[R] How to conduct a PERMANOVA using a dissimilarity matrix

[michael.eisenring at agroscope.admin.ch]

Dear R-List members,

I have to compare how similar two types of forest (old growth=O) and (young forest=Y) in terms of moth communities are.
I sampled moths at 4 O and 4 Y sites.
I need to analyse the data using a PERMANOVA approach. But I am having a really hard time to do this in R.

I found out that I need to create a dissimilarity matrix and read this matrix then into R to conduct a one-way Permanova with forest type (O or Y) as factor.
The package vegan with the function "adonis" seems to be able to do a permanova.

I created the matrix (based on Soerenson (dis)similarities) and imported it into R.

Could anyone help me with the next step? How can I conduct a permanova on my dataset? In the end I would need an R value and significance level telling me if community compositions differ significantly between sites.

Below is my code (not too much) and the data for the matrix.

#dput for matrix:

structure(c("", "O", "Y", "Y", "Y", "O", "O", "Y", "O", "O",
"0", "0.544", "0.519", "0.533", "0.481", "0.548", "0.518", "0.479",
"Y", "0.544", "0", "0.383", "0.416", "0.383", "0.358", "0.434",
"0.399", "Y", "0.519", "0.383", "0", "0.398", "0.359", "0.392",
"0.401", "0.374", "Y", "0.533", "0.416", "0.398", "0", "0.398",
"0.399", "0.358", "0.348", "O", "0.481", "0.383", "0.359", "0.398",
"0", "0.37", "0.317", "0.354", "O", "0.548", "0.358", "0.392",
"0.399", "0.37", "0", "0.39", "0.365", "Y", "0.518", "0.434",
"0.401", "0.358", "0.317", "0.39", "0", "0.371", "O", "0.479",
"0.399", "0.374", "0.348", "0.354", "0.365", "0.371", "0"), .Dim = c(9L,
9L), .Dimnames = list(NULL, c("V1", "V2", "V3", "V4", "V5", "V6",
"V7", "V8", "V9")))


#Code
#load dissimilarity matrix (based on Soerenson similarity)
moth_dta<-read.csv("Geo_sorenson_8.csv",header=T,sep=";")#Creates matrix from imported data
moth_dta<-as.matrix(moth_dta)
moth_dta
library(vegan)


Thank you very much,
Michael

Eisenring Michael, Msc.
PhD Student

Federal Department of Economic Affairs, Education and Research
EAER
Institute of Sustainability Sciences ISS
Biosafety

Reckenholzstrasse 191, CH-8046 Zürich
Tel. +41 44 37 77181
Fax +41 44 37 77201
michael.eisenring at agroscope.admin.ch<mailto:michael.eisenring at agroscope.admin.ch>
www.agroscope.ch<http://www.agroscope.ch/>


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