual covariates, and we shall also describe the use of splines for modelling covariates in general.


This talk will be illustrated by a range of examples, involving red-deer (Cervus elaphus), grey herons (Ardea cinerea), dippers (Cinclus cinclus), snow petrels (Pagodroma nivea) and Soay sheep (Ovis aries).


Key Words: AIC; BIC; conditional inference; integrated population modelling; Kalman Filter; likelihood ratio tests; MARK; M-SURGE; multinomial distribution; numerical optimisation; P-splines; random effects; score tests; simulated annealing; trinomial methodology.

10:30 AM
12:00 PM
Mark Berliner - Hierarchical Bayesian Statistical Modeling and Prediction

Hierarchical Bayesian Statistical Modeling and Prediction

01:30 PM
02:15 PM
Jay Ver Hoef - Ecological Study: Introduction

Ecological Study: Introduction

03:30 PM
05:00 PM
Alan Gelfand - Developing Statistical Models for Analyzing Species Distributions

Statistical models to describe species distributions need to be able to accommodate features such as irregular sampling intensity, transformed landscape, and spatial dependence. We show how to build hierarchical models incorporating spatial random effects that capture these features, enable spatial prediction and adequately quantify uncertainty. We illustrate with a large dataset from the Cape Floristic Region in South Africa.

03:30 PM
05:00 PM
F. Jay Breidt - Uncertainty Analysis for a US Inventory of Soil Organic Carbon Stock Changes

Soil organic matter is an important sink for carbon, and the size of this sink is impacted by agricultural management such as organic amendments and tillage practices. Appropriate management can increase carbon sequestration in soils and mitigate greenhouse emissions of carbon dioxide to the atmosphere. Accounting for the amount of carbon sequestration is difficult due to the long temporal scales and fine spatial scales of interest and the complexity of the dynamics of carbon as it cycles between the atmosphere and biosphere, including soil organic matter pools. CENTURY, a biogeophysical process model, is used to model carbon dynamics in a national-level inventory of soil organic carbon stock changes. Inputs to CENTURY include weather, soils data, cropping history, tillage practices, fertilizer usage, and organic amendments, all of which are available to some degree from different national databases at different spatial scales. CENTURY is used to simulate soil organic matter dynamics at points used by the National Resources Inventory (NRI), a nationally-representative two-stage area sample, for which a standard design-based variance estimator provides a consistent estimate of uncertainty. At these NRI points, detailed soils data and cropping history are available, but tillage, mineral fertilizer use and organic amendments are not. Monte Carlo methods are used in conjunction with the design-based methods to provide accounting for both the sampling uncertainty of NRI and the uncertainty of inputs not available from NRI. Finally, external validation data of actual soil organic carbon measurements are used to account for model uncertainty related to imperfections in the structural relationships represented in CENTURY.


This is joint work with Stephen M. Ogle and Keith Paustian, Natural Resources Ecology Laboratory, Colorado State University.

Tuesday, April 4, 2006
Time Session
08:45 AM
10:15 AM
- Environmental Stochasticity in Age-structured Populations: Ressonance and apparent trends

If one wore to condense the last decades of environmental research into two observations, the following would represent a candidate: (1) humans are changing both terrestrial and marine biota at an ever increasing pace, and (2) ecological networks are sufficiently complicated that the current generation of detailed mechanistic models are as likely to fail as succeed in predicting the consequences of climate or habitat change. In light of this, ecologists rightly and prudently lean on more correlational trend analyses for early warning signs of ecosystem change and degradation. The precautionary line of reasoning is that ecological interactions such as competition or predation are likely to result in variation at the 'few-generation' time-scale. A trend that represent variation (or changes) at the 'many-generation' time-scale could thus be interpreted as systems transition likely reflecting human alterations of habitat or climate. We will discuss how this may be true for deterministic models. However, stochastic age-structured models predicts apparent trends in abundance that are superimposed on the 'deterministic variability' (high-frequency variability) through the cohort resonance effect. We detail the anatomy of these internally generated trends through transfer functions, and thus revisit the rule-of-thumb that long-term changes in abundance can be used as indicators of anthropogenic (or other external) forcing.


REF: Bjornstad, O. N., R. M. Nisbet, and J.-M. Fromentin. 2004. Trends and cohort resonant effects in age-structured populations. Journal of Animal Ecology 73:: 1157-1167.

08:45 AM
10:15 AM
Steve Buckland - Handling Uncertainty in Models of Population Dynamics

Effective management of wild animal populations requires reliable mathematical models, so that the effects of management action can be predicted, and the uncertainty in these predictions quantified. These models must be able to predict the response of populations to change, while handling the major sources of uncertainty. We describe an approach for formulating and fitting complex discrete-time models. We show how Bayesian methods (sequential Monte Carlo and MCMC) can account for observation error, model uncertainty and process variation (demographic and environmental stochasticity).


This work was done in collaboration with K.B. Newman, C. Fernandez, L. Thomas and J. Harwood.

10:45 AM
11:30 AM
Shannon LaDeau - Monitoring Population Effects of an Emergent Disease in Wild Birds

West Nile virus (WNV) is an emergent disease that spread rapidly through-out the contiguous United States following introduction into New York City in 1999. Although the virus is known to have caused several severe epizootics and result in high mortality for some species in lab challenges, there is little known regarding its implications for wild birds. To date, annual censuses collected by "citizen scientists" are the source of avian data with the most extensive temporal and spatial coverage. It is unknown how these data, which include multiple sources of error, perform as a means for evaluating mortality associated with an emerging pathogen. We use hierarchical techniques to evaluate the utility of bird census data in evaluating population effects associated with the introduction and spread of West Nile virus.

10:45 AM
11:30 AM
Devin Johnson - Bayesian Model Selection: An Alternative to AIC for Ecological Inference

The use of AIC for model selection, and averaging, has become nearly ubiquitous in ecological studies. The Bayesian alternative has been largely ignored for regular use. Bayesian model selection implemented via MCMC has some attractive properties that that make it a worthy competitor to AIC. For example, Bayesian MCMC methods allow a priori unequal weighting of predictors in a regression model. In some common cases, the method can also be extended to hierarchical models with relative ease. MCMC model selection and parameter inference is demonstrated on a spatial data set concerning fish abundance.

10:45 AM
11:30 AM
Jarrett Barber - Getting Your Fish through a Tube: The passage of fish through culverts on a tributary of the Yellowstone River

This talk will discuss data consisting of the times of road culvert passage attempts by fish on a spawning run. Interest lies in quantifying the effects of fish, culvert, and stream characteristics on the probability of passing through culverts. I propose a preliminary Bayesian hierarchical model for the data with the intent to foster discussion in the spirit of the workshop.

01:30 PM
03:00 PM
William Link - Detectability, not Detection

Count surveys like the North American Breeding Bird Survey (BBS) and the Christmas Bird Count (CBC) have been much reviled on the grounds that they produce unreliable indices of population size, rather than population estimates. Counts, the argument has gone, can be expressed as C = N p, so that temporal or spatial change in population size N is confounded with changes in detection probability p; what was needed was a means for estimating detection rate p, and obtaining "adjusted counts" to be used as the basis of population inference. In this talk, I argue that what is really needed is model based control for factors influencing detetectability; this, whether one estimates detection rates or not. Estimation of population change is inevitably and inescapably model-based, with inference relying on untestable model assumptions. I illustrate the potential for model based analysis of count survey data using a combined analysis of CBC and BBS data to examine seasonal components of population change without estimating abundance. I illustrate the inevitability of untestable model assumptions using simple examples from closed population mark-recapture.

01:30 PM
03:00 PM
Andy Royle - Hierarchical Models of Animal Abundance

Population ecology is largely concerned with understanding spatial and temporal variation in abundance and occurrence of species. Consistent with this view, many monitoring programs and smaller-scale population studies adopt an explicit focus on estimating or modeling abundance and understanding factors that influence abundance. One important consideration in the conduct of inference about abundance is an acute inability to observe the state variable of interest in most animal sampling problems. That is, individuals in the sampled population may go undetected by sampling and so observations of putative abundance are intrinsically biased. Historically this issue of non-detection bias (or "detectability") has been viewed as being paramount in the conduct of inference about abundance and other demographic parameters, and it provides a conceptual unification of a large and diverse body of methodology dealing with animal sampling.


There are several prevailing views on modeling abundance in the presence of imperfect detection. The classical view adopts a strong focus on modeling the detection process, and subsequent adjustment of sample counts to obtain abundance, or a second stage of modeling in which parameters of the detection process are fixed. An equally prevalent view is that focused on developing complex models directly from sample counts, absent any explicit consideration of detectability. The conceptual middle ground is occupied by a number of related views that share a common methodological formulation as hierarchical models.


In this paper, I advocate this conceptual middle ground, arguing that many estimation and inference problems (and sampling designs) yield naturally to formulation as hierarchical models. These hierarchical models are comprised of component models describing (1) variation in the observations conditional on the latent state variable (spatially and temporally indexed abundance), and (2) variation in the latent state variable, usually expressing the ecological structure that is the focus of inference. A few brief examples of hierarchical models applied to avian survey data will be given.

01:30 PM
03:00 PM
Robert Dorazio - The Dirichlet Process: A Robust Alternative for Modeling Heterogeneity in Abundance and Detection

Various sampling protocols (e.g., repeated point counts, mark-recapture, or multi-observer sampling) are used to estimate the abundance of a demographically-closed population of individuals (animals or species) that cannot be captured or detected with absolute certainty. In some populations heterogeneity in local abundance or detectability is thought to exist but the sources of heterogeneity are either poorly understood or unobservable. These latent sources of variation are often modeled using simple distributional assumptions, and the quantities of scientific interest are computed based on estimates of the assumed distribution's parameters. This approach, though often satisfactory, is vulnerable to errors in model specification that may be difficult or impossible to assess. An alternative approach is to assume a Dirichlet Process prior on the distribution of latent heterogeneity, thereby allowing for model uncertainty and robust estimation of abundance and detection. The benefits of this approach are illustrated in an analysis of removal counts observed while sampling an endangered population of fishes.

Wednesday, April 5, 2006
Time Session
08:45 AM
10:15 AM
Marie-Josee Fortin - Processes, Spatial Patterns, Scales and Their Interactions: A spatial analysis perspective

Ecological processes (demography, behavioral, disturbance) create a wide range of spatial patterns at multiple scales. To quantify and characterize these spatial patterns several spatial statistics are available. Here I present some of the conceptual and statistical challenges that ecologists face while analyzing spatially heterogeneous dynamic landscapes while trying to disentangle the key scales at which ecological processes occur.

08:45 AM
10:15 AM
Chris Wikle - A General Framework for Spatio-Temporal Dynamical Models

Ecological processes often encompass a very extensive range of spatial and temporal scales of variability, and include complicated interactions across domains, variables, and systems. To understand and eventually predict such complicated processes, we must make use of available scientific knowledge, as well as honestly account for uncertainties in that knowledge. A general hierarchical framework is presented for spatio-temporal dynamical processes in which the parameterizations are motivated by classical deterministic models.

08:45 AM
10:15 AM
Subhash Lele - TBA

TBA

10:45 AM
11:30 AM
Mevin Hooten - Spatio-temporal Dynamics of an Invasion

Dynamical systems have long been used to characterize invasions in terms of population growth. This talk provides an example of the statistical estimation and prediction of such spatio-temporal phenomena in the presence of data by utilizing a scientifically based dynamic process while accounting for imperfect knowledge of the process. This specific application involves the ongoing invasion of the Eurasion Collared-Dove.

10:45 AM
11:30 AM
Kiona Ogle - Bayesian Inverse Modeling of "hidden" Belowground Ecosystem Processes

Belowground ecosystem processes (e.g., soil, root, microbial respiration; uptake of water by plant roots) are hidden from view and difficult to measure, thus ecologists know very little about belowground compared to aboveground processes. Understanding the belowground system and how it is coupled to aboveground components is essential to developing general theories of ecosystem dynamics, yet we lack sufficient quantitative methods for disentangling the belowground component. To address this problem, I will present a general framework for inferring belowground processes that combines above- and belowground data, semi-mechanistic models of key ecological processes, and hierarchical Bayesian statistical tools.

10:45 AM
11:30 AM
Bret Elderd - Disease Epidemics: Smallpox Outbreaks & Public Policy

Complex deterministic models are often used to shape public policy regarding outbreaks of highly infectious diseases. These models often forecast disease epidemics and subsequent policy responses based on a single point estimate of the disease reproductive rate (i.e., the number of newly infected individuals arising from a single infected individual). By combining a Markov chain Monte Carlo (MCMC) simulation with a simple set of differential equations, the SEIR model, we were able to estimate the distribution for the reproductive rate of spread of smallpox. Given this distribution, a more informed set of decisions can be reached with regards to the public policy of smallpox inoculation. In general, this method can be widely applied and used to forecast disease outbreaks for other epidemics besides those related to human health.

01:30 PM
03:00 PM
Rachel Fewster - Visualizing Resampled Genetic Distance Data

Our problem is to generate a simple but informative display of genetic relatedness across a community of islands, to help highlight geographical factors affecting genetic isolation such as ocean distance or cliffs. The quality of genetic data from each island location depends on the number of individuals sampled from that island: for example, a rare genetic allele might not be included in a small sample despite being present at that location. We discuss how a Bayesian resampling process may be used to alleviate the difficulties of small samples. This raises the new problem of how to display the information gathered from resampled genetic distances. Some ideas will be discussed.

01:30 PM
03:00 PM
Brian Beckage - Parameter Estimation in a Coupled Landscape Model of Vegetation and Fire in the Florida Everglades

We are developing a landscape simulation model of the Everglades landscape that couples vegetation dynamics with fire, hydrology, and climate. A large number of parameters must be estimated, some of which are obtainable from pre-existing empirical data. Other parameters must be fitted dynamically from simulations. This presents two challenges: First, the simulation model generates data on many aspects of the ecosystem and parameter estimates are likely to be sensitive to the choice of metric(s) to measure model fit. Second, the link between model parameters and the state of the ecosystem is stochastic, but this stochasticity is generated internally in the simulation model. We do not know the "correct" underlying stochastic model and we can only generate distributions of results from summaries provided by multiple individual realizations. This complicates the process of parameter estimation. We describe our model, illustrate these challenges, and discuss potential solutions.

01:30 PM
03:00 PM
Aaron Ellison - Alternative Community States, Regime Shifts, and State-and-transition Models

Community ecologists, ecosystem scientists, and restoration ecologists all recognize that ecological systems are rarely in equilibrium, but they may exist in more than one state for long periods of time. Community ecologists recognize "alternative community states", and ecosystem ecologists recognize "regime shifts"; restoration ecologists have adopted these terms in attempts to manage the long-term dynamics of communities and ecosystems. Statistical discrimination of alternative community states or regime shifts has proven difficult. Community ecologists use ANOVA and its relatives to determine if different community configurations have significantly different responses (state variables) for a single parameter set. Ecosystem ecologists use time-series analysis to determine if parameters are varying through time, and how these parameter shifts can result in new ecosystem dynamics, given a set of state variables. Common statistical methods are needed to bring unity to these different perspectives; restoration ecologists could use these methods to develop statistical benchmarks that can be used to determine if and when a new community state has been reached. Three datasets will be presented for detailed analysis by workshop participants: an experimental study of alternative community states in the Gulf of Maine; a simulation study of phosphorus dynamics in lakes; and a rehabilitation scheme of abandoned mines in western Australia.

03:30 PM
05:00 PM
Gabriel Katul - Multi-scale Approaches to Biosphere-Atmosphere Exchange Rates of H2O and CO2

Models for the uptake or release of H2O and CO2 from terrestrial ecosystems are now needed for developing relationships between anthropogenic perturbations, atmospheric CO2 levels, and alterations to the water cycle. What makes modeling these exchange rates in forested ecosystems a complex task is that key processes relevant to water and carbon transfer and storage can vary over many space and time scales. In time, these fluxes are influenced by fast processes such as turbulent transport mechanics (often measured in seconds) and slow process such forest growth (often measured in years to decades). In space, photosynthesis and water uptake occurs at the leaf scale (often measured in millimeter) while stand level variables such as tree density are often measured in kilometers. To date, a nesting framework that couples fast and slow processes has not been developed for this problem though such a framework may be logical precisely because of the wide scale separation between variability at diurnal scales (important for radiative transfer) and monthly scales (important for carbon allocation and leaf area). In this talk, we report on developments of a multiscale approach that reproduces the spectral features of biosphere-atmosphere exchange of carbon, and water from minutes to multiple years. The testing is conducted for a maturing loblolly pine plantation in the Southern Piedmont region of North Carolina. We use pine plantations as a case study because, in addition to their economic importance, they represent a "simple" (in terms of dominant species) yet a non-equilibrium system that has been studied both extensively and intensively. Four-year eddy-covariance data set along with ecological measurements collected at the Duke Forest pine site is used for this purpose. Based on the annual precipitation measurements, the selected four years include a mild drought at the beginning of the growing season, a severe drought (5th largest on record), and two wet years.


Co-authors: Siqueira, M., Stoy, P., Juang, J., Palmroth, S., McCarthy, H., and Oren, R. from Nicholas School of the Environment and Earth Sciences, Duke University

03:30 PM
05:00 PM
Steve Wofsy - How do we assess uncertainty in analysis of ecosystem data and models?

Ecosystem analysis is prone to the most serious types of hidden errors, particulary when exploring issues surounding shifts in ecosystem composition or climate change hypotheses, i.e. data and modeling purporting to characterize large spatial scales or long time intervals. Using examples drawn from actual data measured or encountered in my work, I will examine several classes of errors in this area of science, and give examples where the nature and magnitude of the errors could be determined.


Spatially distributed data: representation error, spatial correlation, transport error, ecosystem model error (fitting to a wrong model).


Time series data: serial correlation (tree rings vs. climate), overestimation of the # degrees of freedom, accepting a false hypothesis (trend data for ecosystem function debunked with new types of observations), experimental design error (especially sensor drift, e.g. soil T data, psychrometers).


I conclude that effective steps in reducing hidden errors involve (1) improving the experimental design to investigate sources of bias and artifacts, (2) critically selecting, rejecting, and re-selecting underlying models for data analysis, and (3) liberally experimenting with stochastic simulations (especially simple Markovian models) to assess confidence intervals and test null hypotheses.

03:30 PM
05:00 PM
Doug Nychka - Discussion

Discussion

Thursday, April 6, 2006
Time Session
10:45 AM
11:45 AM
Marc Mangel - Uncertainty in Ecology: A Retrospective and Prospective

I will provide an idosyncratic history of uncertainty in ecology, using the classic experiments of Thomas Park on flour beetles (and their analysis by Neyman, Park and Scott, Leslie and Gower, Barnett, and Bartlett) as a motivational framework. This will suggest how we can make the greatest progress going forward and I will connect the challenges of the future with the presentations at the workshop.

Name Email Affiliation
Allen, Linda linda.j.allen@ttu.edu Mathematics and Statistics, Texas Tech University
Barber, Jarrett jarrett@math.montana.edu Mathematical Sciences, Montona State University
Beckage, Brian brian.beckage@uvm.edu Botany Department, University of Vermont
Berliner, Mark mb@stat.osu.edu Statistics, The Ohio State University
Best, Janet jbest@mbi.osu.edu
Boerner, Ralph boerner.1@osu.edu Evolution, Ecology and Organismal Biology, The Ohio State University
Bouchard, Virginie bouchard.8@osu.edu Natural Resources, The Ohio State University
Bravington, Mark mark.bravington@csiro.au CSIRO Mathematical & Information Sciences, Castray Esplanade
Breidt, F. Jay jbreidt@stat.colostate.edu Statistics, Colorado State University
Buckland, Steve steve@mcs.st-and.ac.uk School of Mathematics and Statistics, University of St. Andrews
Burnham, Ken kenb@lamar.colostate.edu Fishery and Wildlife Biology, Colorado State University
Calder, Catherine calder@stat.ohio-state.edu Statistics, The Ohio State University
Calian, Violeta calian@raunvis.hi.is Science Institute, University of Iceland (H'ask'oli Islands)
Clark, Jim jimclark@duke.edu Biology, Duke University
Craigmile, Peter pfc@stat.ohio-state.edu Statistics, The Ohio State University
Cressie, Noel ncressie@stat.ohio-state.edu Statistics, The Ohio State University
Culver, David culver.3@osu.edu EEOB, The Ohio State University
Curtis, Peter curtis.7@osu.edu EEOB, The Ohio State University
De Angelis, Donald don_deangelis@usgs.gov Department of Biology, University of Miami
Dennis, Brian brian@uidaho.edu Fish and Wildlife Resources, University of Idaho
Dixon, Philip pdixon@iastate.edu Statistics, Iowa State University
Djordjevic, Marko mdjordjevic@mbi.osu.edu Mathematical Biosciences Institute (MBI), The Ohio State University
Dorazio, Robert bdorazio@usgs.gov Statistics, University of Florida
Elderd, Bret belderd@uchicago.edu Ecology and Evolution, University of Chicago
Ellison, Aaron aellison@fas.harvard.edu Harvard Forest, Harvard University
Enciso, German German_Enciso@hms.harvard.edu Mathematical Biosciences Institute (MBI), The Ohio State University
Fewster, Rachel r.fewster@auckland.ac.nz Statistics, University of Auckland
Fisher, Susan fisher.14@osu.edu Entomology, The Ohio State University
Fortin, Marie-Josee mjfortin@zoo.utoronto.ca Zoology, University of Toronto
Gelfand, Alan alan@stat.duke.edu Statistics and Decision Sciences, Duke University
Goebel, Charles goebel.11@osu.edu Natural Resources, The Ohio State University
Goel, Pranay goelpra@helix.nih.gov Mathematical Biosciences Institute (MBI), The Ohio State University
Gough, Chris gough.21@osu.edu EEOB, Ohio State University
Grajdeanu, Paula pgrajdeanu@mbi.osu.edu Mathematical Biosciences Institute (MBI), The Ohio State University
Gregoire, Timothy timothy.gregoire@yale.edu School of Forestry & Environmental Studies, Yale University
Gross, Louis Ecology & Evolutionary Biology & Mathematics, University of Tennessee - Knoxville
Hastings, Alan amhastings@ucdavis.edu Department of Environmental Science and Policy, University of California, Davis
He, Chong (Zhuoqiong) hez@vt.edu Statistics, Virginia Tech
Herms, Dan herms.2@osu.edu Entomology, The Ohio State University
Hoeting, Jennifer jah@lamar.colostate.edu Statistics, Colorado State University
Hooten, Mevin hooten@stat.missouri.edu Statistics, University of Missouri
Hsu, Jason hsu.1@osu.edu Statistics, The Ohio State University
Ives, Tony arives@facstaff.wisc.edu Zoology, University of Wisconsin
Johnson, Devin devin.johnson@noaa.gov Mathematical Sciences, University of Alaska
Johnson, Doug Douglas_H_Johnson@usgs.gov Fisheries, Wildlife, and Conservation Biology, U.S.G.S Biological Resources Discipline
Just, Winfried just@math.ohio.edu Math, Ohio University
Kaiser, Mark mskaiser@iastate.edu Statistics, Iowa State University
Kang, Lei lei@stat.ohio-state.edu Statistics, The Ohio State University
Katul, Gabriel gaby@duke.edu Environmental Sciences and Policy, Duke University
Kim, Yongku kim@stat.ohio-state.edu Statistics, The Ohio State University
LaDeau, Shannon ladeaus@si.edu Smithsonian Environmental Research Center
Lal, Rattan lal.1@osu.edu Natural Resources, The Ohio State University
Lam, Eric ericl@stat.ohio-state.edu Statistics, The Ohio State University
Lavine, Michael michael@stat.duke.edu ISDS, Duke University
Lele, Subhash slele@ualberta.ca Mathematical and Statistical Sciences, University of Alberta
Li, Hongfei hongfei@stat.ohio-state.edu Statistics, The Ohio State University
Lim, Sookkyung limsk@math.uc.edu Mathematical Biosciences Institute (MBI), The Ohio State University
Link, William william_link@usgs.gov Patuxent Wildlife Research Center, USGS
Loladze, Irakli iloladze@math.unl.edu MBI, The Ohio State University
Lou, Yuan lou@math.ohio-state.edu Math, The Ohio State University
Malik, Vikas malik.68@osu.edu EEOB, The Ohio State University
Mangel, Marc msmangel@soe.ucsc.edu Applied Math and Statistics, University of California, Santa Cruz
Maunder, Mark mmaunder@iattc.org Inter-American Tropical Tuna Commission
Mitsch, Bill mitsch.1@osu.edu Natural Resources, The Ohio State University
Monestiez, Pascal pascal@avignon.inra.fr Unite de Biometrie, Institut National de la Recherche Agronomique (INRA)
Morgan, Byron B.J.T.Morgan@kent.ac.uk Inst. of Mathematics, Statistics & Actuarial Science, University of Kent at Canterbury
Nevai, Andrew anevai@mbi.osu.edu Mathematical Biosciences Institute (MBI), The Ohio State University
Nychka, Doug nychka@ucar.edu Inst. for Mathematics Applied to Geosciences, National Center for Atmospheric Research
Ogle, Kiona kogle@Princeton.EDU Princeton Environmental Institute, Princeton University
Olsen, Anthony olsen.tony@epamail.epa.gov Western Ecology Division, US EPA
Parent, Eric parent@engref.fr National French Institute for Rural Engineering
Park, Jung park.824@osu.edu Entomology, The Ohio State University
Pol, Diego dpol@mbi.osu.edu Mathematical Biosciences Institute (MBI), The Ohio State University
Quintero, Estela quintero.11@osu.edu EEOB, The Ohio State University
Rathbun, Steve rathbun@uga.edu Biostatistics, University of Georgia
Rodewald, Amanda rodewald.1@osu.edu Natural Resources, The Ohio State University
Rodriguez, Susan rodriguez.219@osu.edu EEOB, The Ohio State University
Royle, Andy aroyle@usgs.gov USGS Patuxent Wildlife Research Center, AMAT
Schmidt, Alexandra alex@im.ufrj.br Departamento de Metodos Estatisticos, Instituto de Matematica
Schugart, Richard richard.schugart@wku.edu Mathematical Biosciences Institute (MBI), The Ohio State University
Shi, Tao shi.79@osu.edu Statistics, The Ohio State University
Srinivasan, Partha p.srinivasan35@csuohio.edu Mathematical Biosciences Institute (MBI), The Ohio State University
Stigler, Brandy bstigler@mbi.osu.edu Mathematical Biosciences Institute (MBI), The Ohio State University
Tian, Paul tianjj@mbi.osu.edu Mathematical Biosciences Institute (MBI), The Ohio State University
Turner, Rolf rolf@math.unb.ca Mathematics and Statistics, University of New Brunswick
Vadrevu, Krishna vadrevu.2@osu.edu Entomology, The Ohio State University
Ver Hoef, Jay jay.verhoef@noaa.gov NOAA, National Oceanographic and Atmospheric Administration (NOAA)
Waite, Tom waite.1@osu.edu EEOB, The Ohio State University
Wali, Mohan wali.1@osu.edu Natural Resources, The Ohio State University
Waller, Lance lwaller@sph.emory.edu Biostatistics, Emory University
Wei, Hu wei.97@osu.edu Geography, The Ohio State University
Wheeler, David Geography, The Ohio State University
Wikle, Chris wikle@missouri.edu Statistics, University of Missouri
Wofsy, Steve wofsy@fas.harvard.edu Harvard University
Xiao, Ningchuan xiao.37@osu.edu Geography, The Ohio State University
Yao, Yonggang yao@stat.ohio-state.edu Statistics, The Ohio State University
Young, Linda LYoung@biostat.ufl.edu Department of Statistics, IFAS, University of Florida
Zhou, Jin jzhou@mbi.osu.edu Mathematical Biosciences Institute (MBI), The Ohio State University
Zimmerman, Dale dzimmer@stat.uiowa.edu Statistics and Actuarial Science, University of Iowa
Getting Your Fish through a Tube: The passage of fish through culverts on a tributary of the Yellowstone River

This talk will discuss data consisting of the times of road culvert passage attempts by fish on a spawning run. Interest lies in quantifying the effects of fish, culvert, and stream characteristics on the probability of passing through culverts. I propose a preliminary Bayesian hierarchical model for the data with the intent to foster discussion in the spirit of the workshop.

Parameter Estimation in a Coupled Landscape Model of Vegetation and Fire in the Florida Everglades

We are developing a landscape simulation model of the Everglades landscape that couples vegetation dynamics with fire, hydrology, and climate. A large number of parameters must be estimated, some of which are obtainable from pre-existing empirical data. Other parameters must be fitted dynamically from simulations. This presents two challenges: First, the simulation model generates data on many aspects of the ecosystem and parameter estimates are likely to be sensitive to the choice of metric(s) to measure model fit. Second, the link between model parameters and the state of the ecosystem is stochastic, but this stochasticity is generated internally in the simulation model. We do not know the "correct" underlying stochastic model and we can only generate distributions of results from summaries provided by multiple individual realizations. This complicates the process of parameter estimation. We describe our model, illustrate these challenges, and discuss potential solutions.

Hierarchical Bayesian Statistical Modeling and Prediction

Hierarchical Bayesian Statistical Modeling and Prediction

Uncertainty Analysis for a US Inventory of Soil Organic Carbon Stock Changes

Soil organic matter is an important sink for carbon, and the size of this sink is impacted by agricultural management such as organic amendments and tillage practices. Appropriate management can increase carbon sequestration in soils and mitigate greenhouse emissions of carbon dioxide to the atmosphere. Accounting for the amount of carbon sequestration is difficult due to the long temporal scales and fine spatial scales of interest and the complexity of the dynamics of carbon as it cycles between the atmosphere and biosphere, including soil organic matter pools. CENTURY, a biogeophysical process model, is used to model carbon dynamics in a national-level inventory of soil organic carbon stock changes. Inputs to CENTURY include weather, soils data, cropping history, tillage practices, fertilizer usage, and organic amendments, all of which are available to some degree from different national databases at different spatial scales. CENTURY is used to simulate soil organic matter dynamics at points used by the National Resources Inventory (NRI), a nationally-representative two-stage area sample, for which a standard design-based variance estimator provides a consistent estimate of uncertainty. At these NRI points, detailed soils data and cropping history are available, but tillage, mineral fertilizer use and organic amendments are not. Monte Carlo methods are used in conjunction with the design-based methods to provide accounting for both the sampling uncertainty of NRI and the uncertainty of inputs not available from NRI. Finally, external validation data of actual soil organic carbon measurements are used to account for model uncertainty related to imperfections in the structural relationships represented in CENTURY.


This is joint work with Stephen M. Ogle and Keith Paustian, Natural Resources Ecology Laboratory, Colorado State University.

Handling Uncertainty in Models of Population Dynamics

Effective management of wild animal populations requires reliable mathematical models, so that the effects of management action can be predicted, and the uncertainty in these predictions quantified. These models must be able to predict the response of populations to change, while handling the major sources of uncertainty. We describe an approach for formulating and fitting complex discrete-time models. We show how Bayesian methods (sequential Monte Carlo and MCMC) can account for observation error, model uncertainty and process variation (demographic and environmental stochasticity).


This work was done in collaboration with K.B. Newman, C. Fernandez, L. Thomas and J. Harwood.

Uncertainty in Ecological Analysis: Introduction

Ecological processes evolve dynamically and spatially. Uncertainties abound as science tries to describe, and then explain, these processes. Statistical modeling and analysis offers a framework within which scientists can work, but the spatio-temporal setting offers special challenges. This talk will address some of these and pay particular attention to one of the most fascinating: change of support.

The Dirichlet Process: A Robust Alternative for Modeling Heterogeneity in Abundance and Detection

Various sampling protocols (e.g., repeated point counts, mark-recapture, or multi-observer sampling) are used to estimate the abundance of a demographically-closed population of individuals (animals or species) that cannot be captured or detected with absolute certainty. In some populations heterogeneity in local abundance or detectability is thought to exist but the sources of heterogeneity are either poorly understood or unobservable. These latent sources of variation are often modeled using simple distributional assumptions, and the quantities of scientific interest are computed based on estimates of the assumed distribution's parameters. This approach, though often satisfactory, is vulnerable to errors in model specification that may be difficult or impossible to assess. An alternative approach is to assume a Dirichlet Process prior on the distribution of latent heterogeneity, thereby allowing for model uncertainty and robust estimation of abundance and detection. The benefits of this approach are illustrated in an analysis of removal counts observed while sampling an endangered population of fishes.

Disease Epidemics: Smallpox Outbreaks & Public Policy

Complex deterministic models are often used to shape public policy regarding outbreaks of highly infectious diseases. These models often forecast disease epidemics and subsequent policy responses based on a single point estimate of the disease reproductive rate (i.e., the number of newly infected individuals arising from a single infected individual). By combining a Markov chain Monte Carlo (MCMC) simulation with a simple set of differential equations, the SEIR model, we were able to estimate the distribution for the reproductive rate of spread of smallpox. Given this distribution, a more informed set of decisions can be reached with regards to the public policy of smallpox inoculation. In general, this method can be widely applied and used to forecast disease outbreaks for other epidemics besides those related to human health.

Alternative Community States, Regime Shifts, and State-and-transition Models

Community ecologists, ecosystem scientists, and restoration ecologists all recognize that ecological systems are rarely in equilibrium, but they may exist in more than one state for long periods of time. Community ecologists recognize "alternative community states", and ecosystem ecologists recognize "regime shifts"; restoration ecologists have adopted these terms in attempts to manage the long-term dynamics of communities and ecosystems. Statistical discrimination of alternative community states or regime shifts has proven difficult. Community ecologists use ANOVA and its relatives to determine if different community configurations have significantly different responses (state variables) for a single parameter set. Ecosystem ecologists use time-series analysis to determine if parameters are varying through time, and how these parameter shifts can result in new ecosystem dynamics, given a set of state variables. Common statistical methods are needed to bring unity to these different perspectives; restoration ecologists could use these methods to develop statistical benchmarks that can be used to determine if and when a new community state has been reached. Three datasets will be presented for detailed analysis by workshop participants: an experimental study of alternative community states in the Gulf of Maine; a simulation study of phosphorus dynamics in lakes; and a rehabilitation scheme of abandoned mines in western Australia.

Visualizing Resampled Genetic Distance Data

Our problem is to generate a simple but informative display of genetic relatedness across a community of islands, to help highlight geographical factors affecting genetic isolation such as ocean distance or cliffs. The quality of genetic data from each island location depends on the number of individuals sampled from that island: for example, a rare genetic allele might not be included in a small sample despite being present at that location. We discuss how a Bayesian resampling process may be used to alleviate the difficulties of small samples. This raises the new problem of how to display the information gathered from resampled genetic distances. Some ideas will be discussed.

Processes, Spatial Patterns, Scales and Their Interactions: A spatial analysis perspective

Ecological processes (demography, behavioral, disturbance) create a wide range of spatial patterns at multiple scales. To quantify and characterize these spatial patterns several spatial statistics are available. Here I present some of the conceptual and statistical challenges that ecologists face while analyzing spatially heterogeneous dynamic landscapes while trying to disentangle the key scales at which ecological processes occur.

Developing Statistical Models for Analyzing Species Distributions

Statistical models to describe species distributions need to be able to accommodate features such as irregular sampling intensity, transformed landscape, and spatial dependence. We show how to build hierarchical models incorporating spatial random effects that capture these features, enable spatial prediction and adequately quantify uncertainty. We illustrate with a large dataset from the Cape Floristic Region in South Africa.

Spatio-temporal Dynamics of an Invasion

Dynamical systems have long been used to characterize invasions in terms of population growth. This talk provides an example of the statistical estimation and prediction of such spatio-temporal phenomena in the presence of data by utilizing a scientifically based dynamic process while accounting for imperfect knowledge of the process. This specific application involves the ongoing invasion of the Eurasion Collared-Dove.

Bayesian Model Selection: An Alternative to AIC for Ecological Inference

The use of AIC for model selection, and averaging, has become nearly ubiquitous in ecological studies. The Bayesian alternative has been largely ignored for regular use. Bayesian model selection implemented via MCMC has some attractive properties that that make it a worthy competitor to AIC. For example, Bayesian MCMC methods allow a priori unequal weighting of predictors in a regression model. In some common cases, the method can also be extended to hierarchical models with relative ease. MCMC model selection and parameter inference is demonstrated on a spatial data set concerning fish abundance.

Multi-scale Approaches to Biosphere-Atmosphere Exchange Rates of H2O and CO2

Models for the uptake or release of H2O and CO2 from terrestrial ecosystems are now needed for developing relationships between anthropogenic perturbations, atmospheric CO2 levels, and alterations to the water cycle. What makes modeling these exchange rates in forested ecosystems a complex task is that key processes relevant to water and carbon transfer and storage can vary over many space and time scales. In time, these fluxes are influenced by fast processes such as turbulent transport mechanics (often measured in seconds) and slow process such forest growth (often measured in years to decades). In space, photosynthesis and water uptake occurs at the leaf scale (often measured in millimeter) while stand level variables such as tree density are often measured in kilometers. To date, a nesting framework that couples fast and slow processes has not been developed for this problem though such a framework may be logical precisely because of the wide scale separation between variability at diurnal scales (important for radiative transfer) and monthly scales (important for carbon allocation and leaf area). In this talk, we report on developments of a multiscale approach that reproduces the spectral features of biosphere-atmosphere exchange of carbon, and water from minutes to multiple years. The testing is conducted for a maturing loblolly pine plantation in the Southern Piedmont region of North Carolina. We use pine plantations as a case study because, in addition to their economic importance, they represent a "simple" (in terms of dominant species) yet a non-equilibrium system that has been studied both extensively and intensively. Four-year eddy-covariance data set along with ecological measurements collected at the Duke Forest pine site is used for this purpose. Based on the annual precipitation measurements, the selected four years include a mild drought at the beginning of the growing season, a severe drought (5th largest on record), and two wet years.


Co-authors: Siqueira, M., Stoy, P., Juang, J., Palmroth, S., McCarthy, H., and Oren, R. from Nicholas School of the Environment and Earth Sciences, Duke University

Monitoring Population Effects of an Emergent Disease in Wild Birds

West Nile virus (WNV) is an emergent disease that spread rapidly through-out the contiguous United States following introduction into New York City in 1999. Although the virus is known to have caused several severe epizootics and result in high mortality for some species in lab challenges, there is little known regarding its implications for wild birds. To date, annual censuses collected by "citizen scientists" are the source of avian data with the most extensive temporal and spatial coverage. It is unknown how these data, which include multiple sources of error, perform as a means for evaluating mortality associated with an emerging pathogen. We use hierarchical techniques to evaluate the utility of bird census data in evaluating population effects associated with the introduction and spread of West Nile virus.

TBA

TBA

Uncertainty in Ecology: A Retrospective and Prospective

I will provide an idosyncratic history of uncertainty in ecology, using the classic experiments of Thomas Park on flour beetles (and their analysis by Neyman, Park and Scott, Leslie and Gower, Barnett, and Bartlett) as a motivational framework. This will suggest how we can make the greatest progress going forward and I will connect the challenges of the future with the presentations at the workshop.

Likelihood Methods in Ecology

Likelihood-based methods have been widely and successfully used for the estimation of wild animal abundance and survival. In this talk we review the many advantages of this classical approach, and also outline a number of recent developments.


We now have tools for choosing between models, for constructing confidence intervals, and for variable selection in appropriate regressions. We can evaluate methods through repeated simulations, and if necessary we can average predictions over models. In addition, we can combine likelihoods if we have relevant different samples of data, and a particular case of this arises when there are data that allow the estimation of demographic rates, as well as data providing appropriate census information.


We shall consider the possible advantages of reparameterisation, and the importance of testing for parameter redundancy, which arises when it is not possible to estimate all of the parameters in a model. An interesting application involves the use of covariates in survival, which may relate to climate and population density, or attributes of individuals, when the covariates may be constant or time-varying. We shall mention a new approach to modelling time-varying individual covariates, and we shall also describe the use of splines for modelling covariates in general.


This talk will be illustrated by a range of examples, involving red-deer (Cervus elaphus), grey herons (Ardea cinerea), dippers (Cinclus cinclus), snow petrels (Pagodroma nivea) and Soay sheep (Ovis aries).


Key Words: AIC; BIC; conditional inference; integrated population modelling; Kalman Filter; likelihood ratio tests; MARK; M-SURGE; multinomial distribution; numerical optimisation; P-splines; random effects; score tests; simulated annealing; trinomial methodology.

Discussion

Discussion

Bayesian Inverse Modeling of "hidden" Belowground Ecosystem Processes

Belowground ecosystem processes (e.g., soil, root, microbial respiration; uptake of water by plant roots) are hidden from view and difficult to measure, thus ecologists know very little about belowground compared to aboveground processes. Understanding the belowground system and how it is coupled to aboveground components is essential to developing general theories of ecosystem dynamics, yet we lack sufficient quantitative methods for disentangling the belowground component. To address this problem, I will present a general framework for inferring belowground processes that combines above- and belowground data, semi-mechanistic models of key ecological processes, and hierarchical Bayesian statistical tools.

Hierarchical Models of Animal Abundance

Population ecology is largely concerned with understanding spatial and temporal variation in abundance and occurrence of species. Consistent with this view, many monitoring programs and smaller-scale population studies adopt an explicit focus on estimating or modeling abundance and understanding factors that influence abundance. One important consideration in the conduct of inference about abundance is an acute inability to observe the state variable of interest in most animal sampling problems. That is, individuals in the sampled population may go undetected by sampling and so observations of putative abundance are intrinsically biased. Historically this issue of non-detection bias (or "detectability") has been viewed as being paramount in the conduct of inference about abundance and other demographic parameters, and it provides a conceptual unification of a large and diverse body of methodology dealing with animal sampling.


There are several prevailing views on modeling abundance in the presence of imperfect detection. The classical view adopts a strong focus on modeling the detection process, and subsequent adjustment of sample counts to obtain abundance, or a second stage of modeling in which parameters of the detection process are fixed. An equally prevalent view is that focused on developing complex models directly from sample counts, absent any explicit consideration of detectability. The conceptual middle ground is occupied by a number of related views that share a common methodological formulation as hierarchical models.


In this paper, I advocate this conceptual middle ground, arguing that many estimation and inference problems (and sampling designs) yield naturally to formulation as hierarchical models. These hierarchical models are comprised of component models describing (1) variation in the observations conditional on the latent state variable (spatially and temporally indexed abundance), and (2) variation in the latent state variable, usually expressing the ecological structure that is the focus of inference. A few brief examples of hierarchical models applied to avian survey data will be given.

Ecological Study: Introduction

Ecological Study: Introduction

A General Framework for Spatio-Temporal Dynamical Models

Ecological processes often encompass a very extensive range of spatial and temporal scales of variability, and include complicated interactions across domains, variables, and systems. To understand and eventually predict such complicated processes, we must make use of available scientific knowledge, as well as honestly account for uncertainties in that knowledge. A general hierarchical framework is presented for spatio-temporal dynamical processes in which the parameterizations are motivated by classical deterministic models.

How do we assess uncertainty in analysis of ecosystem data and models?

Ecosystem analysis is prone to the most serious types of hidden errors, particulary when exploring issues surounding shifts in ecosystem composition or climate change hypotheses, i.e. data and modeling purporting to characterize large spatial scales or long time intervals. Using examples drawn from actual data measured or encountered in my work, I will examine several classes of errors in this area of science, and give examples where the nature and magnitude of the errors could be determined.


Spatially distributed data: representation error, spatial correlation, transport error, ecosystem model error (fitting to a wrong model).


Time series data: serial correlation (tree rings vs. climate), overestimation of the # degrees of freedom, accepting a false hypothesis (trend data for ecosystem function debunked with new types of observations), experimental design error (especially sensor drift, e.g. soil T data, psychrometers).


I conclude that effective steps in reducing hidden errors involve (1) improving the experimental design to investigate sources of bias and artifacts, (2) critically selecting, rejecting, and re-selecting underlying models for data analysis, and (3) liberally experimenting with stochastic simulations (especially simple Markovian models) to assess confidence intervals and test null hypotheses.