title: Summarizing a presence absence, abundance matrix
body: <p>I have a site by species matrix that looks like this:</p>
  
  <pre><code>colA= c("A","A","A","B","B","B","C","C","C")
  colB= c(1,2,3,3,0,1,2,1,0)
  colC= c(0,0,0,1,0,0,0,0,1)
  df= data.frame (site=colA, sp1=colB, sp2=colC)
  </code></pre>
  
  <p>This matrix has three sites A,B,C, and two species sp1, sp2. </p>
  
  <p>I am trying to build code that summarizes the abundance of each species by site. The ultimate output should be a dataframe with one column having the site and a second column having the species name and the third column with the abundance of that species at that site. </p>
  
  <p>I'm guessing this will have to be done in a loop for each site and then have the summaries put into a new dataframe.</p>
  
  <p>The output should look something like this:</p>
  
  <pre><code>colA= c("A","B","C","A","B","C")
  colB= c("sp1","sp1","sp1","sp2","sp2","sp2")
  colC= c(6,4,3,0,1,1)
  output= data.frame (site=colA, species=colB, abundance=colC)
  output
  </code></pre>