Fix version to 3.0.1.9055 and update CLAUDE.md version formula

Uses origin/${defaultbranch} (with a fetch) instead of the local
branch ref so the commit count is never stale after a merge.

https://claude.ai/code/session_01FC43syPbzhGmKgrrVNHjnF

CLAUDE.md

@@ -167,7 +167,8 @@ Then run the following from the repo root to determine the version string to use
 currenttag=$(git describe --tags --abbrev=0 | sed 's/v//')
 currenttagfull=$(git describe --tags --abbrev=0)
 defaultbranch=$(git branch | cut -c 3- | grep -E '^master$|^main$')
-currentcommit=$(git rev-list --count ${currenttagfull}..${defaultbranch})
+git fetch origin ${defaultbranch} --quiet
+currentcommit=$(git rev-list --count ${currenttagfull}..origin/${defaultbranch})
 currentversion="${currenttag}.$((currentcommit + 9001 + 1))"
 echo "$currentversion"
 ```

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.1.9053
+Version: 3.0.1.9055
-Date: 2026-04-27
+Date: 2026-04-30
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9053
+# AMR 3.0.1.9055
 
 This will become release v3.1.0, intended for launch end of May.
 
@@ -7,6 +7,7 @@ This will become release v3.1.0, intended for launch end of May.
 * Support for the [`future`](https://future.futureverse.org) package and its framework, as the previous implementation of parallel computing was slow
   - **Breaking change**: `as.sir()` with `parallel = TRUE` now requires a non-sequential `future::plan()` to be active before the call — e.g., `future::plan(future::multisession)` — and throws an informative error if none is set.
   - New all-core usage setup: 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 and processing time)
+  - `antibiogram()` and `wisca()` gained a `parallel` argument using the same `future`/`future.apply` pattern: for WISCA, Monte Carlo simulations are split into `(group, chunk)` job pairs distributed across workers; for grouped antibiograms, each group is processed by a separate worker (#281)
 * Integration with the *tidymodels* framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
   - `step_mic_log2()` to transform `<mic>` columns with log2, and `step_sir_numeric()` to convert `<sir>` columns to numeric
   - New `tidyselect` helpers:

R/antibiogram.R

@@ -65,6 +65,7 @@
 #' @param simulations (for WISCA) a numerical value to set the number of Monte Carlo simulations.
 #' @param conf_interval A numerical value to set confidence interval (default is `0.95`).
 #' @param interval_side The side of the confidence interval, either `"two-tailed"` (default), `"left"` or `"right"`.
+#' @param parallel A [logical] to indicate if parallel computing must be used, defaults to `FALSE`. Requires the [`future.apply`][future.apply::future_lapply()] package. For WISCA, Monte Carlo simulations are distributed across workers; for grouped antibiograms, each group is processed by a separate worker. **A non-sequential [future::plan()] must already be active before setting `parallel = TRUE`** — for example, `future::plan(future::multisession)`. An error is thrown if `parallel = TRUE` is used without a plan set by the user.
 #' @param info A [logical] to indicate info should be printed - the default is `TRUE` only in interactive mode.
 #' @param object An [antibiogram()] object.
 #' @param ... When used in [R Markdown or Quarto][knitr::kable()]: arguments passed on to [knitr::kable()] (otherwise, has no use).
@@ -413,6 +414,7 @@ antibiogram <- function(x,
                         conf_interval = 0.95,
                         interval_side = "two-tailed",
                         info = interactive(),
+                        parallel = FALSE,
                         ...) {
   UseMethod("antibiogram")
 }
@@ -439,6 +441,7 @@ antibiogram.default <- function(x,
                                 conf_interval = 0.95,
                                 interval_side = "two-tailed",
                                 info = interactive(),
+                                parallel = FALSE,
                                 ...) {
   meet_criteria(x, allow_class = "data.frame")
   x <- ascertain_sir_classes(x, "x")
@@ -478,6 +481,7 @@ antibiogram.default <- function(x,
   meet_criteria(conf_interval, allow_class = c("numeric", "integer"), has_length = 1, is_finite = TRUE, is_positive = TRUE)
   meet_criteria(interval_side, allow_class = "character", has_length = 1, is_in = c("two-tailed", "left", "right"))
   meet_criteria(info, allow_class = "logical", has_length = 1)
+  meet_criteria(parallel, allow_class = "logical", has_length = 1)
 
   # try to find columns based on type
   if (is.null(col_mo)) {
@@ -705,52 +709,113 @@ antibiogram.default <- function(x,
 
     wisca_parameters <- out
 
-    progress <- progress_ticker(
+    # quantile probabilities are constant across all groups
-      n = length(unique(wisca_parameters$group)) * simulations,
+    probs <- if (interval_side == "two-tailed") {
-      n_min = 25,
+      c((1 - conf_interval) / 2, 1 - (1 - conf_interval) / 2)
-      print = info,
+    } else if (interval_side == "left") {
-      title = paste("Calculating WISCA for", length(unique(wisca_parameters$group)), "regimens")
+      c(0, conf_interval)
-    )
+    } else {
-    on.exit(close(progress))
+      c(1 - conf_interval, 1)
-
-    # run WISCA per group
-    for (group in unique(wisca_parameters$group)) {
-      params_current <- wisca_parameters[wisca_parameters$group == group, , drop = FALSE]
-      if (sum(params_current$n_tested, na.rm = TRUE) == 0) {
-        next
-      }
-
-      # prepare priors
-      priors_current <- create_wisca_priors(params_current)
-
-      # Monte Carlo simulations
-      coverage_simulations <- vapply(
-        FUN.VALUE = double(1),
-        seq_len(simulations), function(i) {
-          progress$tick()
-          simulate_coverage(priors_current)
-        }
-      )
-
-      # summarise results
-      coverage_mean <- mean(coverage_simulations)
-
-      if (interval_side == "two-tailed") {
-        probs <- c((1 - conf_interval) / 2, 1 - (1 - conf_interval) / 2)
-      } else if (interval_side == "left") {
-        probs <- c(0, conf_interval)
-      } else if (interval_side == "right") {
-        probs <- c(1 - conf_interval, 1)
-      }
-
-      coverage_ci <- unname(stats::quantile(coverage_simulations, probs = probs))
-
-      out_wisca$coverage[out_wisca$group == group] <- coverage_mean
-      out_wisca$lower_ci[out_wisca$group == group] <- coverage_ci[1]
-      out_wisca$upper_ci[out_wisca$group == group] <- coverage_ci[2]
     }
 
-    close(progress)
+    unique_groups <- unique(wisca_parameters$group)
+
+    # parallel gate for WISCA — identical pattern to as.sir()
+    if (requireNamespace("future.apply", quietly = TRUE) && !inherits(future::plan(), "sequential")) {
+      if (isFALSE(parallel)) {
+        message_("Assuming {.code parallel = TRUE} since parallel computing has been set up using the {.pkg future} package before. Set {.help [{.fun plan}](future::plan)} to sequential to prevent this.")
+      }
+      parallel <- TRUE
+    }
+    if (isTRUE(parallel)) {
+      stop_ifnot(
+        requireNamespace("future.apply", quietly = TRUE),
+        "Setting {.code parallel = TRUE} requires the {.pkg future.apply} package.\n",
+        "Install it with {.code install.packages(\"future.apply\")}."
+      )
+      stop_if(inherits(future::plan(), "sequential"),
+        "Setting {.code parallel = TRUE} requires a non-sequential {.help [{.fun future::plan}](future::plan)} to be active.\n",
+        "For your system, you could first run: {.code library(future); ",
+        ifelse(.Platform$OS.type == "windows" || in_rstudio(),
+          "plan(multisession)",
+          "plan(multicore)"
+        ),
+        "}",
+        call = FALSE
+      )
+      n_workers <- future::nbrOfWorkers()
+    } else {
+      n_workers <- 1L
+    }
+
+    use_parallel_wisca <- isTRUE(parallel) && n_workers > 1L && length(unique_groups) > 0L
+
+    if (use_parallel_wisca) {
+      if (isTRUE(info)) {
+        message_("Running WISCA in parallel mode using ", n_workers, " workers...", as_note = FALSE, appendLF = FALSE)
+      }
+      # chunks_per_group gives ~n_workers total jobs so all workers stay busy
+      # even when the number of regimens is smaller than n_workers
+      chunks_per_group <- max(1L, ceiling(n_workers / length(unique_groups)))
+      chunk_sizes <- diff(c(0L, round(seq_len(chunks_per_group) * simulations / chunks_per_group)))
+
+      # precompute priors per group and build (group, chunk) job list
+      jobs <- unlist(lapply(unique_groups, function(g) {
+        params_g <- wisca_parameters[wisca_parameters$group == g, , drop = FALSE]
+        if (sum(params_g$n_tested, na.rm = TRUE) == 0L) return(NULL)
+        priors_g <- create_wisca_priors(params_g)
+        lapply(seq_along(chunk_sizes), function(ch) {
+          list(group = g, priors = priors_g, n_sims = chunk_sizes[ch])
+        })
+      }), recursive = FALSE)
+      jobs <- Filter(Negate(is.null), jobs)
+
+      flat <- future.apply::future_lapply(jobs, function(job) {
+        vapply(FUN.VALUE = double(1), seq_len(job$n_sims), function(i) {
+          simulate_coverage(job$priors)
+        })
+      }, future.seed = TRUE)
+
+      # reassemble per group: concatenate chunks, then summarise
+      for (g in unique_groups) {
+        g_idx <- vapply(jobs, function(j) identical(j$group, g), logical(1))
+        if (!any(g_idx)) next
+        sims <- unlist(flat[g_idx], use.names = FALSE)
+        out_wisca$coverage[out_wisca$group == g] <- mean(sims)
+        ci_vals <- unname(stats::quantile(sims, probs = probs))
+        out_wisca$lower_ci[out_wisca$group == g] <- ci_vals[1]
+        out_wisca$upper_ci[out_wisca$group == g] <- ci_vals[2]
+      }
+
+      if (isTRUE(info)) message_(font_green_bg(" DONE "), as_note = FALSE)
+
+    } else {
+      progress <- progress_ticker(
+        n = length(unique_groups) * simulations,
+        n_min = 25,
+        print = info,
+        title = paste("Calculating WISCA for", length(unique_groups), "regimens")
+      )
+      on.exit(close(progress), add = TRUE)
+
+      for (group in unique_groups) {
+        params_current <- wisca_parameters[wisca_parameters$group == group, , drop = FALSE]
+        if (sum(params_current$n_tested, na.rm = TRUE) == 0) next
+        priors_current <- create_wisca_priors(params_current)
+        coverage_simulations <- vapply(
+          FUN.VALUE = double(1),
+          seq_len(simulations), function(i) {
+            progress$tick()
+            simulate_coverage(priors_current)
+          }
+        )
+        out_wisca$coverage[out_wisca$group == group] <- mean(coverage_simulations)
+        ci_vals <- unname(stats::quantile(coverage_simulations, probs = probs))
+        out_wisca$lower_ci[out_wisca$group == group] <- ci_vals[1]
+        out_wisca$upper_ci[out_wisca$group == group] <- ci_vals[2]
+      }
+      close(progress)
+    }
 
     # final output preparation
     out <- out_wisca
@@ -997,30 +1062,50 @@ antibiogram.grouped_df <- function(x,
                                    conf_interval = 0.95,
                                    interval_side = "two-tailed",
                                    info = interactive(),
+                                   parallel = FALSE,
                                    ...) {
   stop_ifnot(is.null(mo_transform), "{.arg mo_transform} must not be set if creating an antibiogram using a grouped tibble. The groups will become the variables over which the antimicrobials are calculated, which could include the pathogen information (though not necessary). Nonetheless, this makes {.arg mo_transform} redundant.", call = FALSE)
   stop_ifnot(is.null(syndromic_group), "{.arg syndromic_group} must not be set if creating an antibiogram using a grouped tibble. The groups will become the variables over which the antimicrobials are calculated, making {.arg syndromic_group} redundant.", call = FALSE)
+  meet_criteria(parallel, allow_class = "logical", has_length = 1)
+
   groups <- attributes(x)$groups
   n_groups <- NROW(groups)
-  progress <- progress_ticker(
-    n = n_groups,
-    n_min = 5,
-    print = info,
-    title = paste("Calculating AMR for", n_groups, "groups")
-  )
-  on.exit(close(progress))
 
-  out <- NULL
+  # parallel gate — identical pattern to as.sir()
-  wisca_parameters <- NULL
+  if (requireNamespace("future.apply", quietly = TRUE) && !inherits(future::plan(), "sequential")) {
-  long_numeric <- NULL
+    if (isFALSE(parallel)) {
-
+      message_("Assuming {.code parallel = TRUE} since parallel computing has been set up using the {.pkg future} package before. Set {.help [{.fun plan}](future::plan)} to sequential to prevent this.")
-  for (i in seq_len(n_groups)) {
-    progress$tick()
-    rows <- unlist(groups[i, ]$.rows)
-    if (length(rows) == 0) {
-      next
     }
-    new_out <- antibiogram(as.data.frame(x)[rows, , drop = FALSE],
+    parallel <- TRUE
+  }
+  if (isTRUE(parallel)) {
+    stop_ifnot(
+      requireNamespace("future.apply", quietly = TRUE),
+      "Setting {.code parallel = TRUE} requires the {.pkg future.apply} package.\n",
+      "Install it with {.code install.packages(\"future.apply\")}."
+    )
+    stop_if(inherits(future::plan(), "sequential"),
+      "Setting {.code parallel = TRUE} requires a non-sequential {.help [{.fun future::plan}](future::plan)} to be active.\n",
+      "For your system, you could first run: {.code library(future); ",
+      ifelse(.Platform$OS.type == "windows" || in_rstudio(),
+        "plan(multisession)",
+        "plan(multicore)"
+      ),
+      "}",
+      call = FALSE
+    )
+    n_workers <- future::nbrOfWorkers()
+  } else {
+    n_workers <- 1L
+  }
+
+  use_parallel <- isTRUE(parallel) && n_workers > 1L && n_groups > 1L
+
+  x_df <- as.data.frame(x)
+  run_group <- function(i) {
+    rows <- unlist(groups[i, ]$.rows)
+    if (length(rows) == 0L) return(NULL)
+    antibiogram(x_df[rows, , drop = FALSE],
       antimicrobials = antimicrobials,
       mo_transform = NULL,
       ab_transform = ab_transform,
@@ -1040,12 +1125,42 @@ antibiogram.grouped_df <- function(x,
       conf_interval = conf_interval,
       interval_side = interval_side,
       info = FALSE,
-      ...
+      parallel = FALSE  # never nest parallelism in workers
     )
+  }
+
+  if (use_parallel) {
+    if (isTRUE(info)) {
+      message_("Running antibiogram for ", n_groups, " groups in parallel using ", n_workers, " workers...", as_note = FALSE, appendLF = FALSE)
+    }
+    results_raw <- future.apply::future_lapply(seq_len(n_groups), run_group, future.seed = TRUE)
+    if (isTRUE(info)) message_(font_green_bg(" DONE "), as_note = FALSE)
+  } else {
+    progress <- progress_ticker(
+      n = n_groups,
+      n_min = 5,
+      print = info,
+      title = paste("Calculating AMR for", n_groups, "groups")
+    )
+    on.exit(close(progress), add = TRUE)
+    results_raw <- vector("list", n_groups)
+    for (i in seq_len(n_groups)) {
+      progress$tick()
+      results_raw[[i]] <- run_group(i)
+    }
+    close(progress)
+  }
+
+  out <- NULL
+  wisca_parameters <- NULL
+  long_numeric <- NULL
+
+  for (i in seq_len(n_groups)) {
+    new_out <- results_raw[[i]]
     new_wisca_parameters <- attributes(new_out)$wisca_parameters
     new_long_numeric <- attributes(new_out)$long_numeric
 
-    if (NROW(new_out) == 0) {
+    if (is.null(new_out) || NROW(new_out) == 0) {
       next
     }
 
@@ -1071,8 +1186,7 @@ antibiogram.grouped_df <- function(x,
       new_long_numeric <- new_long_numeric[, c(col_name, setdiff(names(new_long_numeric), col_name))] # set place to 1st col
     }
 
-    if (i == 1) {
+    if (is.null(out)) {
-      # the first go
       out <- new_out
       wisca_parameters <- new_wisca_parameters
       long_numeric <- new_long_numeric
@@ -1083,8 +1197,6 @@ antibiogram.grouped_df <- function(x,
     }
   }
 
-  close(progress)
-
   out <- structure(as_original_data_class(out, class(x), extra_class = "antibiogram"),
     has_syndromic_group = FALSE,
     combine_SI = isTRUE(combine_SI),
@@ -1116,6 +1228,7 @@ wisca <- function(x,
                   conf_interval = 0.95,
                   interval_side = "two-tailed",
                   info = interactive(),
+                  parallel = FALSE,
                   ...) {
   antibiogram(
     x = x,
@@ -1137,6 +1250,7 @@ wisca <- function(x,
     conf_interval = conf_interval,
     interval_side = interval_side,
     info = info,
+    parallel = parallel,
     ...
   )
 }

tests/testthat/test-antibiogram.R

@@ -130,6 +130,74 @@ test_that("test-antibiogram.R", {
     expect_equal(colnames(ab9), c("ward", "gender", "Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))
   }
 
+  # Parallel computing ----------------------------------------------------
+  # Tests must pass even when only 1 core is available; parallel = TRUE then
+  # silently falls back to sequential, but results must still be correct.
+
+  if (AMR:::pkg_is_available("future.apply")) {
+    set.seed(42)
+
+    # sequential reference for WISCA
+    wisca_seq <- suppressWarnings(suppressMessages(
+      wisca(example_isolates, antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"), simulations = 100, info = FALSE)
+    ))
+
+    future::plan(future::multicore)
+
+    # 1. parallel = TRUE produces the same antibiogram structure as sequential
+    wisca_par <- suppressWarnings(suppressMessages(
+      wisca(example_isolates, antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"), simulations = 100, parallel = TRUE, info = FALSE)
+    ))
+    expect_inherits(wisca_par, "antibiogram")
+    expect_equal(colnames(wisca_par), colnames(wisca_seq))
+    expect_true(isTRUE(attributes(wisca_par)$wisca))
+
+    # 2. coverage values fall within [0, 100] (basic sanity)
+    ln <- attributes(wisca_par)$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))
+
+    # 3. a second parallel run gives the same column names
+    wisca_par2 <- suppressWarnings(suppressMessages(
+      wisca(example_isolates, antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"), simulations = 100, parallel = TRUE, info = FALSE)
+    ))
+    expect_equal(colnames(wisca_par), colnames(wisca_par2))
+
+    # 4. parallel with workers = 1 gives same structure as sequential
+    future::plan(future::multicore, workers = 1)
+    wisca_par1 <- suppressWarnings(suppressMessages(
+      wisca(example_isolates, antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"), simulations = 100, parallel = TRUE, info = FALSE)
+    ))
+    expect_equal(colnames(wisca_seq), colnames(wisca_par1))
+
+    # 5. grouped antibiogram in parallel yields identical structure to sequential
+    if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
+      future::plan(future::sequential)
+      ab_grp_seq <- suppressWarnings(suppressMessages(
+        example_isolates %>%
+          group_by(ward) %>%
+          wisca(antimicrobials = c("TZP", "TZP+TOB"), simulations = 50, info = FALSE)
+      ))
+      future::plan(future::multicore)
+      ab_grp_par <- suppressWarnings(suppressMessages(
+        example_isolates %>%
+          group_by(ward) %>%
+          wisca(antimicrobials = c("TZP", "TZP+TOB"), simulations = 50, parallel = TRUE, info = FALSE)
+      ))
+      expect_equal(colnames(ab_grp_seq), colnames(ab_grp_par))
+      expect_equal(nrow(ab_grp_seq), nrow(ab_grp_par))
+    }
+
+    # 6. parallel = TRUE without a plan raises an informative error
+    future::plan(future::sequential)
+    expect_error(
+      suppressWarnings(wisca(example_isolates, antimicrobials = "TZP", parallel = TRUE, info = FALSE)),
+      "non-sequential"
+    )
+
+    future::plan(future::sequential)
+  }
 
   # Generate plots with ggplot2 or base R --------------------------------