This reproducible-research compendium contains all files and commands necessary to reproduce the atmospheric results of Chapter 3 of Ryan Challener's dissertation entitled "Exoplanets: Correlated Noise and Cautionary Tales" The review process for the publication of this chapter may require revisions, so please be sure that you find the compendium associated with the paper, rather than the dissertation, if the paper has been published. This repository makes use of the Bayesian Atmospheric Radiative Transfer code (BART, https://github.com/exosports/BART), and was created in accordance with BART's license. All commands necessary to produce the output are in compendium.sh. File paths have been left as they are on my machine, so as to not change any configuration files. The user may change the paths if they desire, but they must make the corresponding changes in the configuration files. All outputs used in the paper can be found in the output directory, which is subdivided according to the inputs. The lightcurves directory contains FITS files and InfraRed Science Archive (IRSA) tables with photometry, centering, and modeling information for all observations. The lcplots directory contains diagnostic plots from light-curve modeling. The scripts directory contains scripts used to process the BART outputs to make the plots used in the paper.