# pairwiseAdonis

**Repository Path**: openResearch/pairwiseAdonis

## Basic Information

- **Project Name**: pairwiseAdonis
- **Description**: Pairwise multilevel comparison using adonis
- **Primary Language**: Unknown
- **License**: GPL-3.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2025-04-15
- **Last Updated**: 2025-04-15

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# pairwiseAdonis
# version 0.4 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 fuction accepts strata

_________________________________________________________________________________________________
## Install `pairwiseAdonis`

``` r
# Option 1: from github

install.packages("devtools")
devtools::install_github("pmartinezarbizu/pairwiseAdonis", dependencies = TRUE)   


```

``` r
# Option 2: from gitee

install.packages("git2r")
install.packages("remotes")
library(git2r)
library(remotes)
remotes::install_git("https://gitee.com/openResearch/pairwiseAdonis.git")  
```

If the above methods fail, please try downloading the .Zip or .tar.gz file of this R package to your local path of your computer,
and install it using the following method:

``` r
# Option 3: from local

devtools::install_local("E:/R/ggradar2/pairwiseAdonis-master.zip")  # zip file
devtools::install_local("E:/R/ggradar2/pairwiseAdonis_0.3.tar.gz")    # tar.gz file

# Please replace the path and file name with your own. 
```


____________________________________
## 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()```
_____________________________________________
## Citation

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