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Fix parallel WISCA returning all NA; strengthen tests; add sequential hint

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Bug: lapply() over a factor yields length-1 factor elements (integer
codes), while for() over a factor yields character strings.  The job
list stored j\$group as a factor integer, but the reassembly loop
compared it with identical(j\$group, g) where g was character -- always
FALSE, so no simulation chunks were ever assembled and coverage stayed
NA throughout.

Fix: convert unique_groups to character before building jobs so both
the job list and the reassembly loop use the same type.

Tests: replaced na.rm = TRUE guards with explicit anyNA() checks so the
test suite would have caught the all-NA result immediately.

Also adds a sequential-mode performance hint (analogous to sir.R
lines 1116-1127) when simulations >= 500 and >= 3 regimens.

https://claude.ai/code/session_01FC43syPbzhGmKgrrVNHjnF
This commit is contained in:
Claude
2026-04-30 17:23:31 +00:00
parent 48af4b7cdc
commit f5ea4ea4ba
2 changed files with 19 additions and 5 deletions
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13
R/antibiogram.R
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@@ -746,7 +746,7 @@ antibiogram.default <- function(x,
c(1 - conf_interval, 1)
}
unique_groups <- unique(wisca_parameters$group)
unique_groups <- as.character(unique(wisca_parameters$group))
use_parallel_wisca <- isTRUE(parallel) && n_workers > 1L && length(unique_groups) > 0L
@@ -815,6 +815,17 @@ antibiogram.default <- function(x,
out_wisca$upper_ci[out_wisca$group == group] <- ci_vals[2]
}
close(progress)
if (isTRUE(info) && simulations >= 500 && length(unique_groups) >= 3) {
suggest <- ifelse(.Platform$OS.type == "windows" || in_rstudio(),
"plan(multisession)",
"plan(multicore)"
)
if (requireNamespace("future.apply", quietly = TRUE)) {
message_("Running in sequential mode. To speed up WISCA, set a parallel {.help [{.fun future::plan}](future::plan)} such as {.code ", suggest, "} and use {.code parallel = TRUE}.")
} else {
message_("Running in sequential mode. To speed up WISCA, install the {.pkg future.apply} package and then set {.code parallel = TRUE}.")
}
}
}
# final output preparation

11
tests/testthat/test-antibiogram.R
View File

@@ -152,11 +152,14 @@ test_that("test-antibiogram.R", {
expect_equal(colnames(wisca_par), colnames(wisca_seq))
expect_true(isTRUE(attributes(wisca_par)$wisca))
# 2. coverage values fall within [0, 100] (basic sanity)
# 2. coverage values are non-NA and fall within [0, 1]
ln <- attributes(wisca_par)$long_numeric
expect_true(all(ln$coverage >= 0 & ln$coverage <= 1, na.rm = TRUE))
expect_true(all(ln$lower_ci <= ln$coverage, na.rm = TRUE))
expect_true(all(ln$upper_ci >= ln$coverage, na.rm = TRUE))
expect_false(anyNA(ln$coverage))
expect_false(anyNA(ln$lower_ci))
expect_false(anyNA(ln$upper_ci))
expect_true(all(ln$coverage >= 0 & ln$coverage <= 1))
expect_true(all(ln$lower_ci <= ln$coverage))
expect_true(all(ln$upper_ci >= ln$coverage))
# 3. a second parallel run gives the same column names
wisca_par2 <- suppressWarnings(suppressMessages(