Practical Maximum Pseudolikelihood for Spatial Point Patterns(with Discussion)

This paper describes a technique for computing approximate maximum pseudolikelihood estimates of the parameters of a spatial point process. The method is an extension of Berman & Turner's (1992) device for maximizing the likelihoods of inhomogeneous spatial Poisson processes. For a very wide class of spatial point process models the likelihood is intractable, while the pseudolikelihood is known explicitly, except for the computation of an integral over the sampling region. Approximation of this integral by a finite sum in a special way yields an approximate pseudolikelihood which is formally equivalent to the (weighted) likelihood of a loglinear model with Poisson responses. This can be maximized using standard statistical software for generalized linear or additive models, provided the conditional intensity of the process takes an 'exponential family' form. Using this approach a wide variety of spatial point process models of Gibbs type can be fitted rapidly, incorporating spatial trends, interaction between points, dependence on spatial covariates, and mark information.     

Understanding increments in model performance metrics

The area under the receiver operating characteristic curve (AUC) is the most commonly reported measure of discrimination for prediction models with binary outcomes. However, recently it has been criticized for its inability to increase when important risk factors are added to a baseline model with good discrimination. This has led to the claim that the reliance on the AUC as a measure of discrimination may miss important improvements in clinical performance of risk prediction rules derived from a baseline model. In this paper we investigate this claim by relating the AUC to measures of clinical performance based on sensitivity and specificity under the assumption of multivariate normality. The behavior of the AUC is contrasted with that of discrimination slope. We show that unless rules with very good specificity are desired, the change in the AUC does an adequate job as a predictor of the change in measures of clinical performance. However, stronger or more numerous predictors are needed to achieve the same increment in the AUC for baseline models with good versus poor discrimination. When excellent specificity is desired, our results suggest that the discrimination slope might be a better measure of model improvement than AUC. The theoretical results are illustrated using a Framingham Heart Study example of a model for predicting the 10-year incidence of atrial fibrillation.     

An improved comorbidity summary score for measuring disease burden and predicting mortality with applications to two national cohorts

Abstract

Research involving administrative healthcare data to study patient outcomes requires the investigator to account for the patient’s disease burden in order to reduce the potential for biased results. Here we develop a comorbidity summary score based on variable importance measures derived from several statistical and machine learning methods and show it has superior predictive performance to the Elixhauser and Charlson indices when used to predict 1-year, 5-year, and 10-year mortality. We used two large Veterans Administration cohorts to develop and validate the summary score and compared predictive performance using the area under ROC curve (AUC) and the Brier score.     

A generating algorithm for linear trend-free and nearly linear trend-free block designs

The theory and properties of trend-free (TF) and nearly trend-free (NTF) block designs are wel1 developed. Applications have been hampered because a methodology for design construction has not been available.

This article begins with a short review of concepts and properties of TF and NTF block designs. The major contribution is provision of an algorithm for the construction of linear and nearly linear TF block designs. The algorithm is incorporated in a computer program in FORTRAN 77 provided in an appendix for the IBM PC or compatible microcomputer, a program adaptable also to other computers. Three sets of block designs generated by the program are given as examples.

A numerical example of analysis of a linear trend-free balanced incomplete block design is provided.     

Recursive location and scale estimators

It is shown that a recursive estimator with the same asymptotic properties as the median has convergence properties in finite samples which depend heavily on the scale of the data. A simple modification which adjusts for the scale is suggested and its application illustrated on simulated data. The modified estimator has much improved properties which are similar to those of the sample (non-recursive) median.     

On the robustness of the extreme deviate test for a single multivariate outlier against heavy-tailed distributions

In this paper we assess the sensitivity of the multivariate extreme deviate test for a single multivariate outlier to non-normality in the form of heavy tails. We find that the empirical significance levels can be markedly affected by even modest departures from multivariate normality. The effects are particularly severe when the sample size is large relative to the dimension. Finally, by way of example we demonstrate that certain graphical techniques may prove useful in identifying the source of rejection for the multivariate extreme deviate test.     

Principles for Conduct of Pest Risk Analyses: Report of an Expert Workshop

The North American Free Trade Agreement (NAFTA) and the General Agreement on Tariffs and Trade (GATT) have focused attention on risk assessment of potential insect, weed, and animal pests and diseases of livestock. These risks have traditionally been addressed through quarantine protocols ranging from limits on the geographical areas from which a product may originate, postharvest disinfestation procedures like fumigation, and inspections at points of export and import, to outright bans. To ensure that plant and animal protection measures are not used as nontariff trade barriers, GATT and NAFTA require pest risk analysis (PRA) to support quarantine decisions. The increased emphasis on PRA has spurred multiple efforts at the national and international level to design frameworks for the conduct of these analyses. As approaches to pest risk analysis proliferate, and the importance of the analyses grows, concerns have arisen about the scientific and technical conduct of pest risk analysis. In January of 1997, the Harvard Center for Risk Analysis (HCRA) held an invitation-only workshop in Washington, D.C. to bring experts in risk analysis and pest characterization together to develop general principles for pest risk analysis. Workshop participants examined current frameworks for PRA, discussed strengths and weaknesses of the approaches, and formulated principles, based on years of experience with risk analysis in other setting and knowledge of the issues specific to analysis of pests. The principles developed highlight the both the similarities of pest risk analysis to other forms of risk analysis, and its unique attributes.     

A Diversity Index for Model Space Selection in the Estimation of Benchmark and Infectious Doses via Model Averaging

In chemical and microbial risk assessments, risk assessors fit dose‐response models to high‐dose data and extrapolate downward to risk levels in the range of 1–10%. Although multiple dose‐response models may be able to fit the data adequately in the experimental range, the estimated effective dose (ED) corresponding to an extremely small risk can be substantially different from model to model. In this respect, model averaging (MA) provides more robustness than a single dose‐response model in the point and interval estimation of an ED. In MA, accounting for both data uncertainty and model uncertainty is crucial, but addressing model uncertainty is not achieved simply by increasing the number of models in a model space. A plausible set of models for MA can be characterized by goodness of fit and diversity surrounding the truth. We propose a diversity index (DI) to balance between these two characteristics in model space selection. It addresses a collective property of a model space rather than individual performance of each model. Tuning parameters in the DI control the size of the model space for MA.     

Relationship of bird richness,abundance and assemblage to the built environment in a small island tropical urban setting: a Suva,Fiji case study

There have been few studies investigating the relationship between the built environment and the status of bird distributions in small island tropical urban areas. We present a study investigating the relationship between bird species richness, abundance and assemblage to the built environment in Suva, Fiji. Field surveys were taken at 54 randomly selected sites throughout the city, stratified by three building density classes and the central business district (CBD). At each site bird counts were recorded, along with environmental data such as average building height, within a 150 m radius. Land-use information was obtained from screen digitized high-resolution satellite imagery within the same radius. Distance to undeveloped patches of land within the urban area was calculated using a GIS. Analysis of the effects of the built environment was carried out for all species, and for exotic and native species separately. Abundance of exotics was significantly higher in the central business district (CBD) than all other urban density classes, and significantly higher than natives in all other density classes. We found a negative relationship between native species richness and distance to undeveloped patches, but no relationship for exotics. Species assemblage was not related to urban density class. We conclude that the status of native and exotic bird species in Suva is similar to what has been found in urban areas in temperate climates, and conservation efforts should focus on minimizing the amount of heavily urbanized “core areas” and protecting undeveloped areas of forested vegetation to improve bird biodiversity in small tropical islands cities.