Search results for "Likelihood Functions"
showing 10 items of 101 documents
Population genetic analysis of bi-allelic structural variants from low-coverage sequence data with an expectation-maximization algorithm
2014
Background Population genetics and association studies usually rely on a set of known variable sites that are then genotyped in subsequent samples, because it is easier to genotype than to discover the variation. This is also true for structural variation detected from sequence data. However, the genotypes at known variable sites can only be inferred with uncertainty from low coverage data. Thus, statistical approaches that infer genotype likelihoods, test hypotheses, and estimate population parameters without requiring accurate genotypes are becoming popular. Unfortunately, the current implementations of these methods are intended to analyse only single nucleotide and short indel variation…
Melastomeae come full circle: biogeographic reconstruction and molecular clock dating.
2001
Rhexia, with 11 species in the Coastal Plain province of North America, is the only temperate zone endemic of the tropical eudicot family Melastomataceae. It is a member of the only pantropical tribe of that family, Melastomeae. Based on the chloroplast gene ndhF, we use a fossil-calibrated molecular clock to address the question of the geographic origin and age of Rhexia. Sequences from 37 species in 21 genera representing the tribe's geographical range were analyzed together with five outgroups. To obtain better clade support, another chloroplast region, the rpl16 intron, was added for 24 of the species. Parsimony analysis of the combined data and maximum-likelihood analysis of ndhF alone…
Characterizing the collective personality of ant societies: aggressive colonies do not abandon their home.
2011
Animal groups can show consistent behaviors or personalities just like solitary animals. We studied the collective behavior of Temnothorax nylanderi ant colonies, including consistency in behavior and correlations between different behavioral traits. We focused on four collective behaviors (aggression against intruders, nest relocation, removal of infected corpses and nest reconstruction) and also tested for links to the immune defense level of a colony and a fitness component (per-capita productivity). Behaviors leading to an increased exposure of ants to micro-parasites were expected to be positively associated with immune defense measures and indeed colonies that often relocated to other…
Inferential tools in penalized logistic regression for small and sparse data: A comparative study.
2016
This paper focuses on inferential tools in the logistic regression model fitted by the Firth penalized likelihood. In this context, the Likelihood Ratio statistic is often reported to be the preferred choice as compared to the ‘traditional’ Wald statistic. In this work, we consider and discuss a wider range of test statistics, including the robust Wald, the Score, and the recently proposed Gradient statistic. We compare all these asymptotically equivalent statistics in terms of interval estimation and hypothesis testing via simulation experiments and analyses of two real datasets. We find out that the Likelihood Ratio statistic does not appear the best inferential device in the Firth penal…
Weighted Least-Squares Likelihood Ratio Test for Branch Testing in Phylogenies Reconstructed from Distance Measures
2005
A variety of analytical methods is available for branch testing in distance-based phylogenies. However, these methods are rarely used, possibly because the estimation of some of their statistics, especially the covariances, is not always feasible. We show that these difficulties can be overcome if some simplifying assumptions are made, namely distance independence. The weighted least-squares likelihood ratio test (WLS-LRT) we propose is easy to perform, using only the distances and some of their associated variances. If no variances are known, the use of the Felsenstein F-test, also based on weighted least squares, is discussed. Using simulated data and a data set of 43 mammalian mitochondr…
Efficient estimation of generalized linear latent variable models.
2019
Generalized linear latent variable models (GLLVM) are popular tools for modeling multivariate, correlated responses. Such data are often encountered, for instance, in ecological studies, where presence-absences, counts, or biomass of interacting species are collected from a set of sites. Until very recently, the main challenge in fitting GLLVMs has been the lack of computationally efficient estimation methods. For likelihood based estimation, several closed form approximations for the marginal likelihood of GLLVMs have been proposed, but their efficient implementations have been lacking in the literature. To fill this gap, we show in this paper how to obtain computationally convenient estim…
Sample size planning of two-arm superiority and noninferiority survival studies with discrete follow-up
2016
In clinical trials using lifetime as primary outcome variable, it is more the rule than the exception that even for patients who are failing in the course of the study, survival time does not become known exactly since follow-up takes place according to a restricted schedule with fixed, possibly long intervals between successive visits. In practice, the discreteness of the data obtained under such circumstances is plainly ignored both in data analysis and in sample size planning of survival time studies. As a framework for analyzing the impact of making no difference between continuous and discrete recording of failure times, we use a scenario in which the partially observed times are assig…
Use of xylitol chewing gum among Finnish schoolchildren
2000
The preventive, and partly the remineralizing, effect of xylitol was shown in Finland in the Turku Sugar Studies in 1971-73. Since then, several clinical trials in many countries have confirmed these results. In Finland, oral health personnel have recommended daily use of xylitol chewing gum in their dental health education. Moreover, commercial companies have advertised xylitol, emphasizing in particular its caries preventive effects. All Nordic dental associations have given their recommendations for xylitol use. The aim of this study was to describe how this health habit has been adopted by Finnish schoolchildren. The study was part of the comprehensive cross-national survey on Health Be…
A novel family of tRNA-derived SINEs in the colugo and two new retrotransposable markers separating dermopterans from primates.
2003
Abstract Short interspersed nuclear elements (SINEs) provide a near homoplasy free and copious source of molecular evolutionary markers with precisely defined character polarity. Used as molecular cladistic markers in presence/absence analyses, they represent a powerful complement to phylogenetic reconstructions that are based on sequence comparisons on the level of nucleotide substitutions. Recent sequence comparisons of large data sets incorporating a broad eutherian taxonomic sample have led to considerations of the different primate infraorders to constitute a paraphyletic group. Statistically significant support against the monophyly of primates has been obtained by clustering the flyi…
The heritability of depressive symptoms: multiple informants and multiple measures
2002
Background: Earlier research suggests large rater differences in heritability estimates of children's depressive symptoms in the context of significant age and sex-limitation effects. Methods: With data from an ongoing, population-based twin-family study, we estimated genetic and environmental influences on children's depression with models allowing for sex-specific effects. Our assessments of twins included self-reports and ratings made by their classmate peers, their parents and their teachers, allowing estimates of genetic and environmental effects with data from different informants. Model-fitting used maximum likelihood estimation of log-transformed data from a sample of 1,366 11- and …