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docs(man): runnable examples for ms_tally/ms_extract/ms_fit/ms_compare - #91
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ms_tally/ms_extract/ms_fit/ms_compare carried the only four man pages of
the flagship grammar without an \examples{} block (12 of 97 pages had
one). Each example is standalone and tempfile-based, verified by direct
execution against load_all before this commit:
- ms_tally: a 2-record VCF tallied against a minimal in-memory 2bit
genome (little-endian 2bit serialization written inline; variants sit
inside the SBS96 context window so nothing is ledgered as skipped).
- ms_extract/ms_fit/ms_compare: one shared scenario over the bundled
COSMIC SBS96 reference -- simulate three signatures with fixed
activity shares, extract with the default pipeline, refit exposures,
compare against truth under the Jiang protocol with a small null MC
(null_n=200/null_n_draws=500 to stay example-sized while honoring the
>=200 floor).
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What
Adds
@examplesroxygen blocks to the four flagship faces —ms_tally,ms_extract,ms_fit,ms_compare— the working grammar's entry points, which were the only four of the twelve example-bearing-candidate man pages without runnable examples (12/97 pages had\examples{}before; this takes the flagship four off the lacking list).Each example is standalone, tempfile-based, and verified by direct execution against
load_all()before this commit (every block ran end-to-end with no error).Why
The flagship man pages are a new user's first landing spots;
?ms_tallythrough?ms_comparehad no executable usage. Per the docs remediation roster (MEDIUM-1).Notes for reviewers
ms_tally's example builds a minimal little-endian 2bit genome inline (16-byte header, one 9-byte index entry, one 8 bp chromosome record, packed0x19 0xE7= TCACGACG). The two VCF records sit at positions 3 and 6, inside the SBS96 context window, so the tally is exercised end-to-end withn_skipped = 0.ms_extract/ms_fit/ms_compareshare one scenario: bundled COSMIC SBS96 reference subset to three signatures, 24 samples with fixed activity shares,ms_simulate(burden = 4000, seed = 7), then extract → refit → compare.ms_comparepassesnull_n = 200, null_n_draws = 500— example-sized while honoring the>= 200draw floor the Jiang protocol enforces.devtools::document()regenerated the four.Rdfiles; a pre-existing drift inman/plot_catalog_profile.Rd(source fixed in daf7020, Rd lagging) surfaced during regen and was reverted out of this PR — it is doc-sync debt from docs(site): professional README, tiered pkgdown user site, docs/ corpus converted to site articles #75/fix(ci): publish the Pages site instead of only storing its artifact #79, not this change's concern.Test plan
@examplesblock verbatim and ran it viaRscriptagainstload_all()— all four OKdevtools::document()— clean, only the four intended.Rdfiles writtencatalog-tally,ffi-tally,docs-bridgegreen (1 sanctioned skip: lane-site 404 census in R CMD check context)