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Fix as.sir() data.frame: preserve already-<sir> columns, exclude metadata

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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
This commit is contained in:
Claude
2026-04-24 21:30:21 +00:00
parent ce79dd1f75
commit 6ece73cb22
4 changed files with 124 additions and 4 deletions
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24
R/sir.R
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@@ -852,7 +852,6 @@ as.sir.data.frame <- function(x,
i <- 0
ab_cols <- colnames(x)[vapply(FUN.VALUE = logical(1), x, function(y) {
i <<- i + 1
check <- is.mic(y) | is.disk(y)
ab <- colnames(x)[i]
if (!is.null(col_mo) && ab == col_mo) {
return(FALSE)
@@ -861,13 +860,30 @@ as.sir.data.frame <- function(x,
return(FALSE)
}
if (length(sel) == 0 || (length(sel) > 0 && ab %in% sel)) {
# columns already carrying an AMR class are always included
y_bak <- x.bak[, ab, drop = TRUE]
if (is.mic(y_bak) || is.disk(y_bak) || is.sir(y_bak)) {
return(TRUE)
}
ab_coerced <- suppressWarnings(as.ab(ab, info = FALSE))
if (is.na(ab_coerced) || (length(sel) > 0 & !ab %in% sel)) {
# not even a valid AB code
return(FALSE)
} else {
return(TRUE)
}
# Name matches an antibiotic; also verify column content resembles AMR
# data. This prevents false positives on metadata columns whose names
# happen to match a drug code (e.g. 'patient' -> OXY, 'ward' -> PRU).
# Note: all_valid_disks() is intentionally avoided here because it strips
# non-numeric characters (as.disk("Pt_1") == 1), accepting patient IDs.
y_char <- tryCatch(as.character(y), error = function(e) character(0))
y_valid <- y_char[!is.na(y_char) & nzchar(trimws(y_char))]
if (length(y_valid) == 0L) {
return(FALSE)
}
y_numeric <- suppressWarnings(as.numeric(y_valid))
all_valid_mics(y) ||
all(!is.na(y_numeric)) ||
any(y_valid %in% c("S", "SDD", "I", "R", "NI"))
} else {
return(FALSE)
}
@@ -883,7 +899,7 @@ as.sir.data.frame <- function(x,
types[vapply(FUN.VALUE = logical(1), x.bak[, ab_cols, drop = FALSE], is.mic)] <- "mic"
types[types == "" & vapply(FUN.VALUE = logical(1), x[, ab_cols, drop = FALSE], all_valid_disks)] <- "disk"
types[types == "" & vapply(FUN.VALUE = logical(1), x[, ab_cols, drop = FALSE], all_valid_mics)] <- "mic"
types[types == "" & !vapply(FUN.VALUE = logical(1), x.bak[, ab_cols, drop = FALSE], is.sir)] <- "sir"
types[types == ""] <- "sir"
if (any(types %in% c("mic", "disk"), na.rm = TRUE)) {
# now we need an mo column
stop_if(is.null(col_mo), "{.arg col_mo} must be set")