Variable selection and model choice in geoadditive regression models

Summary .  Model choice and variable selection are issues of major concern in practical regression analyses, arising in many biometric applications such as habitat suitability analyses, where the aim is to identify the influence of potentially many environmental conditions on certain species. We describe regression models for breeding bird communities that facilitate both model choice and variable selection, by a boosting algorithm that works within a class of geoadditive regression models comprising spatial effects, nonparametric effects of continuous covariates, interaction surfaces, and varying coefficients. The major modeling components are penalized splines and their bivariate tensor product extensions. All smooth model terms are represented as the sum of a parametric component and a smooth component with one degree of freedom to obtain a fair comparison between the model terms. A generic representation of the geoadditive model allows us to devise a general boosting algorithm that automatically performs model choice and variable selection.     

Model checking in regression via dimension reduction

Lack-of-fit checking for parametric and semiparametric modelsis essential in reducing misspecification. The efficiency ofmost existing model-checking methods drops rapidly as the dimensionof the covariates increases. We propose to check a model byprojecting the fitted residuals along a direction that adaptsto the systematic departure of the residuals from the desiredpattern. Consistency of the method is proved for parametricand semiparametric regression models. A bootstrap implementationis also discussed. Simulation comparisons with several existingmethods are made, suggesting that the proposed methods are moreefficient than the existing methods when the dimension increases.Air pollution data from Chicago are used to illustrate the procedure.     

Evaluation of Root-n Bandwidth Selectors for Kernel Density Estimation

ABSTRACT The kernel density estimator is used commonly for estimating animal utilization distributions from location data. This technique requires estimation of a bandwidth, for which ecologists often use least-squares cross-validation (LSCV). However, LSCV has large variance and a tendency to under-smooth data, and it fails to generate a bandwidth estimate in some situations. We compared performance of 2 new bandwidth estimators (root-n) versus that of LSCV using simulated data and location data from sharp-shinned hawks (Accipter striatus) and red wolves (Canis rufus). With simulated data containing no repeat locations, LSCV often produced a better fit between estimated and true utilization distributions than did root-n estimators on a case-by-case basis. On average, LSCV also provided lower positive relative error in home-range areas with small sample sizes of simulated data. However, root-n estimators tended to produce a better fit than LSCV on average because of extremely poor estimates generated on occasion by LSCV. Furthermore, the relative performance of LSCV decreased substantially as the number of repeat locations in the data increased. Root-n estimators also generally provided a better fit between utilization distributions generated from subsamples of hawk data and the local densities of locations from the full data sets. Least-squares cross-validation generated more unrealistically disjointed estimates of home ranges using real location data from red wolf packs. Most importantly, LSCV failed to generate home-range estimates for >20% of red wolf packs due to presence of repeat locations. We conclude that root-n estimators are superior to LSCV for larger data sets with repeat locations or other extreme clumping of data. In contrast, LSCV may be superior where the primary interest is in generating animal home ranges (rather than the utilization distribution) and data sets are small with limited clumping of locations.     

Generalized additive modeling with implicit variable selection by likelihood-based boosting

The use of generalized additive models in statistical data analysis suffers from the restriction to few explanatory variables and the problems of selection of smoothing parameters. Generalized additive model boosting circumvents these problems by means of stagewise fitting of weak learners. A fitting procedure is derived which works for all simple exponential family distributions, including binomial, Poisson, and normal response variables. The procedure combines the selection of variables and the determination of the appropriate amount of smoothing. Penalized regression splines and the newly introduced penalized stumps are considered as weak learners. Estimates of standard deviations and stopping criteria, which are notorious problems in iterative procedures, are based on an approximate hat matrix. The method is shown to be a strong competitor to common procedures for the fitting of generalized additive models. In particular, in high-dimensional settings with many nuisance predictor variables it performs very well.     

Technical note: A freeware,equitable approach to dental topographic analysis

Dental topographic analysis has proved a valuable tool for quantifying dental morphology. Established workflows often use proprietary software for pre-processing dental surfaces, rendering the method expensive and inaccessible to many. This study explores the use of freeware pre-processing alternatives. We tested 4 decimation tools and 13 smoothing tools across 7 different freeware packages. Surfaces generated via proprietary software could not be replicated, but it was possible to obtain statistically similar measurements using freeware. Based on this investigation, we propose a freeware workflow for researchers to conduct dental topographic analysis, with the expectation that their results will be comparable to that obtained through proprietary methods.     

Statistical modelling and forecasting annual sugarcane production in India: Using various time series models

This paper proposes a comparison of various time series forecasting models to forecast annual data on sugarcane production over 63 years from 1960 to 2022. In this research, the Mean Forecast Model, the Naive Model, the Simple Exponential Smoothing Model, Holt's model, and the Autoregressive Integrated Moving Average time series models have all been used to make effective and accurate predictions for sugarcane. Different scale-dependent error forecasting techniques and residual analysis have been used to examine the forecasting accuracy of these time series models. SE of Residuals, Root Mean Squared Error (RMSE), Mean Absolute Error (MAE) and Akaike's Information Criterion (AIC) are used to analyse the forecast's accuracy. The best model has been selected based on the predictions with the lowest value, according to the three-performance metrics of RMSE, MAE, and AIC. The estimated sugarcane production shows an increasing trend for the next 10 years and is projected to be 37,763.38 million tonnes in the year 2032. Further, empirical results support the plan and execution of viable strategies to advance sugarcane production in India to fulfil the utilisation need of the increasing population and further improve food security.     

Quantile Inference with Multivariate Failure Time Data

Quantiles, especially the medians, of survival times are often used as summary statistics to compare the survival experiences between different groups. Quantiles are robust against outliers and preferred over the mean. Multivariate failure time data often arise in biomedical research. For example, in clinical trials, each patient in the study may experience multiple events which may be of the same type or distinct types, while in family studies of genetic diseases or litter matched mice studies, failure times for subjects in the same cluster may be correlated. In this article, we propose nonparametric procedures for the estimation of quantiles with multivariate failure time data. We show that the proposed estimators asymptotically follow a multivariate normal distribution. The asymptotic variance‐covariance matrix of the estimated quantiles is estimated based on the kernel smoothing and bootstrap techniques. Simulation results show that the proposed estimators perform well in finite samples. The methods are illustrated with the burn‐wound infection data and the Diabetic Retinopathy Study (DRS) data.     

Nonlinear system identification for prostate cancer and optimality of intermittent androgen suppression therapy

These days prostate cancer is one of the most common types of malignant neoplasm in men. Androgen ablation therapy (hormone therapy) has been shown to be effective for advanced prostate cancer. However, continuous hormone therapy often causes recurrence. This results from the progression of androgen-dependent cancer cells to androgen-independent cancer cells during the continuous hormone therapy. One possible method to prevent the progression to the androgen-independent state is intermittent androgen suppression (IAS) therapy, which ceases dosing intermittently. In this paper, we propose two methods to estimate the dynamics of prostate cancer, and investigate the IAS therapy from the viewpoint of optimality. The two methods that we propose for dynamics estimation are a variational Bayesian method for a piecewise affine (PWA) system and a Gaussian process regression method. We apply the proposed methods to real clinical data and compare their predictive performances. Then, using the estimated dynamics of prostate cancer, we observe how prostate cancer behaves for various dosing schedules. It can be seen that the conventional IAS therapy is a way of imposing high cost for dosing while keeping the prostate cancer in a safe state. We would like to dedicate this paper to the memory of Professor Luigi M. Ricciardi.     

Exploring spatial and temporal variations of cadmium concentrations in pacific oysters from british columbia

Oysters from the Pacific Northwest coast of British Columbia, Canada, contain high levels of cadmium, in some cases exceeding some international food safety guidelines. A primary goal of this article is the investigation of the spatial and temporal variation in cadmium concentrations for oysters sampled from coastal British Columbia. Such information is important so that recommendations can be made as to where and when oysters can be cultured such that accumulation of cadmium within these oysters is minimized. Some modern statistical methods are applied to achieve this goal, including monotone spline smoothing, functional principal component analysis, and semi-parametric additive modeling. Oyster growth rates are estimated as the first derivatives of the monotone smoothing growth curves. Some important patterns in cadmium accumulation by oysters are observed. For example, most inland regions tend to have a higher level of cadmium concentration than most coastal regions, so more caution needs to be taken for shellfish aquaculture practices occurring in the inland regions. The semi-parametric additive modeling shows that oyster cadmium concentration decreases with oyster length, and oysters sampled at 7 m have higher average cadmium concentration than those sampled at 1 m.