adonis3: Permutational Multivariate Analysis of Variance Using...

In GUniFrac: Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis

Permutational Multivariate Analysis of Variance Using Distance Matrices (Freedman-Lane permutation)

Description

Analysis of variance using distance matrices — for partitioning distance matrices among sources of variation and fitting linear models (e.g., factors, polynomial regression) to distance matrices; uses a permutation test (Freedman-Lane permutation) with pseudo-F ratios.

Usage

adonis3(formula, data, permutations = 999, method = "bray",
    strata = NULL, contr.unordered = "contr.sum",
    contr.ordered = "contr.poly", parallel = getOption("mc.cores"), ...)

Arguments

formula	model formula. The LHS must be either a community data matrix or a dissimilarity matrix, e.g., from vegdist or dist. If the LHS is a data matrix, function vegdist will be used to find the dissimilarities. The RHS defines the independent variables. These can be continuous variables or factors, they can be transformed within the formula, and they can have interactions as in a typical formula.
data	the data frame for the independent variables.
permutations	a list of control values for the permutations as returned by the function how, or the number of permutations required, or a permutation matrix where each row gives the permuted indices.
method	the name of any method used in vegdist to calculate pairwise distances if the left hand side of the formula was a data frame or a matrix.
strata	groups (strata) within which to constrain permutations.
contr.unordered, contr.ordered	contrasts used for the design matrix (default in R is dummy or treatment contrasts for unordered factors).
parallel	number of parallel processes or a predefined socket cluster. With parallel = 1 uses ordinary, non-parallel processing. The parallel processing is done with parallel package.
...	Other arguments passed to vegdist.

Details

adonis3 is the re-implementation of the adonis function in the vegan package based on the Freedman-Lane permutation scheme (Freedman & Lane (1983), Hu & Satten (2020)). The original implementation in the vegan package is directly based on the algorithm of Anderson (2001) and performs a sequential test of terms. Statistical significance is assessed based on permuting the distance matrix. We found that such permutation will lead to power loss in testing the effect of a covariate of interest while adjusting for other covariates (confounders). The power loss is more evident when the confounders' effects are strong, the correlation between the covariate of interest and the confounders is high, and the sample size is small. When the sample size is large than 100, the difference is usually small. The new implementation is revised on the adonis function with the same interface.

Value

Function adonis3 returns an object of class "adonis" with following components:

aov.tab	typical AOV table showing sources of variation, degrees of freedom, sequential sums of squares, mean squares, F statistics, partial R^2 and P values, based on N permutations.
coefficients	matrix of coefficients of the linear model, with rows representing sources of variation and columns representing species; each column represents a fit of a species abundance to the linear model. These are what you get when you fit one species to your predictors. These are NOT available if you supply the distance matrix in the formula, rather than the site x species matrix
coef.sites	matrix of coefficients of the linear model, with rows representing sources of variation and columns representing sites; each column represents a fit of a sites distances (from all other sites) to the linear model. These are what you get when you fit distances of one site to your predictors.
f.perms	an N by m matrix of the null F statistics for each source of variation based on N permutations of the data. The permutations can be inspected with permustats and its support functions.
model.matrix	the model.matrix for the right hand side of the formula.
terms	the terms component of the model.

Author(s)

Martin Henry H. Stevens (adonis) and Jun Chen (adonis3).

References

Anderson, M.J. 2001. A new method for non-parametric multivariate analysis of variance. Austral Ecology, 26: 32–46.

Freedman D. & Lane D. 1983. A nonstochastic interpretation of reported significance levels. Journal of Business and Economic Statistics, 1292–298.

Hu, Y. J. & Satten, G. A. 2020. Testing hypotheses about the microbiome using the linear decomposition model (LDM). JBioinformatics, 36(14) : 4106-4115.

Examples

## Not run: 
data(throat.otu.tab)
data(throat.tree)
data(throat.meta)

groups <- throat.meta$SmokingStatus

# Rarefaction
otu.tab.rff <- Rarefy(throat.otu.tab)$otu.tab.rff

# Calculate the UniFrac distance
unifracs <- GUniFrac(otu.tab.rff, throat.tree, alpha=c(0, 0.5, 1))$unifracs

# Test the smoking effect based on unweighted UniFrac distance, adjusting sex
adonis3(as.dist(unifracs[, , 'd_UW']) ~ Sex + SmokingStatus, data = throat.meta)

## End(Not run)

GUniFrac documentation built on Sept. 14, 2023, 1:07 a.m.