R - Vegan package. metaMDS error

Question

I would like to know why im getting this error running metaMDS:

'comm' has negative data: 'autotransform', 'noshare' and 'wascores' set to FALSE

I would like to do NMDS and dendogram graphs but can do so with the error above.

My data set is available for download if anyone wants to check DATASET. After importing the data, I transposed the column and rows. Afterwhich, I replaced the NA values with O before trying to run metaMDS.

    abundance <- read.table("1_abundance.txt", header = TRUE)        
    abundance[is.na(abundance)] <- 0
    abundance_trans <- t(abundance)
    metaMDS(abundance_trans, distance = "bray", k = 2, trymax = 50)

Jari Oksanen Jari Oksanen · Accepted Answer · 2017-10-23T12:55:36

It is not an error message but information: metaMDS tells you that you have negative data entries, and it will not make some tricks that it defaults to do with non-negative data.
Second issue is that you ask for Bray-Curtis dissimilarities that are only applicable with non-negative data.

You have two alternatives: either take care of negative values, or use a dissimilarity measure than can handle them. If you think that you do not have negative data, you are wrong: computer knows. You may have an error when reading in your data, and you may have columns or rows that you should not have. Check your data.

R - Vegan package. metaMDS error

1 Answers