R/ subfolder is full of spaghetti

[bryce-carson]

🍝 The spaghetti should be refrigerated, and then baked into a leftover-spaghetti-caserolle; see the branch of that name for progress.

• Refactor the function providing our meat 🍗 and potatoes 🥔🥔🥔, a SVEIRD w/ Bayesian data assimilation #36 simulation
• Clean up the Q matrix #37 code
• Clean up the H matrix #38 code
• Clean up the linear interpolation operator code (old LIO2 function) #42
• Refactor the function which mentioned the RasterStack #39 class but didn't use it

[ashokkrish]

Spaghetti alle vongole? Spaghetti aglio e olio? Spaghetti alla carbonara? :)

[bryce-carson]

Spaghetti alle vongole? Spaghetti aglio e olio? Spaghetti alla carbonara? :)

I haven't heard of any of those, honestly! 😆 Spaghetti code, unfortunately! Maybe pizza code; I'm unsure. They're not really useful terms.

In short, the code is too interdependent to justify splitting it into so many files, and no single file has a clear role other than to call functions from another file, and so on, until some input data is finally needed. I can't test them in isolation or outside of the Shiny app.

I reviewed the function call diagram you shared with me, and I found that it is inaccurate. Some scripts call functions from files that were not listed as dependencies on the graph, and overall these files really aren't independent.

As they sat, they posed a problem for cleaning up the global.R file. Shiny already sources all R files under the R/ folder, so source calls aren't necessary. The source calls and further calls to library in the files underneath R/ make things even more complex and fragile, and prone to breakage.

It'll get better, slowly. Maybe a week to get through all of these files? I hope by the end of Wednesday, actually, I can have these refactored into a single package which will work independently of the Shiny app, and will have plenty of documentation that we can work on together to ensure that it is useful and testable (in isolation from Shiny). Real modularization.

[bryce-carson]

See the mention of this issue in the storyline above this comment.