Brian Cade, Ph.D.
Science and Products
Unexplained heterogeneity in statistical models of animal responses to their physical environment is reasonable to expect because the measured habitat resources are a constraint on—but not the sole determinant of—abundance, survival, fecundity, or fitness. The ecological understanding and reliability of management predictions based on animal habitat models can be improved by shifting focus from estimating expected values (means) of responses to estimating intervals of responses associated with multiple percentiles of a distribution.
Mathematical and statistical models are powerful research tools that play several important roles in conceptualizing and understanding the structure and dynamics of complicated ecological systems, including developing mechanistic hypotheses pertaining to ecological systems, designing studies that elucidate ecosystem structure and function, and extracting information from data.
California spotted owl fledgling counts, climate, and landscape habitat at territories on the Lassen National Forest, CA 1991-2010
This is a comma separated values (CSV) file used to conduct the logistic quantile regression analyses in R provided by Cade et al. (2017). The data set consists of records of California spotted owl fledgling counts on 88 territories on the Lassen National Forest, CA from 1991-2010. Climatic condition data were obtained from PRISM and landscape habitat data were obtained from LANDFIRE.
Effects of environmental variables on invasive amphibian activity: Using model selection on quantiles for counts
Many different factors influence animal activity. Often, the value of an environmental variable may influence significantly the upper or lower tails of the activity distribution. For describing relationships with heterogeneous boundaries, quantile regressions predict a quantile of the conditional distribution of the dependent variable. A quantile...Muller, Benjamin J.; Cade, Brian S.; Schwarzkoph, Lin
Quantile regression applications in ecology and the environmental sciences
No abstract available.Koenker, Roger; Chernozhukov, Victor; He, Xuming ; Peng, Limin; Cade, Brian S.
Logistic quantile regression provides improved estimates for bounded avian counts: A case study of California Spotted Owl fledgling production
Counts of avian fledglings, nestlings, or clutch size that are bounded below by zero and above by some small integer form a discrete random variable distribution that is not approximated well by conventional parametric count distributions such as the Poisson or negative binomial. We developed a logistic quantile regression model to provide...Cade, Brian S.; Noon, Barry R.; Scherer, Rick D.; Keane, John J.
Efficacy of SpayVac® as a contraceptive in feral horses
ABSTRACT We tested the efficacy of 2 formulations of the immunocontraceptive SpayVac1, which packages the immunogen porcine zona pellucida (PZP) and an adjuvant in multilamellar liposomes, as a contraceptive in captive feral horses (Equus caballus) for 3 consecutive breeding seasons (Pauls Valley, OK, USA; 2012–2014) following a single inoculation...Roelle, James E.; Germaine, Stephen; Kane, Albert J.; Cade, Brian S.
Conditional vulnerability of plant diversity to atmospheric nitrogen deposition across the United States
Atmospheric nitrogen (N) deposition has been shown to decrease plant species richness along regional deposition gradients in Europe and in experimental manipulations. However, the general response of species richness to N deposition across different vegetation types, soil conditions, and climates remains largely unknown even though responses may...Simkin, Samuel M.; Allen, Edith B.; Bowman, William D.; Clark, Christopher M.; Belnap, Jayne; Brooks, Matthew L.; Cade, Brian S.; Collins, Scott L.; Geiser, Linda H.; Gilliam, Frank S.; Jovan, Sarah E.; Pardo, Linda H.; Schulz, Bethany K.; Stevens, Carly J.; Suding, Katharine N.; Throop, Heather L.; Waller, Donald M.
Trophic magnification of organic chemicals: A global synthesis
Production of organic chemicals (OCs) is increasing exponentially, and some OCs biomagnify through food webs to potentially toxic levels. Biomagnification under field conditions is best described by trophic magnification factors (TMFs; per trophic level change in log-concentration of a chemical) which have been measured for more than two decades....Walters, David; Jardine, T.D.; Cade, Brian S.; Kidd, K.A.; Muir, D.C.G.; Leipzig-Scott, Peter C.
Model averaging and muddled multimodel inferences
Three flawed practices associated with model averaging coefficients for predictor variables in regression models commonly occur when making multimodel inferences in analyses of ecological data. Model-averaged regression coefficients based on Akaike information criterion (AIC) weights have been recommended for addressing model uncertainty but they...Cade, Brian S.
Assessment of surface water chloride and conductivity trends in areas of unconventional oil and gas development-Why existing national data sets cannot tell us what we would like to know
Heightened concern regarding the potential effects of unconventional oil and gas development on regional water quality has emerged, but the few studies on this topic are limited in geographic scope. Here we evaluate the potential utility of national and publicly available water-quality data sets for addressing questions regarding unconventional...Bowen, Zachary H.; Oelsner, Gretchen P.; Cade, Brian S.; Gallegos, Tanya J.; Farag, Aïda M.; Mott, David N.; Potter, Christopher J.; Cinotto, Peter J.; Clark, Melanie L.; Kappel, William M.; Kresse, Timothy M.; Melcher, Cynthia P.; Paschke, Suzanne; Susong, David D.; Varela, Brian A.
Estimating risks to aquatic life using quantile regression
One of the primary goals of biological assessment is to assess whether contaminants or other stressors limit the ecological potential of running waters. It is important to interpret responses to contaminants relative to other environmental factors, but necessity or convenience limit quantification of all factors that influence ecological potential...Schmidt, Travis S.; Clements, William H.; Cade, Brian S.
Genetic and environmental influences on cold hardiness of native and introduced riparian trees
To explore latitudinal genetic variation in cold hardiness and leaf phenology, we planted a common garden of paired collections of native and introduced riparian trees sampled along a latitudinal gradient. The garden in Fort Collins, Colorado (latitude 40.6°N), included 681 native plains cottonwood (Populus deltoides subsp. monilifera) and...Friedman, Jonathan M.; Roelle, James E.; Cade, Brian S.
Genetic diversity and species diversity of stream fishes covary across a land-use gradient
Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size,...Blum, M.J.; Bagley, M.J.; Walters, D.M.; Jackson, S.A.; Daniel, F.B.; Chaloud, D.J.; Cade, B.S.
Quantile equivalence to evaluate compliance with habitat management objectives
Equivalence estimated with linear quantile regression was used to evaluate compliance with habitat management objectives at Arapaho National Wildlife Refuge based on monitoring data collected in upland (5,781 ha; n = 511 transects) and riparian and meadow (2,856 ha, n = 389 transects) habitats from 2005 to 2008. Quantiles were used because the...Cade, Brian S.; Johnson, Pamela R.
Blossom is an R package with functions for making statistical comparisons with distance-function based permutation tests developed by P.W. Mielke, Jr. and colleagues at Colorado State University, and for testing parameters estimated in linear models with permutation procedures developed by B. S. Cade and colleagues at the U.S. Geological Survey' Fort Collins Science Center, U.S. Geological Survey.