Fix documentation formatting stuff

[araikes]

There are a bunch of documentation formatting things that should be addressed. This includes:

• [ x] Code syntax issues in the References
• [ x] Convert code chunk outputs to live results rather than statically coded. For example, the summary(lm(...)) in exploring-h5.html should actually give outputs.
• Include plots from ggplot when called.
• Update containers.Rmd to reference the correct containers and the possibly the separability of ModelArray and ModelArrayIO. There should be a clear code example of running an Rscript in the container.
• Consider expanding containers.Rmd to include info on custom containers to include other R packages.