FlexMix Version 2: Finite Mixtures with Concomitant Variables and Varying and Constant Parameters

Grün, Bettina; Leisch, Friedrich

doi:10.18637/jss.v028.i04

Cited by 340 publications

(264 citation statements)

References 43 publications

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“…Bacterial community analyses including β-diversity metrics (BC, JA) and analysis of dissimilarity (adonis, which performs a multidimensional ANOVA on distance matrices and was applied to β-diversity metrics) were carried out using the VEGAN R package (24). The JS distance was calculated using the "flexmix" R package (25). Weighted and unweighted UniFrac distance matrices as well as phylogenetic diversity (PD) (26) were calculated from a maximum-likelihood tree constructed by FastTree (27) as implemented in MOTHUR.…”

Section: Methodsmentioning

confidence: 99%

Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice

Wang

Linnenbrink

Künzel

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

151

153

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Understanding the origins of gut microbial community structure is critical for the identification and interpretation of potential fitnessrelated traits for the host. The presence of community clusters characterized by differences in the abundance of signature taxa, referred to as enterotypes, is a debated concept first reported in humans and later extended to other mammalian hosts. In this study, we provide a thorough assessment of their existence in wild house mice using a panel of evaluation criteria. We identify support for two clusters that are compositionally similar to clusters identified in humans, chimpanzees, and laboratory mice, characterized by differences in Bacteroides, Robinsoniella, and unclassified genera belonging to the family Lachnospiraceae. To further evaluate these clusters, we (i) monitored community changes associated with moving mice from the natural to a laboratory environment, (ii) performed functional metagenomic sequencing, and (iii) subjected wild-caught samples to stable isotope analysis to reconstruct dietary patterns. This process reveals differences in the proportions of genes involved in carbohydrate versus protein metabolism in the functional metagenome, as well as differences in plant-versus meat-derived food sources between clusters. In conjunction with wild-caught mice quickly changing their enterotype classification upon transfer to a standard laboratory chow diet, these results provide strong evidence that dietary history contributes to the presence of enterotype-like clustering in wild mice.

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Section: Methodsmentioning

confidence: 99%

Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice

Wang

Linnenbrink

Künzel

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

151

153

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“…To gain more insight into the mixture model hypothesis, we used the flexmix software package (Grün & Leisch, 2008) to fit one-, two-, and three-component mixture models to the log pause data for InWord, Word, and Bursts (the number of events per student for the other event types is too small for the mixture modeling estimation). This package uses the EM algorithm (Dempster, Laird, & Rubin, 1977) to estimate the mean and variance of each mixture component, as well as estimating the probability that each data point comes from each cluster.…”

Section: Distribution Of Lengths Of Pause Data Vectorsmentioning

confidence: 99%

A Preliminary Analysis of Keystroke Log Data From a Timed Writing Task

Almond

Deane

Quinlan

et al. 2012

ETS Research Report Series

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Since its 1947 founding, ETS has conducted and disseminated scientific research to support its products and services, and to advance the measurement and education fields. In keeping with these goals, ETS is committed to making its research freely available to the professional community and to the general public. Published accounts of ETS research, including papers in the ETS Research Report series, undergo a formal peer-review process by ETS staff to ensure that they meet established scientific and professional standards. All such ETS-conducted peer reviews are in addition to any reviews that outside organizations may provide as part of their own publication processes. AbstractThe Fall 2007 and Spring 2008 pilot tests for the CBAL™ Writing assessment included experimental keystroke logging capabilities. This report documents the approaches used to capture the keystroke logs and the algorithms used to process the outputs. It also includes some preliminary findings based on the pilot data. In particular, it notes that the distribution of most of the pause length is consistent with data generated from a mixture of lognormal distributions. This corresponds to a cognitive model in which some pauses are merely part of the transcription (i.e., typing) process and some are part of more involved cognitive process (e.g., attention to writing conventions, word choice, and planning). In the pilot data, many of the features extracted from the keystroke logs were correlated with human scores. Due to the small sample sizes of the pilot studies, these findings are suggestive, not conclusive; however, they suggest a line of analysis for a large sample containing keystroke logging ga thered in the fall of 2009.

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“…to use the name of latent class regression model to refer to regression models in which the dependent variable is partitioned into latent classes as part of estimating the regression model. More than one regression are simultaneously fitted to the data when the latent data partition is unknown (Grün and Leisch 2008). In this article we would rather prefer the name latent class model with covariates or concomitant-variable latent class model.…”

Section: Mixture Models With Covariatesmentioning

confidence: 99%

A latent class analysis of the public attitude towards the euro adoption in Poland

Genge

2013

Adv Data Anal Classif

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Latent class analysis can be viewed as a special case of model-based clustering for multivariate discrete data. It is assumed that each observation comes from one of a number of classes, groups or subpopulations, with its own probability distribution. The overall population thus follows a finite mixture model. When observed, data take the form of categorical responses-as, for example, in public opinion or consumer behavior surveys it is often of interest to identify and characterize clusters of similar objects. In the context of marketing research, one will typically interpret the latent number of mixture components as clusters or segments. In fact, LC analysis provides a powerful new tool to identify important market segments in target marketing. We used the model based clustering approach for grouping and detecting inhomogeneities of Polish opinions on the euro adoption. We analyzed data collected as part of the Polish General Social Survey using the R software.

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FlexMix Version 2: Finite Mixtures with Concomitant Variables and Varying and Constant Parameters

Cited by 340 publications

References 43 publications

Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice

Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice

A Preliminary Analysis of Keystroke Log Data From a Timed Writing Task

A latent class analysis of the public attitude towards the euro adoption in Poland

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