Browse
Submit Data
Databases
API
Help

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Heteroscedastic nonlinear regression models based on scale mixtures of skew-normal distributions.

ABSTRACT: An extension of some standard likelihood based procedures to heteroscedastic nonlinear regression models under scale mixtures of skew-normal (SMSN) distributions is developed. We derive a simple EM-type algorithm for iteratively computing maximum likelihood (ML) estimates and the observed information matrix is derived analytically. Simulation studies demonstrate the robustness of this flexible class against outlying and influential observations, as well as nice asymptotic properties of the proposed EM-type ML estimates. Finally, the methodology is illustrated using an ultrasonic calibration data.

SUBMITTER: Lachos VH

PROVIDER: S-EPMC3126155 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Heteroscedastic nonlinear regression models based on scale mixtures of skew-normal distributions.

Lachos Victor H VH Bandyopadhyay Dipankar D Garay Aldo M AM

Statistics & probability letters 20110801 8

An extension of some standard likelihood based procedures to heteroscedastic nonlinear regression models under scale mixtures of skew-normal (SMSN) distributions is developed. We derive a simple EM-type algorithm for iteratively computing maximum likelihood (ML) estimates and the observed information matrix is derived analytically. Simulation studies demonstrate the robustness of this flexible class against outlying and influential observations, as well as nice asymptotic properties of the propo ...[more]

PMID: 21731152

Similar Datasets

Bayesian Hierarchical Joint Modeling Using Skew-Normal/Independent Distributions.

Project description:The multiple longitudinal outcomes collected in many clinical trials are often analyzed by multilevel item response theory (MLIRT) models. The normality assumption for the continuous outcomes in the MLIRT models can be violated due to skewness and/or outliers. Moreover, patients' follow-up may be stopped by some terminal events (e.g., death or dropout) which are dependent on the multiple longitudinal outcomes. We proposed a joint modeling framework based on the MLIRT model to account for three data features: skewness, outliers, and dependent censoring. Our method development was motivated by a clinical study for Parkinson's disease.

| S-EPMC6114938 | biostudies-literature

A Bayesian Genomic Regression Model with Skew Normal Random Errors.

Project description:Genomic selection (GS) has become a tool for selecting candidates in plant and animal breeding programs. In the case of quantitative traits, it is common to assume that the distribution of the response variable can be approximated by a normal distribution. However, it is known that the selection process leads to skewed distributions. There is vast statistical literature on skewed distributions, but the skew normal distribution is of particular interest in this research. This distribution includes a third parameter that drives the skewness, so that it generalizes the normal distribution. We propose an extension of the Bayesian whole-genome regression to skew normal distribution data in the context of GS applications, where usually the number of predictors vastly exceeds the sample size. However, it can also be applied when the number of predictors is smaller than the sample size. We used a stochastic representation of a skew normal random variable, which allows the implementation of standard Markov Chain Monte Carlo (MCMC) techniques to efficiently fit the proposed model. The predictive ability and goodness of fit of the proposed model were evaluated using simulated and real data, and the results were compared to those obtained by the Bayesian Ridge Regression model. Results indicate that the proposed model has a better fit and is as good as the conventional Bayesian Ridge Regression model for prediction, based on the DIC criterion and cross-validation, respectively. A computing program coded in the R statistical package and C programming language to fit the proposed model is available as supplementary material.

| S-EPMC5940167 | biostudies-literature

Linear and nonlinear mixed-effects models for censored HIV viral loads using normal/independent distributions.

Project description:HIV RNA viral load measures are often subjected to some upper and lower detection limits depending on the quantification assays. Hence, the responses are either left or right censored. Linear (and nonlinear) mixed-effects models (with modifications to accommodate censoring) are routinely used to analyze this type of data and are based on normality assumptions for the random terms. However, those analyses might not provide robust inference when the normality assumptions are questionable. In this article, we develop a Bayesian framework for censored linear (and nonlinear) models replacing the Gaussian assumptions for the random terms with normal/independent (NI) distributions. The NI is an attractive class of symmetric heavy-tailed densities that includes the normal, Student's-t, slash, and the contaminated normal distributions as special cases. The marginal likelihood is tractable (using approximations for nonlinear models) and can be used to develop Bayesian case-deletion influence diagnostics based on the Kullback-Leibler divergence. The newly developed procedures are illustrated with two HIV AIDS studies on viral loads that were initially analyzed using normal (censored) mixed-effects models, as well as simulations.

| S-EPMC6698393 | biostudies-literature

Bayesian multivariate skew meta-regression models for individual patient data.

Project description:We examine a class of multivariate meta-regression models in the presence of individual patient data. The methodology is well motivated from several studies of cholesterol-lowering drugs where the goal is to jointly analyze the multivariate outcomes, low density lipoprotein cholesterol, high density lipoprotein cholesterol, and triglycerides. These three continuous outcome measures are correlated and shed much light on a subject's lipid status. One of the main goals in lipid research is the joint analysis of these three outcome measures in a meta-regression setting. Since these outcome measures are not typically multivariate normal, one must consider classes of distributions that allow for skewness in one or more of the outcomes. In this paper, we consider a new general class of multivariate skew distributions for multivariate meta-regression and examine their theoretical properties. Using these distributions, we construct a Bayesian model for the meta-data and develop an efficient Markov chain Monte Carlo computational scheme for carrying out the computations. In addition, we develop a multivariate L measure for model comparison, Bayesian residuals for model assessment, and a Bayesian procedure for detecting outlying trials. The proposed multivariate L measure, Bayesian residuals, and Bayesian outlying trial detection procedure are particularly suitable and computationally attractive in the multivariate meta-regression setting. A detailed case study demonstrating the usefulness of the proposed methodology is carried out in an individual patient data multivariate meta-regression setting using 26 pivotal Merck clinical trials that compare statins (cholesterol-lowering drugs) in combination with ezetimibe and statins alone on treatment-naïve patients and those continuing on statins at baseline.

| S-EPMC6461541 | biostudies-literature

Modeling absolute differences in life expectancy with a censored skew-normal regression approach.

Project description:Parameter estimates from commonly used multivariable parametric survival regression models do not directly quantify differences in years of life expectancy. Gaussian linear regression models give results in terms of absolute mean differences, but are not appropriate in modeling life expectancy, because in many situations time to death has a negative skewed distribution. A regression approach using a skew-normal distribution would be an alternative to parametric survival models in the modeling of life expectancy, because parameter estimates can be interpreted in terms of survival time differences while allowing for skewness of the distribution. In this paper we show how to use the skew-normal regression so that censored and left-truncated observations are accounted for. With this we model differences in life expectancy using data from the Swiss National Cohort Study and from official life expectancy estimates and compare the results with those derived from commonly used survival regression models. We conclude that a censored skew-normal survival regression approach for left-truncated observations can be used to model differences in life expectancy across covariates of interest.

| S-EPMC4558072 | biostudies-literature

Bayesian Inference of Finite Population Quantiles for Skewed Survey Data Using Skew-Normal Penalized Spline Regression.

Project description:Skewed data are common in sample surveys. In probability proportional to size sampling, we propose two Bayesian model-based predictive methods for estimating finite population quantiles with skewed sample survey data. We assume the survey outcome to follow a skew-normal distribution given the probability of selection and model the location and scale parameters of the skew-normal distribution as functions of the probability of selection. To allow a flexible association between the survey outcome and the probability of selection, the first method models the location parameter with a penalized spline and the scale parameter with a polynomial function, while the second method models both the location and scale parameters with penalized splines. Using a fully Bayesian approach, we obtain the posterior predictive distributions of the nonsampled units in the population and thus the posterior distributions of the finite population quantiles. We show through simulations that our proposed methods are more efficient and yield shorter credible intervals with better coverage rates than the conventional weighted method in estimating finite population quantiles. We demonstrate the application of our proposed methods using data from the 2013 National Drug Abuse Treatment System Survey.

| S-EPMC7473425 | biostudies-literature

Time-scale dependence of solar wind-based regression models of ionospheric electrodynamics

Project description:The solar wind influence on geospace can be described as the sum of a directly driven component, or dayside reconnection, and an unloading component, associated with the release of magnetic energy via nightside reconnection. The two processes are poorly correlated on short time scales, but exactly equal when averaged over long time windows. Because of this peculiar property, regression models of ionospheric electrodynamics that are based on solar wind data are time scale specific: Models derived from 1 min resolution data will be different from models derived from hourly, daily, or monthly data. We explain and quantify this effect on simple linear regression models of various geomagnetic indices. We also derive a time scale-dependent correction factor that can be used with the Average Magnetic field and Polar current System model. Finally, we show how absolute estimates of the nightside reconnection rate can be calculated from solar wind measurements and geomagnetic indices.

| S-EPMC7532543 | biostudies-literature

Bayesian flexible hierarchical skew heavy-tailed multivariate meta regression models for individual patient data with applications.

Project description:A flexible class of multivariate meta-regression models are proposed for Individual Patient Data (IPD). The methodology is well motivated from 26 pivotal Merck clinical trials that compare statins (cholesterol lowering drugs) in combination with ezetimibe and statins alone on treatment-naïve patients and those continuing on statins at baseline. The research goal is to jointly analyze the multivariate outcomes, Low Density Lipoprotein Cholesterol (LDL-C), High Density Lipoprotein Cholesterol (HDL-C), and Triglycerides (TG). These three continuous outcome measures are correlated and shed much light on a subject's lipid status. The proposed multivariate meta-regression models allow for different skewness parameters and different degrees of freedom for the multivariate outcomes from different trials under a general class of skew t-distributions. The theoretical properties of the proposed models are examined and an efficient Markov chain Monte Carlo (MCMC) sampling algorithm is developed for carrying out Bayesian inference under the proposed multivariate meta-regression model. In addition, the Conditional Predictive Ordinates (CPOs) are computed via an efficient Monte Carlo method. Consequently, the logarithm of the pseudo marginal likelihood and Bayesian residuals are obtained for model comparison and assessment, respectively. A detailed analysis of the IPD meta data from the 26 Merck clinical trials is carried out to demonstrate the usefulness of the proposed methodology.

| S-EPMC7448754 | biostudies-literature

Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions.

Project description:Accurate identification of genotypes is an essential part of the analysis of genomic data, including in identification of sequence polymorphisms, linking mutations with disease and determining mutation rates. Biological and technical processes that adversely affect genotyping include copy-number-variation, paralogous sequences, library preparation, sequencing error and reference-mapping biases, among others.We modeled the read depth for all data as a mixture of Dirichlet-multinomial distributions, resulting in significant improvements over previously used models. In most cases the best model was comprised of two distributions. The major-component distribution is similar to a binomial distribution with low error and low reference bias. The minor-component distribution is overdispersed with higher error and reference bias. We also found that sites fitting the minor component are enriched for copy number variants and low complexity regions, which can produce erroneous genotype calls. By removing sites that do not fit the major component, we can improve the accuracy of genotype calls.Methods and data files are available at https://github.com/CartwrightLab/WuEtAl2017/ (doi:10.5281/zenodo.256858).cartwright@asu.edu.Supplementary data is available at Bioinformatics online.

| S-EPMC5860108 | biostudies-literature

Linear mixed models for skew-normal/independent bivariate responses with an application to periodontal disease.

Project description:Bivariate clustered (correlated) data often encountered in epidemiological and clinical research are routinely analyzed under a linear mixed model (LMM) framework with underlying normality assumptions of the random effects and within-subject errors. However, such normality assumptions might be questionable if the data set particularly exhibits skewness and heavy tails. Using a Bayesian paradigm, we use the skew-normal/independent (SNI) distribution as a tool for modeling clustered data with bivariate non-normal responses in an LMM framework. The SNI distribution is an attractive class of asymmetric thick-tailed parametric structure which includes the skew-normal distribution as a special case. We assume that the random effects follow multivariate SNI distributions and the random errors follow SNI distributions which provides substantial robustness over the symmetric normal process in an LMM framework. Specific distributions obtained as special cases, viz. the skew-t, the skew-slash and the skew-contaminated normal distributions are compared, along with the default skew-normal density. The methodology is illustrated through an application to a real data which records the periodontal health status of an interesting population using periodontal pocket depth (PPD) and clinical attachment level (CAL).

| S-EPMC2962692 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data