From f5ea4ea4ba5993b37fdf112aa9766e93310d435f Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Thu, 30 Apr 2026 17:23:31 +0000
Subject: [PATCH] Fix parallel WISCA returning all NA; strengthen tests; add
 sequential hint

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
---
 R/antibiogram.R                   | 13 ++++++++++++-
 tests/testthat/test-antibiogram.R | 11 +++++++----
 2 files changed, 19 insertions(+), 5 deletions(-)

diff --git a/R/antibiogram.R b/R/antibiogram.R
index 0fe11bb71..dc4e707e0 100755
--- a/R/antibiogram.R
+++ b/R/antibiogram.R
@@ -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
diff --git a/tests/testthat/test-antibiogram.R b/tests/testthat/test-antibiogram.R
index f7a74f221..6dab925a4 100644
--- a/tests/testthat/test-antibiogram.R
+++ b/tests/testthat/test-antibiogram.R
@@ -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(