Scatterplot for comparing species abundance - r

Question

I have a homework question that states the following:
The file “channel_islands_counts_edit.csv” contains survey data on temperate rocky reef fishes from the Channel Islands, collected at many sites over many years. The data has columns for Year, Date, Site, count, and SpeciesName (broken into adults and juveniles). The version of the data that I’ve given you looks at 16 sites over 27 years, with count data for 27 categories of fish. Imagine we’re interested in whether the abundance of different species are correlated across sites (to get a sense for whether species have similar habitat preferences and/or interact with each other), and whether the across-site correlations are consistent over time. To visualize this, make some code that does the following:
For each year, draw a scatterplot that compares the abundance of Hypsypops rubicundus (adults) and the abundance of Paralabrax clathratus (adults) across sites. Feel free to transform the data for plotting purposes, if you think that helps you see any patterns.
I imported my data set, and ran the following code which is giving me 27 plots, with Site as x and Count as y, but there is no data shown in the plots.
head(channel_islands)
sapply(channel_islands, class)
levels(channel_islands$SpeciesName)
par(mfrow= c(6,5)) # set the plotting area into a 6 row*5 column array
for (i in 1:27) {
HR11<-subset(channel_islands,SpeciesName=="Hypsypops rubicundus,adult"[i] & Site==11)
PC15<-subset(channel_islands,SpeciesName=="Paralabrax clathratus,adult"[i] & Site==15)
with(HR11,plot(count~Site,type='b',pch=19,ylim=c(0,10),xlim=c(0,16),col='green',main=i))
with(PC15,plot(count~Site,type='b',pch=19,ylim=c(0,10),xlim=c(0,16),col='blue',main=i))
}
If anyone could help me figure out how to compare species abundance across sites, over 27 years, I would really appreciate it.

Answer 1

The code "Hypsypops rubicundus,adult"[i] doesn't really make sense. Technically, it should work for when i == 1 but beyond that it would just return NA. I'm assuming SpeciesName == NA will never be true so you will get an empty subset.
Consider looking into using ggplot2 with facet_grid to quickly make multiple plots without the loop. The R Graphics Cookbook has good examples on using facets.