Q:

Retain row names in package vegan

I'm using vegdist() from the vegan package to calculate Morisita's Index of Similarity. My data have site names stored in the first column. 
TCR 3   0   0   0   
MTF 0   1   2   0   
UTZ 0   1   0   1   
MTC 0   0   0   0   
TMC 0   0   0   0   
RLK 0   0   0   0

Because vegdist doesn't accept non-numeric data, I have to drop the site names by specifying data[-1]
vegdist(data[-1 ], method='morisita')

This works fine, but then I obviously don't have any site names:
           1          2          3          4          5
2 0.02701298                                            
3 0.30256065 0.31838705                                 
4 0.00000000 0.02279212 0.27784052                      
5 0.25158180 0.33946880 0.54253442 0.29648698           
6 0.03720930 0.03925893 0.35777998 0.03406440 0.40862423

Some of these numbers don't seem correct, based on my data and which sites I think they are. So it's very important I have the site names to confirm which one is which. How can I keep my site names when using vegdist()?
As a note, I was able to keep site names when using diversity(), also from vegan, this way:
plyr::ddply(data, ~site, function(x) {
           data.frame(simpson=diversity(x[-1], index='simpson'))
   })

But I wasn't able to figure out how to adapt this to vegdist().

A:

This is what the base R rownames attribute was made for. 
rownames(data) <- data[,1]
data <- data[,-1]
data
#    V2 V3 V4 V5
#TCR  3  0  0  0
#MTF  0  1  2  0
#UTZ  0  1  0  1
#MTC  0  0  0  0
#TMC  0  0  0  0
#RLK  0  0  0  0

Now when you use all those functions from vegan you get more useful results. 
library(vegan)
vegdist(data,method='morisita')
#    TCR MTF UTZ MTC TMC
#MTF   1                
#UTZ   1   0            
#MTC NaN NaN NaN        
#TMC NaN NaN NaN NaN    
#RLK NaN NaN NaN NaN NaN

