Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Summary

The use of both linear and generalized linear mixed-effects models (LMMs and GLMMs) has become popular not only in social and medical sciences, but also in biological sciences, especially in the field of ecology and evolution. Information criteria, such as Akaike Information Criterion (AIC), are usually presented as model comparison tools for mixed-effects models.


The presentation of ‘variance explained’ (R2) as a relevant summarizing statistic of mixed-effects models, however, is rare, even though R2 is routinely reported for linear models (LMs) and also generalized linear models (GLMs). R2 has the extremely useful property of providing an absolute value for the goodness-of-fit of a model, which cannot be given by the information criteria. As a summary statistic that describes the amount of variance explained, R2 can also be a quantity of biological interest.


One reason for the under-appreciation of R2 for mixed-effects models lies in the fact that R2 can be defined in a number of ways. Furthermore, most definitions of R2 for mixed-effects have theoretical problems (e.g. decreased or negative R2 values in larger models) and/or their use is hindered by practical difficulties (e.g. implementation).


Here, we make a case for the importance of reporting R2 for mixed-effects models. We first provide the common definitions of R2 for LMs and GLMs and discuss the key problems associated with calculating R2 for mixed-effects models. We then recommend a general and simple method for calculating two types of R2 (marginal and conditional R2) for both LMMs and GLMMs, which are less susceptible to common problems.


This method is illustrated by examples and can be widely employed by researchers in any fields of research, regardless of software packages used for fitting mixed-effects models. The proposed method has the potential to facilitate the presentation of R2 for a wide range of circumstances.

https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/j.2041-210x.2012.00261.x

A general and simple method for obtaining R2 from generalized linear mixed-effects models

Statistics for Spatial Data.

/pdf/convex-analysisnoer-san-nojin-zhan-nituite-5dl2rbmoyr.pdf

Convex Analysisの二,三の進展について

Convergence of Probability Measures. By P. Billingsley. Chichester, Sussex, Wiley, 1968. xii, 253 p. 9 1/4“. 117s.

Convergence of Probability Measures

The conditional variance function in a heteroscedastic, nonparametric regression model is estimated by linear smoothing of squared residuals. Attention is focused on local polynomial smoothers. Both the mean and variance functions are assumed to be smooth, but neither is assumed to be in a parametric family. The biasing effect of preliminary estimation of the mean is studied, and a degrees-of-freedom correction of bias is proposed. The corrected method is shown to be adaptive in the sense that the variance function can be estimated with the same asymptotic mean and variance as if the mean function were known. A proposal is made for using standard bandwidth selectors for estimating both the mean and variance functions. The proposal is illustrated with data from the LIDAR method of measuring atmospheric pollutants and from turbulence-model computations.

/pdf/local-polynomial-variance-function-estimation-45cwajcgis.pdf

Local polynomial variance-function estimation

In this article we introduce a new type of positive-breakdown regression method, called a generalized S-estimator (or GS-estimator), based on the minimization of a generalized M-estimator of residual scale. We compare the class of GS-estimators with the usual S-estimators, including least median of squares. It turns out that GS-estimators attain a much higher efficiency than S-estimators, at the cost of a slightly increased worst-case bias. We investigate the breakdown point, the maxbias curve, and the influence function of GS-estimators. We also give an algorithm for computing GS-estimators and apply it to real and simulated data.

/pdf/generalized-s-estimators-gqm5kj2u3e.pdf

Generalized S-Estimators

An estimator in the linear model is defined by minimizing an objective function, the derivative of which is a signed rank statistic. The scores are generated from a function h+ : (0, 1) → [0, ∞), which is not necessarily nondecreasing, as is usually assumed. It is shown that this estimator can be chosen with a maximal breakdown point of. 5. Moreover, strong consistency and asymptotic normality (with convergence rate n −1/2 of the proposed estimator are proved under various regularity conditions. Because the objective function generally is not convex in the regression parameters, the usual proofs of asymptotic normality do not carry over. Instead the proof is based on an asymptotic linearity result, similar to that obtained by Huber for M estimates, and some moment estimates for signed rank statistics. Numerical examples illustrate the behavior of the estimator.

Rank-Based Estimates in the Linear Model with High Breakdown Point

We generalize signed rank statistics to dimensions higher than one. This results in a class of orthogonally invariant and distribution free tests that can be used for testing spherical symmetry/location parameter. The corresponding estimator is orthogonally equivariant. Both the test and estimator can be chosen with asymptotic efficiency 1. The breakdown point of the estimator depends only on the scores, not on the dimension of the data. For elliptical distributions, weobtain an affine invariant test with the same asymptotic properties, if the signed rank statisticis applied to standardized data. We also present a method for computing the estimator numerically, and consider a real data example and some simulations. Finally, an application to detection of time-varying signals in spherically symmetric noise is given.

/pdf/generalizing-univariate-signed-rank-statistics-for-testing-3qn2omzxb4.pdf

Ola Hössjer

Papers

Local polynomial variance-function estimation

Generalized S-Estimators

Rank-Based Estimates in the Linear Model with High Breakdown Point

Generalizing univariate signed rank statistics for testing and estimating a multivariate location parameter

Fast kriging of large data sets with Gaussian Markov random fields