Hi!

Thanks for providing great help in R-related statistics. Now, however I'm
stuck. I'm not a statistics person but I was recommended to use R to perform
a nmds plot and PerMANOVA of my dataset.

Sample(treatment) in the columns and species (OTU) in the rows. I have 4
treatments (Ambient Temperature, Ambient temperature+Low pH, High
temperature, High temperature+low pH), and I have 16 different species
(OTUs).

Firstly I want to make a nmds plot and see how different the treatments are.
Meaning how the species covaries with the environment, I can produce a plot
but don't understand how to interpret it and I get an error message. Then I
want to make a PerMANOVA analysis comparing the different treatments with
each other.

I tried to look at similar problems but I get error messages.

Any ideas?

#NMDS
step1<-read.delim2("day20.txt", row.names=1)
library(clusterSim)
step2<-data.Normalization(step1,type="n10")
step3<-asin(sqrt(step2))*57.3
step4<-t(step3)
library(vegan)
step5<-data.matrix(vegdist(step4,method="bray"))
step6<-metaMDS(step5, autotransform=FALSE)
plot(step5)
Warning message:
In ordiplot(x, choices = choices, type = type, display = display,  :
  Species scores not available


#PerMANOVA
step1<-read.delim2("day20.txt", row.names=1)
library(clusterSim)
step2<-data.Normalization(step1,type="n10")
step3<-asin(sqrt(step2))*57.3
step4<-t(step3)
library(vegan)
step5<-data.matrix(vegdist(step4,method="bray"))
attach(step5)
step6<-adonis(step5~Sample1+Sample2+Sample3,data=step5)

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