Check for plane_shape documentation issues

[abenefield1]

Checking/fixing/adding documentation that might have been impacted by the new plane_shape() method. Here are the places I can think to check, but let me know if you think of any others:

• [x] 1. plane_shape() documentation and examples
• [x] 2. plane_score documentation and examples
• [x] 3. interpretation vignette
• [x] 4. individual component vignette
• [x] 5. basic usage vignette
• [x] 6. shiny app

[abenefield1]

@vpnagraj - I think I caught all places where documentation needed to be updated. Also, I found an error in the interpretation vignette that I pushed back to dev. See details and further suggestions below:

• plane_shape() documentation was already completed, though we may want to include the sensitivity/specificity info that we observed in preliminary analyses (e.g., "Based on preliminary analyses, the DTW method has a higher sensitivity and a slightly lower specificity than the "sdiff" method but is much more computationally expensive.")
• plane_score() documentation - Made minor changes in plane_score documentation - added method argument in example where users provide non-default arguments to plane_score().
• Interpretation vignette - I found an error in this vignette implying that we had a sensitivity argument within shape (was the 2nd to last bullet point under "Motivations for weighting"). I think this was based on some deprecated version of the shape component that never made it to a package version release. I fixed this on dev.
• Individual component vignette - Added a couple of sentences under the shape section. We may want to add a subsection about comparing the two methods, but that's a larger task for the future.
• Basic Usage Vignette - no edits needed
• Shiny app - @vpnagraj had already added a choice for default or dtw. IMO, that should be labeled "sdiff (default)" and "Dynamic Time Warping" just to be consistent with documentation. Also need to add a bullet point under the help tab / Modify Defaults for Method (shape) and then a sentence about the two method options. @dwill023 I don't want to mess anything up in the shiny app. Would you mind making those changes?

[vpnagraj]

thanks @abenefield1 .

ive addressed the relevant items mentioned above:

• i added a bit more to the plane_shape() regarding comparisons between sdiff and dtw methods (https://github.com/signaturescience/rplanes/pull/145/commits/6411d09a2a23f8fbbc7389a72cf4d2d0f0d42506)
• i changed the shiny app radio button selections to "sdiff (Default)" and "Dynamic Time Warping" (https://github.com/signaturescience/rplanes/pull/145/commits/8f90e16b4a9ea161457462737bfce7cc62b9887f)

also reminder to always make sure to run devtools::check() on the package when adding new features (even updates to documentation!) ... turns out that we ran into a pesky character limit in one of the examples with one of your commits. here were the check results:

── R CMD check results ───────────────────────────────────────────────────────────────────────────────────────── rplanes 0.0.3.9000 ────
Duration: 1m 2.6s

❯ checking Rd line widths ... NOTE
  Rd file 'plane_score.Rd':
    \examples lines wider than 100 characters:
       comp_args <- list("trend" = list("sig_lvl" = 0.05), "repeat" = list("prepend" = 4, "tolerance" = 8), "shape" = list("method" = "dtw"))

comp_args <- list("trend" = list("sig_lvl" = 0.05), "repeat" = list("prepend" = 4, "tolerance" = 8), "shape" = list("method" = "dtw"))

its a NOTE which would require an explanation for CRAN review. to get around that i broke up the comp_args object definition into a few separate lines (https://github.com/signaturescience/rplanes/pull/145/commits/fcdfc4d604b9ea06b2abdd8a51bb18abb02c74a5) ... check is coming through clean now (no NOTEs, WARNINGs, or ERRORs)