#ORDINATION FUNCTION
#Reads your data file,
#performs ordination (Non-Metric Multidimensional Scale),
#and plots results

#If you haven't already, go to "Install Packages" in the "Tools" menu
#Then, type "vegan" in the box and click on "Install" (wait for it to finish)
#You only need to install the package once, but you need to run step 1 every time you start the program

ordination <- function(groupnum) {
  
  #read your data file
  commdata <- read.csv(paste("https://people.ucsc.edu/~mclapham/eart101/papers/group_",groupnum,"_data.csv", sep=""), row.names=1)

  #perform the ordination analysis
  mdsres <- vegan::metaMDS(t(commdata), autotransform=F)

  #plot the ordination results
  #sites are plotted as solid circles with labels
  #species are plotted as red text
  plot(mdsres, type="n")
  mdsscores <- vegan::scores(mdsres)
  spscores <- vegan::scores(mdsres, display="species")
  points(mdsscores, pch=16)
  text(mdsscores[,1], mdsscores[,2]-0.04, sample_num <- gsub("\\..*","", colnames(commdata)))
  text(spscores[,1], spscores[,2], rownames(commdata), col="red", cex=0.75)
  #End of STEP 5
  
  #To save the plot, click the "export" option above the plot window and then select "save as image."
  #Set the file name and use the "directory" button in the save window to choose the folder where it will be saved.
}