PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).

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PAML 4: Phylogenetic Analysis by Maximum Likelihood

The model selection literature has been generally poor at reflecting the deep foundations of the Akaike information criterion (AIC) and at making appropriate comparisons to the Bayesian information...

https://faculty.washington.edu/skalski/classes/QERM597/papers_xtra/Burnham%20and%20Anderson.pdf

Multimodel Inference Understanding AIC and BIC in Model Selection

Longitudinal data sets are comprised of repeated observations of an outcome and a set of covariates for each of many subjects. One objective of statistical analysis is to describe the marginal expectation of the outcome variable as a function of the covariates while accounting for the correlation among the repeated observations for a given subject. This paper proposes a unifying approach to such analysis for a variety of discrete and continuous outcomes. A class of generalized estimating equations (GEEs) for the regression parameters is proposed. The equations are extensions of those used in quasi-likelihood (Wedderburn, 1974, Biometrika 61, 439-447) methods. The GEEs have solutions which are consistent and asymptotically Gaussian even when the time dependence is misspecified as we often expect. A consistent variance estimate is presented. We illustrate the use of the GEE approach with longitudinal data from a study of the effect of mothers' stress on children's morbidity.

Longitudinal data analysis for discrete and continuous outcomes.

Nonparametric regression is a set of techniques for estimating a regression curve without making strong assumptions about the shape of the true regression function. These techniques are therefore useful for building and checking parametric models, as well as for data description. Kernel and nearest-neighbor regression estimators are local versions of univariate location estimators, and so they can readily be introduced to beginning students and consulting clients who are familiar with such summaries as the sample mean and median.

/pdf/an-introduction-to-kernel-and-nearest-neighbor-nonparametric-2l6wb0z48n.pdf

An Introduction to Kernel and Nearest-Neighbor Nonparametric Regression

Structured additive regression models are perhaps the most commonly used class of models in statistical applications. It includes, among others, (generalized) linear models, (generalized) additive models, smoothing spline models, state space models, semiparametric regression, spatial and spatiotemporal models, log-Gaussian Cox processes and geostatistical and geoadditive models. We consider approximate Bayesian inference in a popular subset of structured additive regression models, latent Gaussian models, where the latent field is Gaussian, controlled by a few hyperparameters and with non-Gaussian response variables. The posterior marginals are not available in closed form owing to the non-Gaussian response variables. For such models, Markov chain Monte Carlo methods can be implemented, but they are not without problems, in terms of both convergence and computational time. In some practical applications, the extent of these problems is such that Markov chain Monte Carlo sampling is simply not an appropriate tool for routine analysis. We show that, by using an integrated nested Laplace approximation and its simplified version, we can directly compute very accurate approximations to the posterior marginals. The main benefit of these approximations is computational: where Markov chain Monte Carlo algorithms need hours or days to run, our approximations provide more precise estimates in seconds or minutes. Another advantage with our approach is its generality, which makes it possible to perform Bayesian analysis in an automatic, streamlined way, and to compute model comparison criteria and various predictive measures so that models can be compared and the model under study can be challenged.

/pdf/approximate-bayesian-inference-for-latent-gaussian-models-by-2m3x22eic2.pdf

Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations

On introduit une nouvelle classe de fonctions de densite dependant du parametre de forme λ, telles que λ=0 corresponde a la densite normale standard

A class of distributions which includes the normal ones

SUMMARY The paper extends earlier work on the so-called skew-normal distribution, a family of distributions including the normal, but with an extra parameter to regulate skewness. The present work introduces a multivariate parametric family such that the marginal densities are scalar skew-normal, and studies its properties, with special emphasis on the bivariate case.

/pdf/the-multivariate-skew-normal-distribution-265gie4y64.pdf

The multivariate skew-normal distribution

1. Density estimation for exploring data 2. Density estimation for inference 3. Nonparametric regression for exploring data 4. Inference with nonparametric regression 5. Checking parametric regression models 6. Comparing regression curves and surfaces 7. Time series data 8. An introduction to semiparametric and additive models References

/pdf/applied-smoothing-techniques-for-data-analysis-the-kernel-1bp2axnqub.pdf

Applied smoothing techniques for data analysis : the kernel approach with S-plus illustrations

Summary. A fairly general procedure is studied to perturb a multivariate density satisfying a weak form of multivariate symmetry, and to generate a whole set of non-symmetric densities. The approach is sufficiently general to encompass some recent proposals in the literature, variously related to the skew normal distribution. The special case of skew elliptical densities is examined in detail, establishing connections with existing similar work. The final part of the paper specializes further to a form of multivariate skew t-density. Likelihood inference for this distribution is examined, and it is illustrated with numerical examples.

Distributions generated by perturbation of symmetry with emphasis on a multivariate skew t‐distribution

A fairly general procedure is studied to perturbate a multivariate density satisfying a weak form of multivariate symmetry, and to generate a whole set of non-symmetric densities. The approach is general enough to encompass a number of recent proposals in the literature, variously related to the skew normal distribution. The special case of skew elliptical densities is examined in detail, establishing connections with existing similar work. The final part of the paper specializes further to a form of multivariate skew $t$ density. Likelihood inference for this distribution is examined, and it is illustrated with numerical examples.

Adelchi Azzalini

Papers

A class of distributions which includes the normal ones

The multivariate skew-normal distribution

Applied smoothing techniques for data analysis : the kernel approach with S-plus illustrations

Distributions generated by perturbation of symmetry with emphasis on a multivariate skew t‐distribution

Distributions generated by perturbation of symmetry with emphasis on a multivariate skew $t$ distribution