2 Commits

Include renames

Author	SHA1	Message	Date
Claude	d770469a63	Update benchmark: two-panel script with warm-up and column-count sweep ... Previous single-panel benchmark was misleading: the first sequential run paid one-time cache-warm-up cost (skewing n=20), and only 6 columns were used so only 6 cores were ever active on a 16-core machine. New two-panel design: Left – vary rows with 16 fixed AB columns (shows memory-bandwidth saturation for large n) Right – vary columns with fixed rows (shows the real speedup profile: parallel wins when n_cols >> 1) Also adds a warm-up pass before measurements to eliminate first-call bias. https://claude.ai/code/session_012DXCXbZUC54Zij1z9bFiHR	2026-04-24 21:42:05 +00:00
Claude	6ece73cb22	Fix as.sir() data.frame: preserve already-<sir> columns, exclude metadata ... Issue #278: two related bugs in the column-detection / type-assignment pipeline. Bug 1 – already-<sir> columns deleted on re-run Line 886 excluded already-sir columns from the type assignment (they stayed type "") causing the result loop to do x[,col] <- NULL, deleting them. Fix: drop the !is.sir() guard so all untyped columns fall through to type "sir" and are re-processed correctly. Bug 2 – metadata columns treated as antibiotics as.ab("patient") -> OXY, as.ab("ward") -> PRU. The column detector accepted any column whose name matched an antibiotic code, regardless of content. Fix: for name-matched columns that do not already carry an AMR class, also verify content looks like AMR data (all_valid_mics, all- numeric, or any SIR-like string). all_valid_disks() is intentionally avoided here because it strips letters from strings (as.disk("Pt_1")==1). Also adds tools/benchmark_parallel.R: a standalone script that times sequential vs parallel as.sir() across n=20/200/2000/20000 rows and saves a ggplot2 PNG to tools/benchmark_parallel.png. https://claude.ai/code/session_012DXCXbZUC54Zij1z9bFiHR	2026-04-24 21:30:21 +00:00