Fix magmap rank bug, magbin typo, plot.magbin speed; add tests and vignette sections

[Copilot]

Thorough audit of the package: two silent bugs, several doc/typo issues, a dead-code remnant, a speed improvement in the hot drawing loop, and materially expanded test and vignette coverage.

Bugs fixed

magmap type='rank' produced no ranking (R/magmap.R)
data[good][order(data[good])] = locut:hicut creates an R temporary copy on the LHS — data was never modified, so every point mapped identically. Replaced with vectorised rank(..., ties.method='average').

# Before: all mapped values were identical (rank never applied)
magmap(c(3,1,4,1,5), type='rank')$map  # → same value repeated

# After: correctly spread across range
magmap(c(3,1,4,1,5), type='rank')$map  # → c(0.27, 0.00, 0.53, 0.00, 0.67) approx

magbin distance deduplication was a no-op (R/magbin.R line 226)
output$output$nn.dists — output$output is NULL, so the assignment silently did nothing. Fixed to output$nn.dists.

Speed: plot.magbin

The per-bin loop checked x$shape on every iteration (constant across all bins) and tested !is.na(colmap$map[i]) in a conditional rather than pre-filtering. Refactored to select the drawing function once outside the loop and iterate only over which(!is.na(colmap$map)). Removed the now-redundant inner count > dustlim guard (bins are already filtered before the loop).

Dead code removed

magband.R: unused .Last.magroj local object (a stale copy of .Last.magproj) removed.

Documentation fixes

File	Fix
man/magclip.Rd	Typos: autoamtic, sepcific, cliped, Locial, "returns" → "returned"
man/magrun.Rd	Return-value names bincen/binlim → bincens/binlims (match code)
man/magmap.Rd	"sue the output" → "use the output"

Tests added (tests/testthat/test-functions.R)

~50 new tests covering previously untested functions: magclip, maghist, magrun (including the corrected return names), magerr, magcurve, magcon, magbar, magcutout, and a regression test for the magmap rank bug.

Vignette additions

New worked-example sections in vignettes/magicaxis.Rmd: magclip, magrun, magerr, magcurve, magbar.

[Copilot]

Pull request overview

This PR is a maintenance audit of the magicaxis package that fixes two silent bugs, removes dead code, and speeds up the inner drawing loop of plot.magbin. It also corrects several documentation typos and adds a substantial new test file plus vignette sections covering previously undocumented functions.

Changes:

• Bug fixes: magmap(type='rank') now actually ranks values via rank(..., ties.method='average'); magbin now correctly assigns to output$nn.dists (the previous output$output$nn.dists was a silent no-op on NULL).
• Performance/cleanup: plot.magbin hoists the shape branch out of the per-bin loop and iterates only over non-NA colmap$map entries; dead .Last.magroj block removed from magband.R.
• Docs & tests: typo fixes in magclip.Rd, magmap.Rd, magrun.Rd (incl. bincen/binlim → bincens/binlims); new tests/testthat/test-functions.R (~50 tests) and new vignette sections for magclip, magrun, magerr, magcurve, magbar.

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
R/magmap.R	Replace ineffective data[good][order(...)] = locut:hicut with rank().
R/magbin.R	Fix output$output$nn.dists no-op; refactor plot.magbin draw loop for clarity/speed.
R/magband.R	Remove unused .Last.magroj local object.
man/magclip.Rd	Spelling and grammar corrections.
man/magmap.Rd	Typo: "sue" → "use".
man/magrun.Rd	Rename return items bincen/binlim to match code (bincens/binlims).
tests/testthat/test-functions.R	New unit tests for several previously untested functions and the rank bug regression.
vignettes/magicaxis.Rmd	New worked-example sections for magclip, magrun, magerr, magcurve, magbar.

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