Robust forward simulations of recurrent hitchhiking

Evolutionary forces shape patterns of genetic diversity within populations and contribute to phenotypic variation. In particular, recurrent positive selection has attracted significant interest in both theoretical and empirical studies. However, most existing theoretical models of recurrent positive selection cannot easily incorporate realistic confounding effects such as interference between selected sites, arbitrary selection schemes, and complicated demographic processes. It is possible to quantify the effects of arbitrarily complex evolutionary models by performing forward population genetic simulations, but forward simulations can be computationally prohibitive for large population sizes ($> 10^5$). A common approach for overcoming these computational limitations is rescaling of the most computationally expensive parameters, especially population size. Here, we show that ad hoc approaches to parameter rescaling under the recurrent hitchhiking model do not always provide sufficiently accurate dynamics, potentially skewing patterns of diversity in simulated DNA sequences. We derive an extension of the recurrent hitchhiking model that is appropriate for strong selection in small population sizes, and use it to develop a method for parameter rescaling that provides the best possible computational performance for a given error tolerance. We perform a detailed theoretical analysis of the robustness of rescaling across the parameter space. Finally, we apply our rescaling algorithms to parameters that were previously inferred for Drosophila, and discuss practical considerations such as interference between selected sites

An autoregressive approach to house price modeling

A statistical model for predicting individual house prices and constructing a house price index is proposed utilizing information regarding sale price, time of sale and location (ZIP code). This model is composed of a fixed time effect and a random ZIP (postal) code effect combined with an autoregressive component. The former two components are applied to all home sales, while the latter is applied only to homes sold repeatedly. The time effect can be converted into a house price index. To evaluate the proposed model and the resulting index, single-family home sales for twenty US metropolitan areas from July 1985 through September 2004 are analyzed. The model is shown to have better predictive abilities than the benchmark S&P/Case--Shiller model, which is a repeat sales model, and a conventional mixed effects model. Finally, Los Angeles, CA, is used to illustrate a historical housing market downturn.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS380 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Nonparametric regression in exponential families

Most results in nonparametric regression theory are developed only for the case of additive noise. In such a setting many smoothing techniques including wavelet thresholding methods have been developed and shown to be highly adaptive. In this paper we consider nonparametric regression in exponential families with the main focus on the natural exponential families with a quadratic variance function, which include, for example, Poisson regression, binomial regression and gamma regression. We propose a unified approach of using a mean-matching variance stabilizing transformation to turn the relatively complicated problem of nonparametric regression in exponential families into a standard homoscedastic Gaussian regression problem. Then in principle any good nonparametric Gaussian regression procedure can be applied to the transformed data. To illustrate our general methodology, in this paper we use wavelet block thresholding to construct the final estimators of the regression function. The procedures are easily implementable. Both theoretical and numerical properties of the estimators are investigated. The estimators are shown to enjoy a high degree of adaptivity and spatial adaptivity with near-optimal asymptotic performance over a wide range of Besov spaces. The estimators also perform well numerically.Comment: Published in at http://dx.doi.org/10.1214/09-AOS762 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Robust nonparametric estimation via wavelet median regression

In this paper we develop a nonparametric regression method that is simultaneously adaptive over a wide range of function classes for the regression function and robust over a large collection of error distributions, including those that are heavy-tailed, and may not even possess variances or means. Our approach is to first use local medians to turn the problem of nonparametric regression with unknown noise distribution into a standard Gaussian regression problem and then apply a wavelet block thresholding procedure to construct an estimator of the regression function. It is shown that the estimator simultaneously attains the optimal rate of convergence over a wide range of the Besov classes, without prior knowledge of the smoothness of the underlying functions or prior knowledge of the error distribution. The estimator also automatically adapts to the local smoothness of the underlying function, and attains the local adaptive minimax rate for estimating functions at a point. A key technical result in our development is a quantile coupling theorem which gives a tight bound for the quantile coupling between the sample medians and a normal variable. This median coupling inequality may be of independent interest.Comment: Published in at http://dx.doi.org/10.1214/07-AOS513 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

A review of applied methods in Europe for flood-frequency analysis in a changing environment

The report presents a review of methods used in Europe for trend analysis, climate change projections and non-stationary analysis of extreme precipitation and flood frequency. In addition, main findings of the analyses are presented, including a comparison of trend analysis results and climate change projections. Existing guidelines in Europe on design flood and design rainfall estimation that incorporate climate change are reviewed. The report concludes with a discussion of research needs on non-stationary frequency analysis for considering the effects of climate change and inclusion in design guidelines. Trend analyses are reported for 21 countries in Europe with results for extreme precipitation, extreme streamflow or both. A large number of national and regional trend studies have been carried out. Most studies are based on statistical methods applied to individual time series of extreme precipitation or extreme streamflow using the non-parametric Mann-Kendall trend test or regression analysis. Some studies have been reported that use field significance or regional consistency tests to analyse trends over larger areas. Some of the studies also include analysis of trend attribution. The studies reviewed indicate that there is some evidence of a general increase in extreme precipitation, whereas there are no clear indications of significant increasing trends at regional or national level of extreme streamflow. For some smaller regions increases in extreme streamflow are reported. Several studies from regions dominated by snowmelt-induced peak flows report decreases in extreme streamflow and earlier spring snowmelt peak flows. Climate change projections have been reported for 14 countries in Europe with results for extreme precipitation, extreme streamflow or both. The review shows various approaches for producing climate projections of extreme precipitation and flood frequency based on alternative climate forcing scenarios, climate projections from available global and regional climate models, methods for statistical downscaling and bias correction, and alternative hydrological models. A large number of the reported studies are based on an ensemble modelling approach that use several climate forcing scenarios and climate model projections in order to address the uncertainty on the projections of extreme precipitation and flood frequency. Some studies also include alternative statistical downscaling and bias correction methods and hydrological modelling approaches. Most studies reviewed indicate an increase in extreme precipitation under a future climate, which is consistent with the observed trend of extreme precipitation. Hydrological projections of peak flows and flood frequency show both positive and negative changes. Large increases in peak flows are reported for some catchments with rainfall-dominated peak flows, whereas a general decrease in flood magnitude and earlier spring floods are reported for catchments with snowmelt-dominated peak flows. The latter is consistent with the observed trends. The review of existing guidelines in Europe on design floods and design rainfalls shows that only few countries explicitly address climate change. These design guidelines are based on climate change adjustment factors to be applied to current design estimates and may depend on design return period and projection horizon. The review indicates a gap between the need for considering climate change impacts in design and actual published guidelines that incorporate climate change in extreme precipitation and flood frequency. Most of the studies reported are based on frequency analysis assuming stationary conditions in a certain time window (typically 30 years) representing current and future climate. There is a need for developing more consistent non-stationary frequency analysis methods that can account for the transient nature of a changing climate

Gamma ray pulsar analysis from photon probability maps

A new method is presented of analyzing skymap-type gamma ray data. Each photon event is replaced by a probability distribution on the sky corresponding to the observing instrument's point spread function. The skymap produced by this process may be used for source detection or identification. Most important, the use of these photon weights for pulsar analysis promises significant improvement over traditional techniques