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Permutational MANOVA or adonis in Excel

2017-12-12

This tutorial will help you set up and interpret a permutational Multivariate Analysis of Variance or adonis based on Distance Matrices in Excel using the XLSTAT-R engine in Excel.

What is adonis?

Adonis is a technique used in ecology to explain communities with environmental variables. Its goal is similar to Multivariate Analysis of Variance (MANOVA).
The adonis function developed in XLSTAT-R calls the adonis function from the vegan package in R (Martin Henry H. Stevens and Jari Oksanen).

Data set for launching an adonis analysis in XLSTAT-R

An Excel sheet with both the data and the results can be downloaded by clicking on the button below:
Download the data
The data was extracted from Vegetation and Environment in Dutch Dune Meadows [Jongman, R.H.G, ter Braak, C.J.F & van Tongeren, O.F.R. (1987). Data Analysis in Community and Landscape Ecology. Pudoc, Wageningen]. The data is available in the vegan package in R.
The first 30 columns correspond to abundances of 30 plant species measured on 20 sites. Two environmental variables measured on the sites were also included:
  • A1: Thickness of the A1 soil horizon
  • Management: BF (Biological farming), HF (Hobby farming), NM (Nature Conservation Management), and SF (Standard Farming).
The goal here is to investigate the effects of A1, management, and the interaction between both on the plant community.

Setting up an adonis analysis in XLSTAT-R

Open XLSTAT-R / vegan / Permutational MANOVA using Distance Matrices(adonis)
XLSTAT-R Menu in Excel, adonis permutational ANOVA, vegan package
In the general tab, select the plant community in the dependent variables field.
Select A1 in the Quantitative explanatory variables field and Management in the Qualitative explanatory variables field.
XLSTAT-R adonis dialog box, general tab
In the Options tab, activate the interactions, set permutations at 999 and select Marginal effects. Marginal effects are equivalent to the type III sum of squares table.
XLSTAT-R adonis dialog box, Options tab
Click OK to launch computations.
A dialog box appears allowing you to select the terms you want to include in your model. Select all the terms and click OK.
XLSTAT-R adonis, Factors & Interactions dialog box

Interpretation of an adonis output

The adonis ANOVA table shows that A1 & Management have significant effects on the community at alfa = 0.05. The interaction effect is not significant.
XLSTAT-R adonis, ANOVA table with marginal SS
 
 
 
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