Cadence bands

[muschellij2]

This is to address #13 but I'm not sure if this is the right classification given what @ang-zhao envisioned or implemented

[Copilot]

Pull request overview

This PR addresses issue #13 by fixing the cadence band classification logic and implementing several infrastructure improvements. The main fix corrects the cut() function behavior in cadence band computation by setting right = FALSE and adjusting break points to properly classify step counts into their intended bands.

Changes:

• Fixed cadence band classification by updating break points and setting right = FALSE in the cut() function
• Renamed package from rnhanescadence to cadence across all files
• Changed default group_cols parameter from hardcoded c("SEQN", "PAXDAYM") to NULL and introduced nhanes_group_cols() helper function
• Added comprehensive vignette documenting cadence computation functionality
• Updated utility function to handle NULL group_cols parameter

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
R/cadence_bands.R	Core fix for band classification: updated breaks, added right = FALSE, removed fast_walk and very_fast_walk bands
R/nhanes_group_cols.R	New helper function returning default NHANES grouping columns
R/aaa_utils.R	Updated to handle NULL group_cols parameter
R/summarize_cadence.R	Changed group_cols default from hardcoded value to NULL
R/compute_peak_cadence.R	Changed group_cols default from hardcoded value to NULL
vignettes/calculate_cadence.Rmd	New vignette documenting cadence calculation workflow
tests/testthat/*.R	Updated test calls to explicitly pass group_cols parameter
tests/testthat.R	Updated library name from rnhanescadence to cadence
DESCRIPTION	Package rename and added vignette dependencies
man/*.Rd	Updated documentation for changed function signatures
.Rbuildignore	Updated for new package name
.gitignore	Added inst/doc to ignore vignette build output
vignettes/.gitignore	Added to ignore vignette build artifacts
cadence.Rproj	New RStudio project file for renamed package

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[Copilot]

The description for peak_60min incorrectly says "Peak 30-minute cadence" when it should say "Peak 60-minute cadence".

Suggested change

	- `peak_60min`: Peak 30-minute cadence.
	- `peak_60min`: Peak 60-minute cadence.

[Copilot]

The documentation lists fast_walk and very_fast_walk as separate cadence bands with specific ranges (90-99 and 100-119 steps/min), but these bands were removed from the code. The actual bands now only include "zero", "incidental", "sporadic", "purposeful", "slow_walk", "medium_walk", "brisk_walk", and "all_out" (8 bands total), with breaks at [0, 1), [1, 20), [20, 40), [40, 60), [60, 80), [80, 100), [100, 120), and [120, Inf). The documentation should be updated to reflect the actual implemented bands and their ranges.

Suggested change

	- `zero`: Time spent in zero cadence band.
	- `incidental`: Time spent in incidental cadence band.
	- `sporadic`: Time spent in sporadic cadence band.
	- `purposeful`: Time spent in purposeful cadence band.
	- `slow_walk`: Time spent in slow walking cadence band.
	- `medium_walk`: Time spent in medium walking cadence band.
	- `brisk_walk`: Time spent in brisk walking cadence band.
	- `fast_walk`: Time spent in fast walking cadence band: 90-99 steps/min.
	- `very_fast_walk`: Time spent in very fast walking cadence band: 100-119 steps/min.
	- `all_out`: Time spent in all-out cadence band: 119+ steps/min.
	- `zero`: Time spent in zero cadence band: 0 steps/min.
	- `incidental`: Time spent in incidental cadence band: 1-19 steps/min.
	- `sporadic`: Time spent in sporadic cadence band: 20-39 steps/min.
	- `purposeful`: Time spent in purposeful cadence band: 40-59 steps/min.
	- `slow_walk`: Time spent in slow walking cadence band: 60-79 steps/min.
	- `medium_walk`: Time spent in medium walking cadence band: 80-99 steps/min.
	- `brisk_walk`: Time spent in brisk walking cadence band: 100-119 steps/min.
	- `all_out`: Time spent in all-out cadence band: 120+ steps/min.

[Copilot]

The documentation for cadence bands (lines 61-67) does not specify the step ranges for each band. Since the code now uses specific break points [0, 1, 20, 40, 60, 80, 100, 120, Inf] with right = FALSE, the documentation should clearly state the ranges for each band to help users understand the classification (e.g., zero: 0 steps/min, incidental: 1-19 steps/min, sporadic: 20-39 steps/min, etc.).

Suggested change

	Cadence Bands:
	- `zero`: Time spent in zero cadence band.
	- `incidental`: Time spent in incidental cadence band.
	- `sporadic`: Time spent in sporadic cadence band.
	- `purposeful`: Time spent in purposeful cadence band.
	- `slow_walk`: Time spent in slow walking cadence band.
	- `medium_walk`: Time spent in medium walking cadence band.
	- `brisk_walk`: Time spent in brisk walking cadence band.
	- `fast_walk`: Time spent in fast walking cadence band: 90-99 steps/min.
	- `very_fast_walk`: Time spent in very fast walking cadence band: 100-119 steps/min.
	- `all_out`: Time spent in all-out cadence band: 119+ steps/min.
	Cadence Bands (steps per minute, using breaks [0, 1, 20, 40, 60, 80, 100, 120, Inf] with `right = FALSE`):
	- `zero`: Time spent at 0 steps/min.
	- `incidental`: Time spent at 1–19 steps/min.
	- `sporadic`: Time spent at 20–39 steps/min.
	- `purposeful`: Time spent at 40–59 steps/min.
	- `slow_walk`: Time spent at 60–79 steps/min.
	- `medium_walk`: Time spent at 80–99 steps/min.
	- `brisk_walk`: Time spent at 100–119 steps/min.
	- `all_out`: Time spent at 120+ steps/min.

[muschellij2]

Can you comment @ang-zhao on this vs. not