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Maximum Likelihood Methods (maximum + likelihood_methods)
Selected AbstractsFlexible Maximum Likelihood Methods for Bivariate Proportional Hazards ModelsBIOMETRICS, Issue 4 2003Wenqing He Summary. This article presents methodology for multivariate proportional hazards (PH) regression models. The methods employ flexible piecewise constant or spline specifications for baseline hazard functions in either marginal or conditional PH models, along with assumptions about the association among lifetimes. Because the models are parametric, ordinary maximum likelihood can be applied; it is able to deal easily with such data features as interval censoring or sequentially observed lifetimes, unlike existing semiparametric methods. A bivariate Clayton model (1978, Biometrika65, 141,151) is used to illustrate the approach taken. Because a parametric assumption about association is made, efficiency and robustness comparisons are made between estimation based on the bivariate Clayton model and "working independence" methods that specify only marginal distributions for each lifetime variable. [source] Maximum Likelihood Methods for Nonignorable Missing Responses and Covariates in Random Effects ModelsBIOMETRICS, Issue 4 2003Amy L. Stubbendick Summary. This article analyzes quality of life (QOL) data from an Eastern Cooperative Oncology Group (ECOG) melanoma trial that compared treatment with ganglioside vaccination to treatment with high-dose interferon. The analysis of this data set is challenging due to several difficulties, namely, nonignorable missing longitudinal responses and baseline covariates. Hence, we propose a selection model for estimating parameters in the normal random effects model with nonignorable missing responses and covariates. Parameters are estimated via maximum likelihood using the Gibbs sampler and a Monte Carlo expectation maximization (EM) algorithm. Standard errors are calculated using the bootstrap. The method allows for nonmonotone patterns of missing data in both the response variable and the covariates. We model the missing data mechanism and the missing covariate distribution via a sequence of one-dimensional conditional distributions, allowing the missing covariates to be either categorical or continuous, as well as time-varying. We apply the proposed approach to the ECOG quality-of-life data and conduct a small simulation study evaluating the performance of the maximum likelihood estimates. Our results indicate that a patient treated with the vaccine has a higher QOL score on average at a given time point than a patient treated with high-dose interferon. [source] Scales of association: hierarchical linear models and the measurement of ecological systemsECOLOGY LETTERS, Issue 6 2007Sean M. McMahon Abstract A fundamental challenge to understanding patterns in ecological systems lies in employing methods that can analyse, test and draw inference from measured associations between variables across scales. Hierarchical linear models (HLM) use advanced estimation algorithms to measure regression relationships and variance,covariance parameters in hierarchically structured data. Although hierarchical models have occasionally been used in the analysis of ecological data, their full potential to describe scales of association, diagnose variance explained, and to partition uncertainty has not been employed. In this paper we argue that the use of the HLM framework can enable significantly improved inference about ecological processes across levels of organization. After briefly describing the principals behind HLM, we give two examples that demonstrate a protocol for building hierarchical models and answering questions about the relationships between variables at multiple scales. The first example employs maximum likelihood methods to construct a two-level linear model predicting herbivore damage to a perennial plant at the individual- and patch-scale; the second example uses Bayesian estimation techniques to develop a three-level logistic model of plant flowering probability across individual plants, microsites and populations. HLM model development and diagnostics illustrate the importance of incorporating scale when modelling associations in ecological systems and offer a sophisticated yet accessible method for studies of populations, communities and ecosystems. We suggest that a greater coupling of hierarchical study designs and hierarchical analysis will yield significant insights on how ecological processes operate across scales. [source] Feedforward joint phase and timing estimation for MSK,type signalsEUROPEAN TRANSACTIONS ON TELECOMMUNICATIONS, Issue 4 2001Michele Morelli Novel non data,aided (NDA) algorithms are proposed for joint estimation of timing and carrier phase in MSK,type modulations. They are based on maximum likelihood methods and have a feedforward structure which is suitable to fully digital implementation. Performance with MSK and Gaussian MSK. (GMSK) is assessed by computer simulations and compared with that of other existing estimation schemes. [source] A global study of relationships between leaf traits, climate and soil measures of nutrient fertilityGLOBAL ECOLOGY, Issue 2 2009Jenny C. Ordoñez ABSTRACT Aim This first global quantification of the relationship between leaf traits and soil nutrient fertility reflects the trade-off between growth and nutrient conservation. The power of soils versus climate in predicting leaf trait values is assessed in bivariate and multivariate analyses and is compared with the distribution of growth forms (as a discrete classification of vegetation) across gradients of soil fertility and climate. Location All continents except for Antarctica. Methods Data on specific leaf area (SLA), leaf N concentration (LNC), leaf P concentration (LPC) and leaf N:P were collected for 474 species distributed across 99 sites (809 records), together with abiotic information from each study site. Individual and combined effects of soils and climate on leaf traits were quantified using maximum likelihood methods. Differences in occurrence of growth form across soil fertility and climate were determined by one-way ANOVA. Results There was a consistent increase in SLA, LNC and LPC with increasing soil fertility. SLA was related to proxies of N supply, LNC to both soil total N and P and LPC was only related to proxies of P supply. Soil nutrient measures explained more variance in leaf traits among sites than climate in bivariate analysis. Multivariate analysis showed that climate interacted with soil nutrients for SLA and area-based LNC. Mass-based LNC and LPC were determined mostly by soil fertility, but soil P was highly correlated to precipitation. Relationships of leaf traits to soil nutrients were stronger than those of growth form versus soil nutrients. In contrast, climate determined distribution of growth form more strongly than it did leaf traits. Main conclusions We provide the first global quantification of the trade-off between traits associated with growth and resource conservation ,strategies' in relation to soil fertility. Precipitation but not temperature affected this trade-off. Continuous leaf traits might be better predictors of plant responses to nutrient supply than growth form, but growth forms reflect important aspects of plant species distribution with climate. [source] Inverse Modeling of Coastal Aquifers Using Tidal Response and Hydraulic TestsGROUND WATER, Issue 6 2007Andrés Alcolea Remediation of contaminated aquifers demands a reliable characterization of hydraulic connectivity patterns. Hydraulic diffusivity is possibly the best indicator of connectivity. It can be derived using the tidal response method (TRM), which is based on fitting observations to a closed-form solution. Unfortunately, the conventional TRM assumes homogeneity. The objective of this study was to overcome this limitation and use tidal response to identify preferential flowpaths. Additionally, the procedure requires joint inversion with hydraulic test data. These provide further information on connectivity and are needed to resolve diffusivity into transmissivity and storage coefficient. Spatial variability is characterized using the regularized pilot points method. Actual application may be complicated by the need to filter tidal effects from the response to pumping and by the need to deal with different types of data, which we have addressed using maximum likelihood methods. Application to a contaminated artificial coastal fill leads to flowpaths that are consistent with the materials used during construction and to solute transport predictions that compare well with observations. We conclude that tidal response can be used to identify connectivity patterns. As such, it should be useful when designing measures to control sea water intrusion. [source] Heritability of human cranial dimensions: comparing the evolvability of different cranial regionsJOURNAL OF ANATOMY, Issue 1 2009Neus Martínez-Abadías Abstract Quantitative craniometrical traits have been successfully incorporated into population genetic methods to provide insight into human population structure. However, little is known about the degree of genetic and non-genetic influences on the phenotypic expression of functionally based traits. Many studies have assessed the heritability of craniofacial traits, but complex patterns of correlation among traits have been disregarded. This is a pitfall as the human skull is strongly integrated. Here we reconsider the evolutionary potential of craniometric traits by assessing their heritability values as well as their patterns of genetic and phenotypic correlation using a large pedigree-structured skull series from Hallstatt (Austria). The sample includes 355 complete adult skulls that have been analysed using 3D geometric morphometric techniques. Heritability estimates for 58 cranial linear distances were computed using maximum likelihood methods. These distances were assigned to the main functional and developmental regions of the skull. Results showed that the human skull has substantial amounts of genetic variation, and a t -test showed that there are no statistically significant differences among the heritabilities of facial, neurocranial and basal dimensions. However, skull evolvability is limited by complex patterns of genetic correlation. Phenotypic and genetic patterns of correlation are consistent but do not support traditional hypotheses of integration of the human shape, showing that the classification between brachy- and dolicephalic skulls is not grounded on the genetic level. Here we support previous findings in the mouse cranium and provide empirical evidence that covariation between the maximum widths of the main developmental regions of the skull is the dominant factor of integration in the human skull. [source] SOME PHYLOGENETIC RELATIONSHIPS WITHIN THE OSCILLATORIALES (CYANOBACTERIA) CLADE USING 16S RDNA GENE SEQUENCE DATAJOURNAL OF PHYCOLOGY, Issue 2000D.A. Casamatta An approximately 1400 base pair region of the 16S rDNA gene was sequenced from taxa within the Oscillatoriales in order to assess phylogenetic relationships. Ten previously unsequenced strains were obtained from the University of Toronto Culture Collection. New sequence data were combined with previously published sequences from a wide representation of cyanobacteria including all currently available, complete Oscillatorialian taxa. Trees constructed using parsimony, distance, and maximum likelihood methods were similar in topology, although a few taxa were variable in their placement depending on the phylogenetic method employed. Newly sequenced taxa of the genera Phormidium, Oscillatoria, and Lyngbya did not form monophyletic clades based on traditional generic designations. Two Lyngbya strains (UTCC296 and 313) and Phormidium subfuscum (UTCC474) formed a well supported monophyletic clade, but the affinity of this clade with other groups was uncertain due to lack of bootstrap support. Oscillatoria sp. (UTCC393) was closely related to the previously sequenced Oscillatoria limnetica and likewise, Phormidium molle (UTCC77) and Phormidium tenue (UTCC473) were placed in a well supported clade with other Oscillatoriales. The other four taxa were variously placed in the trees and their phylogenetic positions could not be determined with certainty. [source] Maximum likelihood inference on a mixed conditionally and marginally specified regression model for genetic epidemiologic studies with two-phase samplingJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES B (STATISTICAL METHODOLOGY), Issue 2 2007Nilanjan Chatterjee Summary., Two-phase stratified sampling designs can reduce the cost of genetic epidemiologic studies by limiting expensive ascertainments of genetic and environmental exposure to an efficiently selected subsample (phase II) of the main study (phase I). Family history and some covariate information, which may be cheaply gathered for all subjects at phase I, can be used for sampling of informative subjects at phase II. We develop alternative maximum likelihood methods for analysis of data from such studies by using a novel regression model that permits the estimation of ,marginal' risk parameters that are associated with the genetic and environmental covariates of interest, while simultaneously characterizing the ,conditional' risk of the disease associated with family history after adjusting for the other covariates. The methods and appropriate asymptotic theories are developed with and without an assumption of gene,environment independence, allowing the distribution of the environmental factors to remain non-parametric. The performance of the alternative methods and of sampling strategies is studied by using simulated data involving rare and common genetic variants. An application of the methods proposed is illustrated by using a case,control study of colorectal adenoma embedded within the prostate, lung, colorectal and ovarian cancer screening trial. [source] Estimating the transmission probability of human immunodeficiency virus in injecting drug users in ThailandJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES C (APPLIED STATISTICS), Issue 1 2001Michael G. Hudgens We estimate the transmission probability for the human immunodeficiency virus from seroconversion data of a cohort of injecting drug users (IDUs) in Thailand. The transmission probability model developed accounts for interval censoring and incorporates each IDU's reported frequency of needle sharing and injecting acts. Using maximum likelihood methods, the per needle sharing act transmission probability estimate between infectious and susceptible IDUs is 0.008. The effects of covariates, disease dynamics, mismeasured exposure information and the uncertainty of the disease prevalence on the transmission probability estimate are considered. [source] Bayesian analysis of switching ARCH modelsJOURNAL OF TIME SERIES ANALYSIS, Issue 4 2002SYLVIA KAUFMANN We consider a time series model with autoregressive conditional heteroscedasticity that is subject to changes in regime. The regimes evolve according to a multistate latent Markov switching process with unknown transition probabilities, and it is the constant in the variance process of the innovations that is subject to regime shifts. The joint estimation of the latent process and all model parameters is performed within a Bayesian framework using the method of Markov chain Monte Carlo (MCMC) simulation. We perform model selection with respect to the number of states and the number of autoregressive parameters in the variance process using Bayes factors and model likelihoods. To this aim, the model likelihood is estimated by the method of bridge sampling. The usefulness of the sampler is demonstrated by applying it to the data set previously used by Hamilton and Susmel (1994) who investigated models with switching autoregressive conditional heteroscedasticity using maximum likelihood methods. The paper concludes with some issues related to maximum likelihood methods, to classical model selection, and to potential straightforward extensions of the model presented here. [source] Phylogenetic inference regarding Parergodrilidae and Hrabeiella periglandulata (,Polychaeta', Annelida) based on 18S rDNA, 28S rDNA and COI sequencesJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2004J. Jördens Abstract Parergodrilidae and Hrabeiella periglandulata are Annelida showing different combinations of clitellate-like and aclitellate characters. Similarities between both of these taxa and Clitellata have widely been regarded as the result of convergent evolution due to similar selection pressures. The position of the three taxa in the phylogenetic system of Annelida is still in debate. However, in analyses based on 18S rDNA sequences a close relationship of Parergodrilidae with Orbiniidae and Questidae was suggested. To infer their phylogeny the sequences of the 28S rDNA and of the cytochrome oxidase I (COI) gene of Stygocapitella subterranea, Parergodrilus heideri and H. periglandulata were determined. The data were extended by sequences of various species including species from Clitellata and Orbiniidae. Prior to tree reconstruction the dataset was analysed in detail for phylogenetic content by applying a sliding window analysis, a likelihood mapping and Modeltest V.3.04. Subsequently, generalized parsimony and maximum likelihood methods were employed. Clade robustness was estimated by bootstrapping. In addition, combined analyses of the sequences of 18S rDNA and 28S rDNA as well as of 18S rDNA, 28S rDNA and COI were performed. The combination of the data of the two structure genes and a mitochondrial gene improved the resolution obtained with the single datasets slightly. These analyses support a close relationship of Parergodrilidae and Orbiniidae but cannot resolve the position of H. periglandulata. In every analysis Clitellata cluster within ,Polychaeta', confirming previous investigations. Zusammenfassung Die Parergodrilidae und Hrabeiella periglandulata sind Annelida, die unterschiedliche Kombinationen von Clitellaten- und Nicht-Clitellaten-Merkmalen aufweisen. Die Übereinstimmungen zwischen Parergodrilidae, H. periglandulata und Clitellata sind jedoch meistens als Ergebnis konvergenter Evolution auf Grund ähnlicher Selektionsdrücke gedeutet worden. Die Stellung der drei Taxa im phylogenetischen System der Annelida ist noch immer in Diskussion. Analysen, die auf 18S rDNA Sequenzen basieren, weisen jedoch auf eine wahrscheinliche engere Verwandtschaft der Parergodrilidae mit den Orbiniidae und Questidae hin. Um die Phylogenie dieser Taxa aufzuklären, wurden die Sequenzen der 28S rDNA und des COI Gens von Stygocapitella subterranea, P. heideri and H. periglandulata bestimmt. Die Daten wurden durch Sequenzen verschiedener weiterer Arten erweitert, die auch Arten der Clitellata und Orbiniidae umfassen. Vor der phylogenetischen Rekonstruktion wurde der Datensatz im Detail auf das enthaltene phylogenetische Signal durch eine Sliding Window Analyse, ein Likelihood Mapping und Modeltest V.3.04 getestet. Anschließend wurden generalisierte Parsimonie und Maximum Likelihood Methoden angewendet. Die Robustheit der Bäume wurde durch Parsimonie-Bootstrapping abgeschätzt. Zusätzlich wurden kombinierte Analysen der Sequenzen von 18S rDNA und 28S rDNA als auch von 18S rDNA, 28S rDNA und COI durchgeführt. Die Kombination der Daten der beiden Strukturgene und eines mitochondrialen Gens verbesserten geringfügig die Auflösung verglichen mit den Einzelanalysen. Diese Analysen unterstützen eine nahe Verwandtschaft der Parergodrilidae mit den Orbiniidae aber die Stellung von H. periglandulata kann nicht angegeben werden. In jeder Analyse bilden die Clitellata ein Cluster innerhalb der ,Polychaeta', eine Bestätigung früherer Untersuchungen. [source] Molecular identification of some forensically important blowflies of southern Africa and AustraliaMEDICAL AND VETERINARY ENTOMOLOGY, Issue 4 2003M. L. Harvey Abstract., One major aspect of research in forensic entomology is the investigation of molecular techniques for the accurate identification of insects. Studies to date have addressed the corpse fauna of many geographical regions, but generally neglected the southern African calliphorid species. In this study, forensically significant calliphorids from South Africa, Swaziland, Botswana and Zimbabwe and Australia were sequenced over an 1167 base pair region of the COI gene. Phylogenetic analysis was performed to examine the ability of the region to resolve species identities and taxonomic relationships between species. Analyses by neighbour-joining, maximum parsimony and maximum likelihood methods all showed the potential of this region to provide the necessary species-level identifications for application to post-mortem interval (PMI) estimation; however, higher level taxonomic relationships did vary according to method of analysis. Intraspecific variation was also considered in relation to determining suitable maximum levels of variation to be expected during analysis. Individuals of some species in the study represented populations from both South Africa and the east coast of Australia, yet maximum intraspecific variation over this gene region was calculated at 0.8%, with minimum interspecific variation at 3%, indicating distinct ranges of variation to be expected at intra- and interspecific levels. This region therefore appears to provide southern African forensic entomologists with a new technique for providing accurate identification for application to estimation of PMI. [source] A quantitative genetic analysis of intermediate asthma phenotypesALLERGY, Issue 3 2009S. F. Thomsen Aim:, To study the relative contribution of genetic and environmental factors to the correlation between exhaled nitric oxide (FeNO), airway responsiveness, airway obstruction, and serum total immunoglobulin E (IgE). Methods:, Within a sampling frame of 21 162 twin subjects, 20,49 years of age, from the Danish Twin Registry, a total of 575 subjects (256 intact pairs and 63 single twins) who either themselves and/or their co-twins reported a history of asthma at a nationwide questionnaire survey, were clinically examined. Traits were measured using standard techniques. Latent factor models were fitted to the observed data using maximum likelihood methods. Results:, Additive genetic factors explained 67% of the variation in FeNO, 43% in airway responsiveness, 22% in airway obstruction, and 81% in serum total IgE. In general, traits had genetically and environmentally distinct variance structures. The most substantial genetic similarity was observed between FeNO and serum total IgE, genetic correlation (,A) = 0.37, whereas the strongest environmental resemblance was observed between airway responsiveness and airway obstruction, specific environmental correlation (,E) = ,0.46, and between FeNO and airway responsiveness, ,E = 0.34. Conclusions:, Asthma is a complex disease characterized by a set of etiologically heterogeneous biomarkers, which likely constitute diverse targets of intervention. [source] Revisiting the Phylogenetic Position of Synchroma grandeTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 4 2009VISHWANATH PATIL ABSTRACT. Two new classes Synchromophyceae and Picophagea, belonging to the heterokonts, have been proposed recently in separate studies of 18S rRNA phylogenies. Here we revise the 18S phylogeny of these classes by including all available sequenced species and applying Bayesian and maximum likelihood methods; Synchroma grande groups with the photophagotrophic Chlamydomyxa labyrinthuloides with high statistical support. This clade is sister to Chrysophyceae, together they share a common ancestry. Our results show that the creation of class Synchromophyceae by Horn et al. was premature, because they did not include data from the closely related C. labyrinthuloides and Picophagus flagellatus species. A revision of these classes should include additional species and most likely multigene phylogenies. [source] | ||||||||||||||||