pairwiseAdonis

version 0.3 includes 2 functions

pairwise.adonis

pairwise.adonis2

pairwise.adonis

This is a wrapper function for multilevel pairwise comparison using adonis (~Permanova) from package 'vegan'. The function returns adjusted p-values using p.adjust(). It does not accept interaction between factors neither strata.

pairwise.adonis2

This function accepts strata

NOTE: This is still a developing version -- results using interactions may not be right. Please validate. I would appreciate feed back.

update 28 April 2020: Function now adapts the permutation matrix for each combination of factors before applying adonis. The p-value when using strata (block) looks correct now. Check syntax in example below.

This function accepts a model formula like in adonis from vegan. You can use interactions between factors and define strata to constrain permutations. For pairwise comparison a list of unique pairwise combination of factors is produced. Then for each pair, following objects are reduced accordingly to include only the subset of cases belonging to the pair:

• the left hand side of the formula (dissimilarity matrix or community matrix)

• the right hand side of the formula (factors)

• the strata if used.

The reduced data are passed to adonis and the summary of the anova table for each pair is saved in a list, together with the anova table of the full model and the original 'parent call'.

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INSTALLATION

For linux

Note: I have experience myself an Error when installing from github.

Error converted from warning ... (r-lib/remotes#403) To avoid this, load devtools and type first in your R session:

Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS"=TRUE)

.... follow below

make sure you have devtools installed and loaded, for windows also install Rtools

In your R session

install_github("pmartinezarbizu/pairwiseAdonis/pairwiseAdonis")

That's it

Or...

For windows

first install Rtools from here https://cran.r-project.org/bin/windows/Rtools/

in R install devtools

install.packages('devtools')

load devtools

library(devtools)

In your R session

install_github("pmartinezarbizu/pairwiseAdonis/pairwiseAdonis")

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Usage

library(pairwiseAdonis)
data(iris)
pairwise.adonis(iris[,1:4],iris$Species)

# For strata (blocks), following example of Jari Oksanen in adonis2. 
dat <- expand.grid(rep=gl(2,1), NO3=factor(c(0,10,30)),field=gl(3,1) )
Agropyron <- with(dat, as.numeric(field) + as.numeric(NO3)+2) +rnorm(18)/2
Schizachyrium <- with(dat, as.numeric(field) - as.numeric(NO3)+2) +rnorm(18)/2
Y <- data.frame(Agropyron, Schizachyrium)

pairwise.adonis2(Y ~ NO3, data = dat, strata = 'field')

for more examples see also ?pairwise.adonis() ?pairwise.adonis2()

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Citation

Martinez Arbizu, P. (2020). pairwiseAdonis: Pairwise multilevel comparison using adonis. R package version 0.4