Currently it is including all possible lines of data that have either EURY or RHITHRO as the species (ie all values) however I did not dissect Juveniles and so the prevalence data for some of the EURY and RHITHRO is NA instead of a number value. How would I get R to give an accurate count of how many values are getting used in the plot per group?
na.omit may do what you want. It will remove any row with missing data. Depending on how your data looks this can work well or be the the equivalent of using a sledge hammer to shell an almond. It might help if we saw a bit of your data.
A handy way to supply some sample data is the dput() function. In the case of a large dataset something like dput(head(mydata, 100)) should supply the data we need. Just do dput(mydata) where mydata is your data. Copy the output and paste it here.
Some but it would be much better to have the data in dput() format. As it is I cannot read the data into R. The data seems to be in three blocks and the third block with the variable names " Acan_Prev Micro_Prev Total_Richness Total_Prevalence, ..." is garbled.
It would be much better to have dput() output. There is an example below of how to do it.
Just going on the data I have managed to import you have a lot of missing data. Applying na.omit to the entire data set might leave you with N = 1
I think this may give you something a bit like what you want where we only drop NA's in the variables being plotted.