P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-05-31 10:21:46 +02:00
Code Releases Activity

Fix info=FALSE ignored when no breakpoints found in as_sir_method

Browse Source 
Operator-precedence bug at line 1601:

  if (isTRUE(info) && nrow(df_unique) < 10 || nrow(breakpoints) == 0)

R evaluates && before ||, so this was equivalent to:

  (isTRUE(info) && nrow(df_unique) < 10) || (nrow(breakpoints) == 0)

When nrow(breakpoints) == 0 (e.g. cefoxitin / flucloxacillin / mupirocin
against E. coli in EUCAST) the intro message was always printed regardless
of info. Fix: add parentheses so info gates both conditions:

  isTRUE(info) && (nrow(df_unique) < 10 || nrow(breakpoints) == 0)

Also pass print = isTRUE(info) to progress_ticker so the progress bar
(which prints intro_txt as its title) is suppressed when info = FALSE.

https://claude.ai/code/session_012DXCXbZUC54Zij1z9bFiHR
This commit is contained in:
Claude
2026-04-24 22:14:54 +00:00
parent 060449e234
commit bf102f644e
2 changed files with 3 additions and 2 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
NEWS.md
View File

@@ -38,6 +38,7 @@
* Fixed `as.sir()` for data frames silently deleting columns whose AB class was already `<sir>` when called a second time (re-running on already-converted data) (#278)
* Fixed `as.sir()` for data frames incorrectly treating metadata columns (e.g. `patient`, `ward`) as antibiotic columns when their names coincidentally matched an antibiotic code; column content is now validated against AMR data patterns before inclusion
* Improved parallel computing in `as.sir()`: when the number of AB columns is smaller than the number of available cores, rows are now split into batches so all cores stay active (row-batch mode). Previously, a 6-column dataset on a 16-core machine would only use 6 cores; now all 16 are used, with each worker processing a smaller row slice (lower per-worker memory pressure)
* Fixed `as.sir()` ignoring `info = FALSE` for columns with no breakpoints (e.g. cefoxitin against *E. coli*): an operator-precedence bug (`&&`/`||`) caused the "Interpreting MIC values" intro message to fire unconditionally when `nrow(breakpoints) == 0`, regardless of `info`; the progress bar title was also not gated by `info`
### Updates
* Extensive `cli` integration for better message handling and clickable links in messages and warnings (#191, #265)

4
R/sir.R
View File

@@ -1598,11 +1598,11 @@ as_sir_method <- function(method_short,
add_intrinsic_resistance_to_AMR_env()
}
if (isTRUE(info) && nrow(df_unique) < 10 || nrow(breakpoints) == 0) {
if (isTRUE(info) && (nrow(df_unique) < 10 || nrow(breakpoints) == 0)) {
# only print intro under 10 items, otherwise progressbar will print this and then it will be printed double
message_(intro_txt, appendLF = FALSE, as_note = FALSE)
}
p <- progress_ticker(n = nrow(df_unique), n_min = 10, title = intro_txt, only_bar_percent = TRUE)
p <- progress_ticker(n = nrow(df_unique), n_min = 10, print = isTRUE(info), title = intro_txt, only_bar_percent = TRUE)
has_progress_bar <- !is.null(import_fn("progress_bar", "progress", error_on_fail = FALSE)) && nrow(df_unique) >= 10
on.exit(close(p))