Converting Bray Curtis dissimilarity for SIMPER:vegan

Question

I want to use SIMPER with vegan package to see which species are contributing the most given each year.

#4th root transformation
BBcounts_transformed<-siteBB^(1/4)
BBcounts_transformed.matrix<-as.matrix(BBcounts_transformed)
#Bray-Curtis Diss.
BBtrans_bray<-vegdist(BBcounts_transformed.matrix, method="bray")

SIMPER requires the dissimilarity matrix be put into a dataframe, however I'm struggling with this as data.frame function just puts all the distance values into a single column which wont align with the measuring factor. The bray is looking at distances between years with the species matrix(species in columns x 12 separate years in rows). They are either cold or hot years.

BBtrans_bray.df<-as.data.frame(BBtrans_bray)
BBtrans.simper_result<-simper(BBtrans_bray,site_BB2$TempH)

I am still fairly new to Bray and SIMPER so any help would be appreciated at this point.

Answer 1

The "simper" function itself calculates Bray Curtis dissimilarity directly from the community data. You have to put your species matrix as the first argument instead of an object with a dissimilarity matrix. Try this:

#4th root transformation
BBcounts_transformed<-siteBB^(1/4)
BBcounts_transformed.matrix<-as.matrix(BBcounts_transformed)
BBtrans.simper_result<-simper(BBcounts_transformed.matrix,site_BB2$TempH)

For more information please see:

?simper