You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I have an OTU table of the original sparse matrix (most species have an abundance of 0 in the sample, otutab.txt), and use it for neutral model analysis. When using Neutral.fit(otu), the generated freq.pred is 0. In the end, my results are not so satisfactory. Can you help me see where I can improve? Here is my complete code:
otutab <- read.delim("otutab.txt",row.names = 1)
otu_rel <- sweep(otutab, 2, colSums(otutab), FUN = "/")
otu <- t(otu_rel)
res<-neutral.fit(otu)
Note: The otutab.txt file is a raw absolute abundance matrix, which has not been flattened and converted to a relative abundance matrix.