fix claude suggestions

Author: kristinawlai

R/check_parallel_cores.R

@@ -11,7 +11,8 @@ check_parallel_cores <- function(num_cores) {
       c(
         "This computer appears to have
         {parallel::detectCores()} cores available.
-        Reducing `num_cores` argument to {num_cores}
+        `est_seroincidence_by()` has reduced its
+        `num_cores` argument to {num_cores}
         to avoid destabilizing the computer."
       )
     )

R/sim_pop_data_multi.R

@@ -7,6 +7,7 @@
 #' @param lambdas incidence rate, in events/person*year
 #' @param num_cores number of cores to use for parallel computations
 #' @param verbose whether to report verbose information
+#' @param ... arguments passed to [sim.cs()]
 #' @inheritDotParams sim_pop_data
 #' @return a [tibble::tibble()]
 #' @export
@@ -26,7 +27,32 @@ sim_pop_data_multi <- function(
 
   if (num_cores > 1L) {
 
+    chk <- Sys.getenv("_R_CHECK_LIMIT_CORES_", "")
+
+    if (nzchar(chk)) {
+      chk_u <- toupper(chk)
+
+      if (chk_u %in% c("TRUE", "T", "YES", "Y")) {
+        # In check environments, be polite: cap at 2
+        num_cores <- min(num_cores, 2L)
+
+      } else if (chk_u %in% c("FALSE", "F", "NO", "N")) {
+        # No cap requested
+
+      } else {
+        # Often this is a numeric string like "2"
+        chk_n <- suppressWarnings(as.integer(chk))
+        if (!is.na(chk_n) && chk_n >= 1L) {
+          num_cores <- min(num_cores, chk_n)
+        } else {
+          # Unrecognized value: be conservative
+          num_cores <- min(num_cores, 2L)
+        }
+      }
+    }
+
     # Apply existing safety checker after any cap
+
     num_cores <- num_cores |> check_parallel_cores()
 
   }

cran-comments.md

@@ -10,7 +10,7 @@
 
 ## R CMD check results
 
-0 errors | 0 warnings | 2 notes
+0 errors | 0 warnings | 1 note
 
 * There are some words flagged by checks as misspelled, but they are listed in `inst/WORDLIST` and are correctly spelled. 
 * 1 note regarding package archive on 2026-01-16 due to issues not addressed in time. We have addressed these issues in this release. 

vignettes/articles/simulate_xsectionalData.qmd

@@ -293,7 +293,7 @@ autoplot(est1, log_x = TRUE)
 
 ```{r "init-parallel"}
 library(parallel)
-n_cores <- min(2, parallel::detectCores())
+n_cores <- n_cores <- min(2, parallel::detectCores())
 print(n_cores)
 ```