I am currently carrying out an analysis on a species community data matrix. I have an abundance of each bird species against the plots they were found in. My Analysis was working well until I realised a lot of my values are zero as some species of bird were not found in all of the plots.
This is my current code and the errors associated
abundmat <- read.csv("matrix.csv",row.names=1)
groupmat <- read.csv("Matrix Group.csv",row.names=1)
abundmat.rel <- decostand(abundmat,method = "total")
abund.distmat <- vegdist(abundmat.rel,method="bray")
as.matrix(abund.distmat,labels = T)
abundmat_NMDS <- metaMDS(abund.distmat,
distance = "bray",
k = 3,
maxit = 999,
trymax = 250,
wascores = TRUE)
In metaMDS(abund.distmat, distance = "bray", k = 3, maxit = 999, :
stress is (nearly) zero: you may have insufficient data
the stress plot had no correlation and the non metric fit and linear fit was =1.
is there any way I can change this ?