I am a little new to conducting microbiome analyses and doing it in R. I am interested in performing a SIMPER test to see what species are driving compositional differences in different sampling sites. I was successful in performing the SIMPER test using vegan. I am working with a very large dataset and when I summarize the test summary(simper), it returns thousands of lines of text on the console and I cannot get through it all, and the lines cut off after 1000. I am wondering if it's possible to ONLY return those species of statistical significance?
Here is my code:
pc = read.csv("water.csv", header = TRUE)
com = pc[,6:ncol(pc)]
m_com = as.matrix(com)
simper <- simper(m_com, group = pc$Location, permutations = 999)
summary(simper)
I played around with the 'digits' portion of the 'summary' option (summary(simper, ordered = TRUE, digits = max(3)) but this only changed the number of decimal places in the results. I have also increased the output using options(max.print=1000000) but there is still so much data.
I would like to only view those of significance if possible. Any help is appreciated. Thank you all.