scholarly journals Phylogenetic ANOVA: Group-clade aggregation, biological challenges, and a refined permutation procedure

Evolution ◽  
2018 ◽  
Vol 72 (6) ◽  
pp. 1204-1215 ◽  
Author(s):  
Dean C. Adams ◽  
Michael L. Collyer
Keyword(s):  
Permutation Procedure

A Fortran Program for Permutation Covariate Analyses of Residuals Based on Euclidean Distance

1998 ◽  
Vol 82 (2) ◽  
pp. 371-375 ◽  
Author(s):  
Kenneth J. Berry ◽  
Paul W. Mielke
Keyword(s):  
Euclidean Distance ◽  
Latin Square ◽  
Fortran Program ◽  
Experimental Designs ◽  
Permutation Procedure ◽  
Split Plot

A FORTRAN program is presented to analyze the results of experimental designs. A Euclidean distance permutation procedure is used to evaluate residuals obtained from least sum of absolute deviations regression. Applications include completely randomized and randomized block configurations including one-way, factorial, split plot, and Latin square designs, with or without covariates.

scholarly journals Phylogenetic Diversity of Plant Metacommunity of the Dnieper River Arena Terrace Within the ‘Dnieper-Orilskiy ’ Nature Reserve

2017 ◽  
Vol 36 (4) ◽  
pp. 352-365
Author(s):  
Olexander Zhukov ◽  
Olga Kunah ◽  
Yulia Dubinina ◽  
Dmitry Ganga ◽  
Galina Zadorozhnaya
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Diversity ◽  
Nature Reserve ◽  
Species Abundance ◽  
Remote Sensing Data ◽  
Principal Coordinate Analysis ◽  
Permutation Procedure ◽  
Additional Information ◽  
Plant Phylogeny ◽  
Steppe Meadow

Abstract This article presents the features of the phylogenetic organization of the plant communities of the Dnieper River terrace within the ‘Dnieper-Orilskiy’ Nature Reserve and the patterns of its spatial variation involving remote sensing data of the Earth’s surface. The research materials were collected in the period 2012−2016 from within the nature reserve. The research polygon is within the first terrace (arena) of the Dnieper valley. Sandy steppe, meadow, forest and marsh communities within the Protoch river floodplain and the Orlova ravine, as well as artificial pine plantations were the habitats present within the research polygon. The vegetation description was carried out on 10×10 m (100 m2) plots. A total of 94 geobotanical descriptions were made. Data on plant phylogeny was obtained by the Phylomatic service. Phylogenetic diversity of the communities was assessed by the Faith, Simpson and Shannon indices. Phylogenetic analysis was performed by means of a double principal coordinate analysis (DPCoA). The vegetation cover within the investigated polygon was represented by 189 species. Abundance Phylogenetic Deviation (APD) for the investigated metacommunity was evaluated to −0.53, which is statistically significantly different from random alternatives (p = 0.001). The APD negative value indicates that phylogenetic organization of the investigated metacommunity is overdispersed. The permutation procedure allowed us to establish that the eigenvalues of the DPCoA-axes obtained as a result of the real phylogenetic tree were significantly higher than their own number for the random phylogenetic trees for the first seven axes. This indicates that the first seven axes are useful for additional information on the ordination structure of the metacommunity.

Multivariate Multiple Regression Analyses: A Permutation Method for Linear Models

2002 ◽  
Vol 91 (1) ◽  
pp. 3-9 ◽  
Author(s):  
Paul W. Mielke ◽  
Kenneth J. Berry
Keyword(s):  
Multiple Regression ◽  
Euclidean Distance ◽  
Linear Models ◽  
Latin Square ◽  
Experimental Designs ◽  
Regression Analyses ◽  
Permutation Procedure ◽  
Multivariate Extension ◽  
Multivariate Multiple Regression ◽  
Euclidean Distances

A multivariate extension of a univariate procedure for the analysis of experimental designs is presented. A Euclidean-distance permutation procedure is used to evaluate multivariate residuals obtained from a regression algorithm, also based on Euclidean distances. Applications include various completely randomized and randomized block experimental designs such as one-way, Latin square, factorial, nested, and split-plot designs, with and without covariates. Unlike parametric procedures, the only required assumption is the randomization of subjects to treatments.

scholarly journals Importance of allochthonous resources in the diet ofAstyanax aff. fasciatus (Osteichthyes: Characidae) in streams: a longitudinal approach

2014 ◽  
Vol 14 (3) ◽  
Author(s):  
Marlene R. Silva ◽  
Rosemara Fugi ◽  
Natália Carniatto ◽  
Maria Júlia M. Ganassin
Keyword(s):  
Stomach Contents ◽  
Principal Coordinate Analysis ◽  
Fish Diet ◽  
Longitudinal Gradient ◽  
Permutation Procedure ◽  
Allochthonous Resources ◽  
Fish Samples ◽  
Longitudinal Approach ◽  
Ordination Analysis ◽  
Spatial Differences

The aim of this investigation was to respond the following question: is the consumption of allochthonous resources by Astyanax aff.fasciatus influenced by the longitudinal gradient in streams? To respond this question we sampled fish in the headwater, middle and mouth stretches of four streams (Upper Paraná River basin). Samplings were carried out from July 2007 to June 2008 using electrical fishing. Fish were identified, measured and their stomach contents identified and quantified. Spatial variations (among longitudinal stretches) in the diet were summarized using a principal coordinate analysis (PCoA). Spatial differences in the diet were tested with a multiresponse permutation procedure (MRPP). Allochthonous resources had the highest percentage of the A. aff.fasciatus diet in all stretches; however, the increased importance of autochthonous resources in the fish diet in the stream mouths made these stretches to differ significantly from the middle and headwater ones. The ordination analysis separated the fish diet sampled in the stream mouth from the diet of most fish samples in the headwater and middle stretches. The results highlight the importance of allochthonous resources, mainly insects, in the diet of A. aff. fasciatus. However, the diet was affected by longitudinal gradient and followed the pattern described for these ecosystems, where fish depend basically of allochthonous material in the headwaters and the importance of these resources decrease along the longitudinal gradient.

scholarly journals Testing the Mantel statistic with a spatially‐constrained permutation procedure

2019 ◽  
Vol 10 (4) ◽  
pp. 532-540 ◽  
Author(s):  
Julie Crabot ◽  
Sylvie Clappe ◽  
Stéphane Dray ◽  
Thibault Datry
Keyword(s):  
Permutation Procedure

scholarly journals overlappingCGM: Automatic detection and analysis of overlapping co-expressed gene modules

2021 ◽  
Author(s):  
Quang-Huy Nguyen ◽  
Duc-Hau Le
Keyword(s):  
Statistical Approach ◽  
State Of The Art ◽  
Decomposition Methods ◽  
Optimal Number ◽  
Gene Module ◽  
Analysis Framework ◽  
Human Breast ◽  
Permutation Procedure ◽  
Module Detection ◽  
Gene Modules

When it comes to the co-expressed gene module detection, its typical challenges consist of overlap between identified modules and local co-expression in a subset of biological samples. A recent study have reported that the decomposition methods are the most appropriate ones for solving these challenges. In this study, we represent a R tool, termed overlapping co-expressed gene module (overlappingCGM), which possesses those methods with a wholly automatic analysis framework to help non-technical users to easily perform complicated statistical analyses and then gain robust results. We also develop a novel auxiliary statistical approach to select the optimal number of principle components using a permutation procedure. Two example datasets are used, related to human breast cancer and mouse metabolic syndrome, to enable the illustration of the straightforward use of the tool. Computational experiment results show that overlappingCGM outperforms state-of-the-art techniques. The R scripts used in the study, including all information on the tool and its usage are made publicly available at https://github.com/huynguyen250896/overlappingCGM.

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