Model-robust regression and a Bayesian ``sandwich'' estimator

We present a new Bayesian approach to model-robust linear regression that leads to uncertainty estimates with the same robustness properties as the Huber--White sandwich estimator. The sandwich estimator is known to provide asymptotically correct frequentist inference, even when standard modeling assumptions such as linearity and homoscedasticity in the data-generating mechanism are violated. Our derivation provides a compelling Bayesian justification for using this simple and popular tool, and it also clarifies what is being estimated when the data-generating mechanism is not linear. We demonstrate the applicability of our approach using a simulation study and health care cost data from an evaluation of the Washington State Basic Health Plan.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS362 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Sea turtle nesting in the Ten Thousand Islands of Florida

Loggerhead sea turtles (Caretta caretta) nest in numerous substrate and beach types within the Ten Thousand Islands (TTl) of southwest Florida. Nesting beach selection was analyzed on 12 islands within this archipelago. Numerous physical characteristics were recorded to identify the relatedness of these variables and determine their importance for nesting beach selection in C. caretta. These variables were chosen after evaluating the islands, conducting literature searches and soliciting personal communications. Along transects, data were collected, on the following: height of canopy, beach width, overall slope (beach slope and slope of offshore approach) and sand samples analyzed for pH, percentage of water, percentage of organic content, percentage of carbonate and particle size (8 size classes). Data on ordinal aspect of beaches and beach length were also recorded and included in the analysis. All of the variables were analyzed by tree regression, incorporating the nesting data into the analysis. In the TTl, loggerheads appear to prefer wider beaches (p< 0.001; R2 = 0.56) that inherently have less slope, and secondarily, wider beaches that have low amounts of carbonate (p< O.00 1). In addition, C. caretta favors nest sites within or in close proximity to the supra-littoral vegetation zone of beaches in the TTl (p< 0.001). (86 page document

Estimating Sighting Proportions of American Alligator Nests during Helicopter Survey

Proportions of American alligator (Alligator mississippiensis) nests sighted during aerial survey in Florida were estimated based upon multiple surveys by different observers. We compared sighting proportions across habitats, nesting seasons, and observer experience levels. The mean sighting proportion across all habitats and years was 0.736 (SE=0.024). Survey counts corrected by the mean sighting proportion reliably predicted total nest counts (R2=0.933). Sighting proportions did not differ by habitat type (P=0.668) or year P=0.328). Experienced observers detected a greater proportion of nests (P<O.OOOl) than did either less experienced or inexperienced observers. Reliable estimates of nest abundance can be derived from aerial counts of alligator nests when corrected by the appropriate sighting proportion

Herpetofaunal Inventories of the National Parks of South Florida and the Caribbean: Volume III. Big Cypress National Preserve

Amphibian declines and extinctions have been documented around the world, often in protected natural areas. Concern for this trend has prompted the U.S. Geological Survey and the National Park Service to document all species of amphibians that occur within U.S. National Parks and to search for any signs that amphibians may be declining. This study, an inventory of amphibian species in Big Cypress National Preserve, was conducted from 2002 to 2003. The goals of the project were to create a georeferenced inventory of amphibian species, use new analytical techniques to estimate proportion of sites occupied by each species, look for any signs of amphibian decline (missing species, disease, die-offs, and so forth.), and to establish a protocol that could be used for future monitoring efforts. Several sampling methods were used to accomplish these goals. Visual encounter surveys and anuran vocalization surveys were conducted in all habitats throughout the park to estimate the proportion of sites or proportion of area occupied (PAO) by each amphibian species in each habitat. Opportunistic collections, as well as limited drift fence data, were used to augment the visual encounter methods for highly aquatic or cryptic species. A total of 545 visits to 104 sites were conducted for standard sampling alone, and 2,358 individual amphibians and 374 reptiles were encountered. Data analysis was conducted in program PRESENCE to provide PAO estimates for each of the anuran species. All of the amphibian species historically found in Big Cypress National Preserve were detected during this project. At least one individual of each of the four salamander species was captured during sampling. Each of the anuran species in the preserve was adequately sampled using standard herpetological sampling methods, and PAO estimates were produced for each species of anuran by habitat. This information serves as an indicator of habitat associations of the species and relative abundance of sites occupied, but it will also be useful as a comparative baseline for future monitoring efforts. In addition to sampling for amphibians, all encounters with reptiles were documented. The sampling methods used for detecting amphibians are also appropriate for many reptile species. These reptile locations are included in this report, but the number of reptile observations was not sufficient to estimate PAO for reptile species. We encountered 35 of the 46 species of reptiles believed to be present in Big Cypress National Preserve during this study, and evidence exists of the presence of four other reptile species in the Preserve. This study found no evidence of amphibian decline in Big Cypress National Preserve. Although no evidence of decline was observed, several threats to amphibians were identified. Introduced species, especially the Cuban treefrog (Osteopilus septentrionalis), are predators and competitors with several native frog species. The recreational use of off-road vehicles has the potential to affect some amphibian populations, and a study on those potential impacts is currently underway. Also, interference by humans with the natural hydrologic cycle of south Florida has the potential to alter the amphibian community. Continued monitoring of the amphibian species in Big Cypress National Preserve is recommended. The methods used in this study were adequate to produce reliable estimates of the proportion of sites occupied by most anuran species, and are a cost-effective means of determining the status of their populations

Model-Robust Bayesian Regression and the Sandwich Estimator

PLEASE NOTE THAT AN UPDATED VERSION OF THIS RESEARCH IS AVAILABLE AS WORKING PAPER 338 IN THE UNIVERSITY OF WASHINGTON BIOSTATISTICS WORKING PAPER SERIES (http://www.bepress.com/uwbiostat/paper338). In applied regression problems there is often sufficient data for accurate estimation, but standard parametric models do not accurately describe the source of the data, so associated uncertainty estimates are not reliable. We describe a simple Bayesian approach to inference in linear regression that recovers least-squares point estimates while providing correct uncertainty bounds by explicitly recognizing that standard modeling assumptions need not be valid. Our model-robust development parallels frequentist estimating equations and leads to intervals with the same robustness properties as the ’sandwich’ estimator

Trading Bias for Precision: Decision Theory for Intervals and Sets

Interval- and set-valued decisions are an essential part of statistical inference. Despite this, the justification behind them is often unclear, leading in practice to a great deal of confusion about exactly what is being presented. In this paper we review and attempt to unify several competing methods of interval-construction, within a formal decision-theoretic framework. The result is a new emphasis on interval-estimation as a distinct goal, and not as an afterthought to point estimation. We also see that representing intervals as trade-offs between measures of precision and bias unifies many existing approaches -- as well as suggesting interpretable criteria to calibrate this trade-off. The novel statistical arguments produced allow many extensions, and we apply these to resolve several outstanding areas of disagreement between Bayesians and frequentists

Antimicrobial Resistance in Neisseria gonorrhoeae: Proceedings of the STAR Sexually Transmitted Infection-Clinical Trial Group Programmatic Meeting.

The goal of the Sexually Transmitted Infection Clinical Trial Group's Antimicrobial Resistance (AMR) in Neisseria gonorrhoeae (NG) meeting was to assemble experts from academia, government, nonprofit and industry to discuss the current state of research, gaps and challenges in research and technology and priorities and new directions to address the continued emergence of multidrug-resistant NG infections. Topics discussed at the meeting, which will be the focus of this article, include AMR NG global surveillance initiatives, the use of whole genome sequencing and bioinformatics to understand mutations associated with AMR, mechanisms of AMR, and novel antibiotics, vaccines and other methods to treat AMR NG. Key points highlighted during the meeting include: (i) US and International surveillance programs to understand AMR in NG; (ii) the US National Strategy for combating antimicrobial-resistant bacteria; (iii) surveillance needs, challenges, and novel technologies; (iv) plasmid-mediated and chromosomally mediated mechanisms of AMR in NG; (v) novel therapeutic (eg, sialic acid analogs, factor H [FH]/Fc fusion molecule, monoclonal antibodies, topoisomerase inhibitors, fluoroketolides, LpxC inhibitors) and preventative (eg, peptide mimic) strategies to combat infection. The way forward will require renewed political will, new funding initiatives, and collaborations across academic and commercial research and public health programs

Biotechnology and the European Corn Borer: Measuring Historical Farmer Perceptions and Adoption of Transgenic Bt Corn as a Pest Management Strategy

A 3-yr, multi-state survey of farmers who had planted transgenic Bacillus thuringiensis (Bt) corn was conducted to evaluate perceptions of Bt corn performance and its utility as a management option for European corn borer, Ostrinia nubilalis (Hu¨ bner). A questionnaire was sent to farmers in Illinois, Iowa, Kansas, Minnesota, Nebraska, and Pennsylvania who had grown Bt corn during the growing seasons of 1996, 1997, or 1998. There were 7,427 usable questionnaires returned with the following response percentages: 1996 (42.1%), 1997 (35.0%), and 1998 (22.6%). Adoption rates, based on percentage of acreage planted to Bt corn, increased dramatically from 1996 (10.5%) to 1998 (40.7%). The states growing the highest percentage of Bt corn were Minnesota, Iowa, and then Nebraska. However, Illinois, was adopting Bt corn at the fastest rate. Historical use of insecticides did not inßuence the adoption of Bt corn. In addition, of those farmers who used insecticides to control European corn borer, the percentage that decreased their use of insecticides nearly doubled from 13.2% (1996) to 26.0% (1998) over this 3-yr period. The primary reason farmers planted Bt corn was to eliminate the yield loss caused by European corn borer. Scouting for European corn borers decreased from 91% (scouting 2.2 times a year) in 1996 to 75% (scouting 1.8 times a year) in 1998. The percentage of farmers not scouting for European corn borers increased from 9.6% (1996) to 25% (1998). Most farmers believed yields of Bt hybrids were either similar to or greater than the yields of non-Bt hybrids. Minnesota farmers perceived the greatest yield advantages. Farmers are becoming more aware of insect resistance management guidelines; however, they also clearly show preferences for having the ßexibility to use different spatial plantings of Bt and non-Bt corn. Finally, after having planted Bt corn and obtained excellent control of European corn borer, most farmers believed that this insect had been causing more yield loss than they previously had suspected in their non-Bt corn. The data represented here provide an historical foundation for how transgenic Bt corn was used by farmers during the Þrst 3 yr of commercial availability, their initial perceptions on the performance of this technology, and their attitudes regarding management of the European corn borer