prepping FastReseg for handoff to software

[patrickjdanaher]

We want to get this package to a point where we can hand it over to the software team to integrate into our pipelines. For that we'll need:

1. Easy-to-understand, highly modular code
2. Thorough documentation
3. Confidence that it improves / doesn't hurt downstream analysis

1: architecture / modular code:

• Move more code from the big wrapper into its subsidiary functions. See here for an example of a wrapper function that contains almost nothing but calls to subsidiary functions. Data checks should be moved within subsidiary functions when possible.
• The ideal modular function performs a single task, and has relatively few inputs / outputs. A function can call as many subsidiary functions as needed.
• I recommend starting by diagraming out the flow of data through the pipeline. See the readme here for an example of such a diagram. This is useful both to help you organize your functions and to help readers understand the code.

2: documentation

• Easy-to-follow vignettes will be key. A vignette should usually only have a couple dozen R commands; all the extra/supporting stuff would ideally go into functions.
• A thorough README is essential. It should include installation instructions and an explanation of the main things the package does.

3: getting confidence it works:

You've done a lot here already. I think the best thing now is to put the package in people's hands and let them try it out. Note they'll only try it if it's well-documented and easy to use, so move onto this after 1 & 2 are done.

[lidanwu]

Here is the current data flow of the FastReseg. It seems better if I break the big wrapper into 4 different sections of the vignettes (or 4 different wrappers?) and move more intermediate codes that connect the results between functions into the wrapper for individual functions. @patrickjdanaher Please let me know what you think.

[lidanwu]

updated diagram for architecture

[lidanwu]

done.