James Hines
Jim Hines is a computer scientist, working with USGS and non-agency biologists developing methods and computer software for estimation of ecological parameters. He also maintains a web-server used to communicate results of the North American Breeding Bird Survey as well as software written by current and former EESC scientists.
Jim Hines started with the USFWS in 1977 as a part-time computer clerk. After obtaining a BS in Math, he became a full-time computer programmer, then computer specialist and computer scientist. He is co-author on 2 books,
Professional Experience
1977-present USFWS, NBS, USGS - Computer clerk, programmer, specialist, scientist.
Education and Certifications
Hon Dsc. University of Florda, 2023
B.S. University of Maryland, Mathematics, 1979.
Honors and Awards
2016 - Biometrics Working Group Special Recognition Award
2015 - U.S. Geological Survey Distinguished Service Award
2012 - U.S. Geological Survey Meritorious Service Award
2012 - The Wildlife Society's Wildlife Publication Award for Book
1991 - The Wildlife Society's Wildlife Publication Award for Monograph
Science and Products
Relaxing the closure assumption in single-season occupancy models: staggered arrival and departure times
Joint estimation of habitat dynamics and species interactions: Disturbance reduces co-occurrence of non-native predators with an endangered toad
Neighborhood and habitat effects on vital rates: expansion of the Barred Owl in the Oregon Coast Ranges
Habitat fragmentation effects on annual survival of the federally protected eastern indigo snake
Adult tree swallow survival on the polychlorinated biphenyl-contaminated Hudson River, New York, USA, between 2006 and 2010
Estimating parameters of hidden Markov models based on marked individuals: use of robust design data
On valuing patches: Estimating contributions to metapopulation growth with reverse-time capture-recapture modelling
Program SPACECAP: software for estimating animal density using spatially explicit capture-recapture models
Integrating occupancy modeling and interview data for corridor identification: A case study for jaguars in Nicaragua
Demographic consequences of migratory stopover: Linking red knot survival to horseshoe crab spawning abundance
Simultaneous modeling of habitat suitability, occupancy, and relative abundance: African elephants in Zimbabwe
Two-species occupancy models: A new parameterization applied to co-occurrence of secretive rails
Science and Products
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Filter Total Items: 223
Relaxing the closure assumption in single-season occupancy models: staggered arrival and departure times
Occupancy statistical models that account for imperfect detection have proved very useful in several areas of ecology, including species distribution and spatial dynamics, disease ecology, and ecological responses to climate change. These models are based on the collection of multiple samples at each of a number of sites within a given season, during which it is assumed the species is either absenAuthorsWilliam L. Kendall, James E. Hines, James D. Nichols, Evan H. Campbell GrantJoint estimation of habitat dynamics and species interactions: Disturbance reduces co-occurrence of non-native predators with an endangered toad
1. Ecologists have long been interested in the processes that determine patterns of species occurrence and co-occurrence. Potential short-comings of many existing empirical approaches that address these questions include a reliance on patterns of occurrence at a single time point, failure to account properly for imperfect detection and treating the environment as a static variable.2. We fit detectAuthorsDavid A.W. Miller, Cheryl S. Brehme, James E. Hines, James D. Nichols, Robert N. FisherNeighborhood and habitat effects on vital rates: expansion of the Barred Owl in the Oregon Coast Ranges
In this paper, we modify dynamic occupancy models developed for detection-nondetection data to allow for the dependence of local vital rates on neighborhood occupancy, where neighborhood is defined very flexibly. Such dependence of occupancy dynamics on the status of a relevant neighborhood is pervasive, yet frequently ignored. Our framework permits joint inference about the importance of neighborAuthorsCharles B. Yackulic, Janice Reid, Raymond Davis, James E. Hines, James D. Nichols, Eric ForsmanHabitat fragmentation effects on annual survival of the federally protected eastern indigo snake
The eastern indigo snake (Drymarchon couperi) is a federally listed species, most recently threatened by habitat loss and habitat degradation. In an effort to estimate snake survival, a total of 103 individuals (59 males, 44 females) were followed using radio-tracking from January 1998 to March 2004 in three landscape types that had increasing levels of habitat fragmentation: (1) conservation coreAuthorsD.R. Breininger, M. J. Mazerolle, M.R. Bolt, M.L. Legare, J.H. Drese, J. E. HinesAdult tree swallow survival on the polychlorinated biphenyl-contaminated Hudson River, New York, USA, between 2006 and 2010
The upper Hudson River basin in east central New York, USA, is highly contaminated, primarily with polychlorinated biphenyls (PCBs). Reduced adult survival has been documented in tree swallows (Tachycineta bicolor) at a similarly PCB-contaminated river system in western Massachusetts. The purpose of the present study was to assess whether adult survival of tree swallows was likewise affected in thAuthorsChristine M. Custer, Thomas W. Custer, James E. HinesEstimating parameters of hidden Markov models based on marked individuals: use of robust design data
Development and use of multistate mark-recapture models, which provide estimates of parameters of Markov processes in the face of imperfect detection, have become common over the last twenty years. Recently, estimating parameters of hidden Markov models, where the state of an individual can be uncertain even when it is detected, has received attention. Previous work has shown that ignoring state uAuthorsWilliam L. Kendall, Gary C. White, James E. Hines, Catherine A. Langtimm, Jun YoshizakiOn valuing patches: Estimating contributions to metapopulation growth with reverse-time capture-recapture modelling
Metapopulation ecology has historically been rich in theory, yet analytical approaches for inferring demographic relationships among local populations have been few. We show how reverse-time multi-state capture–recapture models can be used to estimate the importance of local recruitment and interpopulation dispersal to metapopulation growth. We use ‘contribution metrics’ to infer demographic conneAuthorsJ.S. Sanderlin, P.M. Waser, J. E. Hines, J. D. NicholsProgram SPACECAP: software for estimating animal density using spatially explicit capture-recapture models
1. The advent of spatially explicit capture-recapture models is changing the way ecologists analyse capture-recapture data. However, the advantages offered by these new models are not fully exploited because they can be difficult to implement. 2. To address this need, we developed a user-friendly software package, created within the R programming environment, called SPACECAP. This package implAuthorsArjun M. Gopalaswamy, J. Andrew Royle, James E. Hines, Pallavi Singh, Devcharan Jathanna, N. Samba Kumar, K. Ullas KaranthIntegrating occupancy modeling and interview data for corridor identification: A case study for jaguars in Nicaragua
Corridors are critical elements in the long-term conservation of wide-ranging species like the jaguar (Panthera onca). Jaguar corridors across the range of the species were initially identified using a GIS-based least-cost corridor model. However, due to inherent errors in remotely sensed data and model uncertainties, these corridors warrant field verification before conservation efforts can beginAuthorsK.A. Zeller, S. Nijhawan, R. Salom-Perez, S.H. Potosme, James E. HinesDemographic consequences of migratory stopover: Linking red knot survival to horseshoe crab spawning abundance
Understanding how events during one period of the annual cycle carry over to affect survival and other fitness components in other periods is essential to understanding migratory bird demography and conservation needs. Previous research has suggested that western Atlantic red knot (Calidris canutus rufa) populations are greatly affected by horseshoe crab (Limulus polyphemus) egg availability at DeAuthorsConor P. McGowan, James E. Hines, James D. Nichols, James E. Lyons, David Smith, Kevin S. Kalasz, Lawrence J. Niles, Amanda D. Dey, Nigel A. Clark, Philip W. Atkinson, Clive D.T. Minton, William KendallSimultaneous modeling of habitat suitability, occupancy, and relative abundance: African elephants in Zimbabwe
The recent development of statistical models such as dynamic site occupancy models provides the opportunity to address fairly complex management and conservation problems with relatively simple models. However, surprisingly few empirical studies have simultaneously modeled habitat suitability and occupancy status of organisms over large landscapes for management purposes. Joint modeling of these cAuthorsJulien Martin, Simon Chamaille-Jammes, James D. Nichols, Herve Fritz, James E. Hines, Christopher J. Fonnesbeck, Darryl I. MacKenzie, Larissa L. BaileyTwo-species occupancy models: A new parameterization applied to co-occurrence of secretive rails
Two-species occupancy models that account for false absences provide a robust method for testing for evidence of competitive exclusion, but previous model parameteriza-tions were inadequate for incorporating covariates. We present a new parameterization that is stable when covariates are included: the conditional two-species occupancy model, which can be used to examine alternative hypotheses forAuthorsO.M.W. Richmond, J. E. Hines, S. R. Beissinger - Web Tools
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