everything done on canned soup

[morganbale]

@marcdotson I will start working on the modeling branch now and you can delete this one. I have pushed everything from my local computer.

[marcdotson]

@morganbale there are a number of merge conflicts. It'll help following the revised repo structure:

• Code includes actual code, so the .stan files and the .rds compiled models.
• Figures is where all figures should go, and you'll want to name them (I'd recommend to match the corresponding chunks in your .Rmd) instead of relying on a whole bunch of unnamed files.
• Writing is where the actual writing goes, so basically any .Rmd files, whether they be the manuscript itself which knits to a PDF or one of these blog/vignette things that just knits as a GitHub document. It will of course draw from Figures and Code (well, probably just showing what's in Code since you won't want it to run when you knit everything again).

I may have borked my local repo trying to work through the merge conflicts. Can you make these changes to the canned-soup-cleaning branch, let me know, and I'll try again to merge?

[marcdotson]

Include this at the beginning of your Rmd file after the YAML:

```{r opts, echo = FALSE}
knitr::opts_chunk$set(
  fig.path = "../Figures/folder_name/"
)

[morganbale]

@marcdotson I named all the chunks and set the figures to save in the figures folder. I moved the model folder which has the .stan files to the code folder. I moved the .Rmd files to the main folder (not in any folder), because I only had a paper folder and not a writing folder. I thought you can move these into writing folder when you merge? Let me know if it doesnt work.