Literature DB >> 19067331

Parametric models for estimating the number of classes.

John Bunge1, Kathryn Barger.   

Abstract

We consider parametric distributions intended to model heterogeneity in population size estimation, especially parametric stochastic abundance models for species richness estimation. We briefly review (conditional) maximum likelihood estimation of the number of species, and summarize the results of fitting 7 candidate models to frequency-count data, from a database of >40000 such instances, mostly arising from microbial ecology. We consider error estimation, goodness-of-fit assessment, data subsetting, and other practical matters. We find that, although the array of candidate models can be improved, finite mixtures of a small number of components (point masses or simple diffuse distributions) represent a promising direction. Finally we consider the connections between parametric models for abundance and incidence data, again noting the usefulness of finite mixture models. ((c) 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim).

Mesh:

Year:  2008        PMID: 19067331     DOI: 10.1002/bimj.200810452

Source DB:  PubMed          Journal:  Biom J        ISSN: 0323-3847            Impact factor:   2.207


  8 in total

1.  Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation.

Authors:  Les Dethlefsen; David A Relman
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-16       Impact factor: 11.205

2.  Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness.

Authors:  Virginia Edgcomb; William Orsi; John Bunge; Sunok Jeon; Richard Christen; Chesley Leslin; Mark Holder; Gordon T Taylor; Paula Suarez; Ramon Varela; Slava Epstein
Journal:  ISME J       Date:  2011-03-10       Impact factor: 10.302

3.  Rapid shifts in the structure and composition of a protistan assemblage during bottle incubations affect estimates of total protistan species richness.

Authors:  Diane Y Kim; Peter D Countway; Rebecca J Gast; David A Caron
Journal:  Microb Ecol       Date:  2011-03-04       Impact factor: 4.552

4.  Estimating population diversity with CatchAll.

Authors:  John Bunge; Linda Woodard; Dankmar Böhning; James A Foster; Sean Connolly; Heather K Allen
Journal:  Bioinformatics       Date:  2012-02-13       Impact factor: 6.937

5.  Estimating animal abundance in ground beef batches assayed with molecular markers.

Authors:  Xin-Sheng Hu; Janika Simila; Sindey Schueler Platz; Stephen S Moore; Graham Plastow; Ciaran N Meghen
Journal:  PLoS One       Date:  2012-03-30       Impact factor: 3.240

Review 6.  Assessing Species Diversity Using Metavirome Data: Methods and Challenges.

Authors:  Damayanthi Herath; Duleepa Jayasundara; David Ackland; Isaam Saeed; Sen-Lin Tang; Saman Halgamuge
Journal:  Comput Struct Biotechnol J       Date:  2017-09-21       Impact factor: 7.271

7.  Different effects of soil bacterial communities affected by biocontrol agent YH-07 on tomato Fusarium wilt inhibition.

Authors:  Tongtong Tang; Xing Sun; Qin Liu; Yuanhua Dong; Yuyong Xiang
Journal:  RSC Adv       Date:  2020-09-21       Impact factor: 4.036

8.  Microbial comparative pan-genomics using binomial mixture models.

Authors:  Lars Snipen; Trygve Almøy; David W Ussery
Journal:  BMC Genomics       Date:  2009-08-19       Impact factor: 3.969

  8 in total

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