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1. microbiome.github.io › course_2021_radboud › beta-diversityChapter 8 Beta diversity | Introduction to microbiome data...

   microbiome.github.io › course_2021_radboud › beta-diversity

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   Investigate the influence of the data transformations on statistical analysis: Visualize community variation with PCoA with the following options: 1) Bray-Curtis distances for compositional data; 2) Euclidean distances for CLR-transformed data.

   • 4 Reproducible Reporting With Rmarkdown

     4 Reproducible Reporting With Rmarkdown - Chapter 8 Beta...

   • 9 Differential Abundance Analysis

     9.3 ANCOM-BC. The analysis of composition of microbiomes...

   • 6 Microbiome Data Exploration

     If you are sharp, you have by now noticed that all the...

   • Chapter 7 Alpha Diversity

     7.2 Statistical testing and comparisons. To further...

2. uw.pressbooks.pub › appliedmultivariatestatistics › chapterCommon Distance Measures – Applied Multivariate Statistics in R

   uw.pressbooks.pub › appliedmultivariatestatistics › chapter

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   Bray-Curtis Distance. When the formula for Sorensen dissimilarity is extended from presence/absence data to species abundance data, it results in the Bray-Curtis distance measure:

3. dyerlab.github.io › applied_population_genetics › genetic-distancesApplied Population Genetics - GitHub Pages

   dyerlab.github.io › applied_population_genetics › genetic-distances

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   20.1.3 Bray-Curtis Individual Distance. A distance metric that can be used to test differences among individuals or populations is that of Bray-Curtis. This distance is a transformation of Jaccard’s distance (see below) and is derived from an ecological ordination paper by Bray & Curtis (1957).

4. scikit.bio › docs › latestCommunity Diversity (skbio.diversity) — scikit-bio 0.6.1...

   scikit.bio › docs › latest

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   Next we’ll do some work with these beta diversity distance matrices. First, we’ll determine if the UniFrac and Bray-Curtis distance matrices are significantly correlated by computing the Mantel correlation between them. Then we’ll determine if the p-value is significant based on an alpha of 0.05.

5. stackoverflow.com › questions › 51200770vegan - Bray-Curtis Pairwise Analysis in R - Stack Overflow

   stackoverflow.com › questions › 51200770

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   6 lip 2018 · I am trying to calculate and visualize the Bray-Curtis dissimilarity between communities at paired/pooled sites using the Vegan package in R. Below is a simplified example dataframe:

6. rdrr.io › cran › veganvegdist : Dissimilarity Indices for Community Ecologists

   rdrr.io › cran › vegan

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   29 maj 2024 · Jaccard index is metric, and probably should be preferred instead of the default Bray-Curtis which is semimetric. Aitchison distance (1986) and robust Aitchison distance (Martino et al. 2019) are metrics that deal with compositional data.

7. www.nhm.uio.no › english › researchSimilarity and distance indices - UiO

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   Bray-Curtis. Bray-Curtis is a popular similarity index for abundance data (Bray and Curtis 1957). Many authors operate with a Bray-Curtis distance, which is simply 1-d. Cosine. The inner product of abundances each normalised to unit norm, i.e. the cosine of the angle between the vectors. Morisita. For abundance data. Horn