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
A multi-state occupancy modelling framework for robust estimation of disease prevalence in multi-tissue disease systems
Demography of snowshoe hare population cycles
Scale‐dependent effects of isolation on seasonal patch colonisation by two Neotropical freshwater fishes
Factors affecting species richness and distribution spatially and temporally within a protected area using multi-season occupancy models
Impact of prey occupancy and other ecological and anthropogenic factors on Tiger distribution in Thailand’s Western Forest Complex
Size-specific apparent survival rate estimates of white sharks using mark-recapture models
Partitioning global change: Assessing the relative importance of changes in climate and land cover for changes in avian distribution
Occupancy in community-level studies
Are ranger patrols effective in reducing poaching-related threats within protected areas?
Territory occupancy and breeding success of Peregrine Falcons Falco peregrinus at various stages of population recovery
Evaluation of nutria (Myocastor coypus) detection methods in Maryland, USA
Roseate Tern breeding dispersal and fidelity: Responses to two newly restored colony sites
PROGRAM SPACECAP
A Program to Estimate Animal Abundance and Density using Spatially-Explicit Capture-Recapture
JOLLY
Computes estimates of survival and capture probability for 1-age class open population capture-recapture models.
MSSRVMIS
Computes estimates of survival and capture probability adjusted for missclassification.
CountRemoval
A removal model for estimating detection probabilities from point count surveys.
ORDSURVIV
Computes estimates of survival and recovery rates for band-recovery data with additional models for estimating reporting rate.
DOBSERV
A Double-observer approach for estimating detection probability and abundance from avian point counts.
MSSRVRD
Computes survival-movement, capture and recovery probabilities from multi-strata capture-recapture-recovery data.
JOLLYAGE
Computes estimates of survival and capture probability for 2-age class open population capture-recapture models.
TMSURVIV
Computes estimates of survival and capture probability and the proportion of transients in open population capture-recapture data.
DOSECOMP
Analyzes dose responses for two populations, using the PROBIT model and the abbreviated protocol as described by Link et al(1996).
MSSURVIV
Computes estimates of survival-movement and capture probability for open capture-recapture models.
CONTRAST
Compares estimates of survival (or any normally distributed parameter estimates).
Science and Products
- Science
- Data
- Publications
Filter Total Items: 223
A multi-state occupancy modelling framework for robust estimation of disease prevalence in multi-tissue disease systems
Given the public health, economic and conservation implications of zoonotic diseases, their effective surveillance is of paramount importance. The traditional approach to estimating pathogen prevalence as the proportion of infected individuals in the population is biased because it fails to account for imperfect detection. A statistically robust way to reduce bias in prevalence estimates is to obtAuthorsVratika Chaudhary, Samantha M Wisely, Felipe A Hernandez, James E. Hines, James D. Nichols, Madan K. OliDemography of snowshoe hare population cycles
Cyclic fluctuations in abundance exhibited by some mammalian populations in northern habitats (“population cycles”) are key processes in the functioning of many boreal and tundra ecosystems. Understanding population cycles, essentially demographic processes, necessitates discerning the demographic mechanisms that underlie numerical changes. Using mark–recapture data spanning five population cyclesAuthorsMadan K. Oli, Charles J Krebs, Alice J Kenney, Rudy Boonstra, Stan Boutin, James E. HinesScale‐dependent effects of isolation on seasonal patch colonisation by two Neotropical freshwater fishes
The metapopulation paradigm has been central to improve the conservation and management of natural populations. However, despite the large number of studies on metapopulation dynamics, the overall support for the relationships on which the paradigm is based has not been strong. Here, we studied the occupancy dynamics of two Neotropical fishes (i.e., Pimelodella gracilis and Leporinus friderici) toAuthorsJerry Penha, Karlo Y. P. Hakamada, James E. Hines, James D. NicholsFactors affecting species richness and distribution spatially and temporally within a protected area using multi-season occupancy models
Exploring trends in species richness and the distribution of individual species over time as well as the factors affecting these trends informs conservation priorities in protecting species and ecosystems as a whole. We used data from 41 park-wide line transect surveys in 2009 and 2014 and multi-season occupancy models with multi-species data to explore trends in species richness and distributionAuthorsJennifer F. Moore, James E. Hines, Michel K. MasozeraImpact of prey occupancy and other ecological and anthropogenic factors on Tiger distribution in Thailand’s Western Forest Complex
Despite conservation efforts, large mammals such as tigers (Panthera tigris) and their main prey, gaur (Bos gaurus), banteng (Bos javanicus), and sambar (Rusa unicolor), are highly threatened and declining across their entire range. The only large viable source population of tigers in mainland Southeast Asia occurs in Thailand's Western Forest Complex (WEFCOM), an approximately 19,000 km 2 landscaAuthorsSomphot Duangchatrasiri, Pornkamol Jornburom, Sitthichai Jinamoy, Anak Pattanvibool, James E. Hines, Todd W. Arnold, John Fieberg, James L D SmithSize-specific apparent survival rate estimates of white sharks using mark-recapture models
For species that exist at low abundance or are otherwise difficult to study, it is challenging to estimate vital rates such as survival and fecundity and common to assume that survival rates are constant across ages and sexes. Population assessments based on overly simplistic vital rates can lead to erroneous conclusions. We estimated sex and length-based annual apparent survival rates for white sAuthorsPaul E. Kanive, Jay J. Rotella, S. J. Jorgensen, T. K. chapple, James E. Hines, S.D. Anderson, B. A. BlockPartitioning global change: Assessing the relative importance of changes in climate and land cover for changes in avian distribution
Understanding the relative impact of climate change and land cover change on changes in avian distribution has implications for the future course of avian distributions and appropriate management strategies. Due to the dynamic nature of climate change, our goal was to investigate the processes that shape species distributions, rather than the current distributional patterns. To this end, we analyzAuthorsMatthew J. Clement, James D. Nichols, Jaime A. Collazo, Adam Terando, James E. Hines, Steven G. WilliamsOccupancy in community-level studies
Another type of multi-species studies, are those focused on community-level metrics such as species richness. In this chapter we detail how some of the single-species occupancy models described in earlier chapters have been applied, or extended, for use in such studies, while accounting for imperfect detection. We highlight how Bayesian methods using MCMC are particularly useful in such settings tAuthorsDarryl I. MacKenzie, James D. Nichols, Andy Royle, Kenneth H. Pollock, Larissa L. Bailey, James E. HinesAre ranger patrols effective in reducing poaching-related threats within protected areas?
Poaching is one of the greatest threats to wildlife conservation world-wide. However, the spatial and temporal patterns of poaching activities within protected areas, and the effectiveness of ranger patrols and ranger posts in mitigating these threats, are relatively unknown.We used 10 years (2006–2015) of ranger-based monitoring data and dynamic multi-season occupancy models to quantify poaching-AuthorsJennnifer F. Moore, Felix Mulindahabi, Michel K. Masozera, James D. Nichols, James E. Hines, Ezechiel Turikunkiko, Madan K. OliTerritory occupancy and breeding success of Peregrine Falcons Falco peregrinus at various stages of population recovery
Organochlorine pesticides disrupted reproduction and killed many raptorial birds, and contributed to population declines during the 1940s to 1970s. We sought to discern whether and to what extent territory occupancy and breeding success changed from the pesticide era to recent years in a resident population of Peregrine Falcons Falco peregrinus in southern Scotland using long-term (1964–2015) fielAuthorsMichael J. McGrady, James E. Hines, Chris Rollie, George D. Smith, Elise R. Morton, Jennifer F. Moore, Richard M. Mearns, Ian Newton, Oscar E. Murillo-Garcia, Madan K. OliEvaluation of nutria (Myocastor coypus) detection methods in Maryland, USA
Nutria (Myocaster coypus), invasive, semi-aquatic rodents native to South America, were introduced into Maryland near Blackwater National Wildlife Refuge (BNWR) in 1943. Irruptive population growth, expansion, and destructive feeding habits resulted in the destruction of thousands of acres of emergent marshes at and surrounding BNWR. In 2002, a partnership of federal, state and private entities inAuthorsMargaret A. Pepper, Valentine Herrmann, James E. Hines, James D. Nichols, Stephen R KendrotRoseate Tern breeding dispersal and fidelity: Responses to two newly restored colony sites
We used 22 yr of capture–mark–reencounter (CMR) data collected from 1988 to 2009 on about 12,500 birds at what went from three to five coastal colony sites in Massachusetts, New York, and Connecticut, United States, to examine spatial and temporal variation in breeding dispersal/fidelity rates of adult Roseate Terns (Sterna dougallii). At the start of our study, Roseate Terns nested at only one siAuthorsJeffrey A. Spendelow, David Monticelli, James D. Nichols, James E. Hines, Ian Nisbet, Grace Cormons, Helen Hays, Jeremy Hatch, Carolyn Mostello - Web Tools
- Software
Filter Total Items: 35
PROGRAM SPACECAP
A Program to Estimate Animal Abundance and Density using Spatially-Explicit Capture-Recapture
JOLLY
Computes estimates of survival and capture probability for 1-age class open population capture-recapture models.
MSSRVMIS
Computes estimates of survival and capture probability adjusted for missclassification.
CountRemoval
A removal model for estimating detection probabilities from point count surveys.
ORDSURVIV
Computes estimates of survival and recovery rates for band-recovery data with additional models for estimating reporting rate.
DOBSERV
A Double-observer approach for estimating detection probability and abundance from avian point counts.
MSSRVRD
Computes survival-movement, capture and recovery probabilities from multi-strata capture-recapture-recovery data.
JOLLYAGE
Computes estimates of survival and capture probability for 2-age class open population capture-recapture models.
TMSURVIV
Computes estimates of survival and capture probability and the proportion of transients in open population capture-recapture data.
DOSECOMP
Analyzes dose responses for two populations, using the PROBIT model and the abbreviated protocol as described by Link et al(1996).
MSSURVIV
Computes estimates of survival-movement and capture probability for open capture-recapture models.
CONTRAST
Compares estimates of survival (or any normally distributed parameter estimates).
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