32,388 research outputs found
Generalized structured additive regression based on Bayesian P-splines
Generalized additive models (GAM) for modelling nonlinear effects of continuous covariates are now well established tools for the applied statistician. In this paper we develop Bayesian GAM's and extensions to generalized structured additive regression based on one or two dimensional P-splines as the main building block. The approach extends previous work by Lang und Brezger (2003) for Gaussian responses. Inference relies on Markov chain Monte Carlo (MCMC) simulation techniques, and is either based on iteratively weighted least squares (IWLS) proposals or on latent utility representations of (multi)categorical regression models. Our approach covers the most common univariate response distributions, e.g. the Binomial, Poisson or Gamma distribution, as well as multicategorical responses. For the first time, we present Bayesian semiparametric inference for the widely used multinomial logit models. As we will demonstrate through two applications on the forest health status of trees and a space-time analysis of health insurance data, the approach allows realistic modelling of complex problems. We consider the enormous flexibility and extendability of our approach as a main advantage of Bayesian inference based on MCMC techniques compared to more traditional approaches. Software for the methodology presented in the paper is provided within the public domain package BayesX
Inbreeding depression in red deer calves
BACKGROUND Understanding the fitness consequences of inbreeding is of major importance for evolutionary and conservation biology. However, there are few studies using pedigree-based estimates of inbreeding or investigating the influence of environment and age variation on inbreeding depression in natural populations. Here we investigated the consequences of variation in inbreeding coefficient for three juvenile traits, birth date, birth weight and first year survival, in a wild population of red deer, considering both calf and mother's inbreeding coefficient. We also tested whether inbreeding depression varied with environmental conditions and maternal age. RESULTS We detected non-zero inbreeding coefficients for 22% of individuals with both parents and at least one grandparent known (increasing to 42% if the dataset was restricted to those with four known grandparents). Inbreeding depression was evident for birth weight and first year survival but not for birth date: the first year survival of offspring with an inbreeding coefficient of 0.25 was reduced by 77% compared to offspring with an inbreeding coefficient of zero. However, it was independent of measures of environmental variation and maternal age. The effect of inbreeding on birth weight appeared to be driven by highly inbred individuals (F = 0.25). On the other hand first year survival showed strong inbreeding depression that was not solely driven by individuals with the highest inbreeding coefficients, corresponding to an estimate of 4.35 lethal equivalents. CONCLUSIONS These results represent a rare demonstration of inbreeding depression using pedigree-based estimates in a wild mammal population and highlight the potential strength of effects on key components of fitness.This research was
supported by a NERC grant to LEBK, JMP and THCB, NERC and BBSRC
fellowships to DHN and a Royal Society fellowship to LEBK
Bayesian Model Comparison in Genetic Association Analysis: Linear Mixed Modeling and SNP Set Testing
We consider the problems of hypothesis testing and model comparison under a
flexible Bayesian linear regression model whose formulation is closely
connected with the linear mixed effect model and the parametric models for SNP
set analysis in genetic association studies. We derive a class of analytic
approximate Bayes factors and illustrate their connections with a variety of
frequentist test statistics, including the Wald statistic and the variance
component score statistic. Taking advantage of Bayesian model averaging and
hierarchical modeling, we demonstrate some distinct advantages and
flexibilities in the approaches utilizing the derived Bayes factors in the
context of genetic association studies. We demonstrate our proposed methods
using real or simulated numerical examples in applications of single SNP
association testing, multi-locus fine-mapping and SNP set association testing
Methods for Population Adjustment with Limited Access to Individual Patient Data: A Review and Simulation Study
Population-adjusted indirect comparisons estimate treatment effects when
access to individual patient data is limited and there are cross-trial
differences in effect modifiers. Popular methods include matching-adjusted
indirect comparison (MAIC) and simulated treatment comparison (STC). There is
limited formal evaluation of these methods and whether they can be used to
accurately compare treatments. Thus, we undertake a comprehensive simulation
study to compare standard unadjusted indirect comparisons, MAIC and STC across
162 scenarios. This simulation study assumes that the trials are investigating
survival outcomes and measure continuous covariates, with the log hazard ratio
as the measure of effect. MAIC yields unbiased treatment effect estimates under
no failures of assumptions. The typical usage of STC produces bias because it
targets a conditional treatment effect where the target estimand should be a
marginal treatment effect. The incompatibility of estimates in the indirect
comparison leads to bias as the measure of effect is non-collapsible. Standard
indirect comparisons are systematically biased, particularly under stronger
covariate imbalance and interaction effects. Standard errors and coverage rates
are often valid in MAIC but the robust sandwich variance estimator
underestimates variability where effective sample sizes are small. Interval
estimates for the standard indirect comparison are too narrow and STC suffers
from bias-induced undercoverage. MAIC provides the most accurate estimates and,
with lower degrees of covariate overlap, its bias reduction outweighs the loss
in effective sample size and precision under no failures of assumptions. An
important future objective is the development of an alternative formulation to
STC that targets a marginal treatment effect.Comment: 73 pages (34 are supplementary appendices and references), 8 figures,
2 tables. Full article (following Round 4 of minor revisions). arXiv admin
note: text overlap with arXiv:2008.0595
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