Update vignette

[zenalapp]

• [x] Add link to good review: https://pubmed.ncbi.nlm.nih.gov/28513284/
• [x] Add tree building recommendations
• [x] Code to bin get_frac_intra() output (data frame and plot)
• [x] Fix environmental sample example (#42)
• [x] Add code to assign each isolate to a cluster based on the get_clusters output (maybe include as package function instead?) (#19)
• [x] Update vignette to show manuscript figures (#27)
• [x] Update text to flow based on updates described above
• [x] Explain how to make get_clusters run faster using a parallelization scheme
• [x] Add pre-processing figure to vignette
• [x] Organize files to not get notes in devtools::check()
• [ ] Check link to vignette on GitHub and change if broken