A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses.
暂无分享,去创建一个
[1] J. Schank,et al. Pseudoreplication is a pseudoproblem. , 2009, Journal of comparative psychology.
[2] P. Legendre,et al. ANALYZING BETA DIVERSITY: PARTITIONING THE SPATIAL VARIATION OF COMMUNITY COMPOSITION DATA , 2005 .
[3] Susan Holmes,et al. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data , 2013, PloS one.
[4] Stuart H. Hurlbert,et al. On misinterpretations of pseudoreplication and related matters: a reply to Oksanen , 2004 .
[5] M. Gessner,et al. Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors , 2011, The ISME Journal.
[6] Pierre Legendre,et al. All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices , 2002 .
[7] Lauri Oksanen,et al. Logic of experiments in ecology: is pseudoreplication a pseudoissue? , 2001 .
[8] Kalle Ruokolainen,et al. Analyzing or explaining beta diversity? Understanding the targets of different methods of analysis. , 2006, Ecology.
[9] W. Ziebis,et al. Biodiversity of benthic microbial communities in bioturbated coastal sediments is controlled by geochemical microniches , 2009, The ISME Journal.
[10] Alain F. Zuur,et al. A protocol for data exploration to avoid common statistical problems , 2010 .
[11] J. Schank,et al. An ancient black art. , 2009, Journal of comparative psychology.
[12] Thomas W Yee,et al. Constrained additive ordination. , 2006, Ecology.
[13] Renzo Kottmann,et al. Megx.net: integrated database resource for marine ecological genomics , 2009, Nucleic Acids Res..
[14] Susan M. Huse,et al. Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems , 2011, PloS one.
[15] William A. Walters,et al. QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.
[16] Regina Nuzzo,et al. Scientific method: Statistical errors , 2014, Nature.
[17] P. Couteron,et al. ANALYZING OR EXPLAINING BETA DIVERSITY? COMMENT. , 2008, Ecology.
[18] Laura E. Green,et al. The role of ecological theory in microbial ecology , 2007, Nature Reviews Microbiology.
[19] J. Prosser. Replicate or lie. , 2010, Environmental microbiology.
[20] R. Coss. Pseudoreplication conventions are testable hypotheses. , 2009, Journal of comparative psychology.
[21] Celia M. Lombardi,et al. The Ancient Black Art and Transdisciplinary Extent of Pseudoreplication Entreaty of a Youthful Offender , 2022 .
[22] D. Chessel,et al. From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis. , 2004, Journal of theoretical biology.
[23] W. Härdle,et al. Applied Multivariate Statistical Analysis , 2003 .
[24] Charles E. McCulloch,et al. MULTIVARIATE ANALYSIS IN ECOLOGY AND SYSTEMATICS: PANACEA OR PANDORA'S BOX? , 1990 .
[25] S. Hurlbert. Pseudoreplication and the Design of Ecological Field Experiments , 1984 .
[26] Mary Ann Moran,et al. Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill , 2013, The ISME Journal.
[27] Pierre Legendre,et al. Studying beta diversity: ecological variation partitioning by multiple regression and canonical analysis , 2008 .
[28] Rune Halvorsen Økland,et al. Wise use of statistical tools in ecological field studies , 2007, Folia Geobotanica.
[29] A. Boetius,et al. Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands , 2009, The ISME Journal.
[30] Richard A. Johnson,et al. Applied Multivariate Statistical Analysis , 1983 .
[31] Pierre Legendre,et al. Numerical Ecology with R , 2011 .
[32] Jizhong Zhou,et al. Random Sampling Process Leads to Overestimation of β-Diversity of Microbial Communities , 2013, mBio.
[33] L. Zinger,et al. Two decades of describing the unseen majority of aquatic microbial diversity , 2012, Molecular ecology.
[34] P. Legendre,et al. Variation partitioning of species data matrices: estimation and comparison of fractions. , 2006, Ecology.
[35] P. Legendre,et al. Spatial and Temporal Variation in a Caribbean Herbivorous Fish Assemblage , 2010 .
[36] John Haigh,et al. Applied multivariate statistical analysis (2nd edition) , by R. A. Johnson and D. W. Wichern. Pp 607. £17·95. 1988. ISBN 0-13-041138-8 (Prentice-Hall) , 1988, The Mathematical Gazette.
[37] S. Wright. The Method of Path Coefficients , 1934 .
[38] A. Ramette. Multivariate analyses in microbial ecology , 2007, FEMS microbiology ecology.
[39] K. R. Clarke,et al. Non‐parametric multivariate analyses of changes in community structure , 1993 .
[40] C. Quince,et al. Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets , 2010, Nucleic acids research.
[41] H. Tuomisto,et al. ANALYZING OR EXPLAINING BETA DIVERSITY? REPLY. , 2008, Ecology.
[42] David I Warton,et al. Regularized Sandwich Estimators for Analysis of High‐Dimensional Data Using Generalized Estimating Equations , 2011, Biometrics.
[43] Jean Thioulouse,et al. Multivariate analyses in soil microbial ecology: a new paradigm , 2012, Environmental and Ecological Statistics.
[44] William A. Walters,et al. Experimental and analytical tools for studying the human microbiome , 2011, Nature Reviews Genetics.
[45] A. Halpern,et al. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific , 2007, PLoS biology.
[46] Pierre Legendre,et al. ANALYZING OR EXPLAINING BETA DIVERSITY? COMMENT. , 2008, Ecology.
[47] Karl Cottenie,et al. Comment to Oksanen (2001): reconciling Oksanen (2001) and Hurlbert (1984) , 2003 .
[48] Stéphane Dray,et al. Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM) , 2006 .
[49] P. Legendre. Species associations: the Kendall coefficient of concordance revisited , 2005 .
[50] E. Laliberté. ANALYZING OR EXPLAINING BETA DIVERSITY? COMMENT. , 2008, Ecology.
[51] T Jombart,et al. Genetic markers in the playground of multivariate analysis , 2009, Heredity.
[52] A. Boetius,et al. The energy–diversity relationship of complex bacterial communities in Arctic deep-sea sediments , 2011, The ISME Journal.
[53] Charles E. Heckler,et al. Applied Multivariate Statistical Analysis , 2005, Technometrics.
[54] R. Tibshirani,et al. Sparse Principal Component Analysis , 2006 .
[55] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[56] Marti J. Anderson,et al. A new method for non-parametric multivariate analysis of variance in ecology , 2001 .
[57] H. Hudson,et al. A MANOVA STATISTIC IS JUST AS POWERFUL AS DISTANCE-BASED STATISTICS, FOR MULTIVARIATE ABUNDANCES , 2004 .
[58] P. Bork,et al. A Holistic Approach to Marine Eco-Systems Biology , 2011, PLoS biology.
[59] Martin Hartmann,et al. Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.
[60] D. Christopher Dryer,et al. Wizards, guides, and beyond: rational and empirical methods for selecting optimal intelligent user interface agents , 1997, IUI '97.
[61] D. Warton,et al. Distance‐based multivariate analyses confound location and dispersion effects , 2012 .
[62] Pierre Legendre,et al. DISTANCE‐BASED REDUNDANCY ANALYSIS: TESTING MULTISPECIES RESPONSES IN MULTIFACTORIAL ECOLOGICAL EXPERIMENTS , 1999 .
[63] Lauri Oksanen,et al. The devil lies in details: reply to Stuart Hurlbert , 2004 .
[64] Kessy Abarenkov,et al. Resistance and resilience of the forest soil microbiome to logging-associated compaction , 2013, The ISME Journal.