From cac9baa55d549e910be64b30ea10fe895a893e53 Mon Sep 17 00:00:00 2001
From: Sima Najafzadehkhoei <u1418987@umail.utah.edu>
Date: Tue, 10 Dec 2024 14:55:49 -0700
Subject: [PATCH] yaml is updated

---
 .github/workflows/R-CMD-check.yaml | 35 +----------
 R/run_simulations.R                | 95 +++++++++++++++---------------
 vignettes/calibrate.Rmd            |  2 +
 3 files changed, 52 insertions(+), 80 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 3ab71de..1e16cb2 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -1,32 +1,3 @@
-jobs:
-  R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: macos-12,   r: 'release'}
-          - {os: windows-latest, r: 'release', build-vignettes: false}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::rcmdcheck
-          needs: check
-
-      - uses: r-lib/actions/check-r-package@v2
-        with:
-          build_args: ${{ matrix.config.build-vignettes && '--compact-vignettes=gs+qpdf' || '--no-build-vignettes' }}
-
 on:
   push:
     branches: [main]
@@ -44,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macos-12,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -53,7 +24,8 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
- steps:
+
+    steps:
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
@@ -83,4 +55,3 @@ jobs:
         with:
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
-
diff --git a/R/run_simulations.R b/R/run_simulations.R
index 2e9e3c3..2a9c6ac 100644
--- a/R/run_simulations.R
+++ b/R/run_simulations.R
@@ -15,59 +15,58 @@
 
 run_simulations <- function(N, n, ndays, ncores, theta, seeds) {
   library(epiworldR)
-  matrices <- parallel::mclapply(1:N, FUN = function(i) {
-    set.seed(seeds[i])
-    m <- epiworldR:: ModelSIRCONN(
-      "mycon",
-      prevalence        = theta$preval[i],
-      contact_rate      = theta$crate[i],
-      transmission_rate = theta$ptran[i],
-      recovery_rate     = theta$prec[i],
-      n                 = n
-    )
+  library(parallel)
 
-    verbose_off(m)
-    run(m, ndays = ndays)
-    ans <- prepare_data(m,max_days=ndays)
+  # Detect the operating system
+  os_type <- .Platform$OS.type
 
-    return(ans)
-  }, mc.cores = ncores)
+  if (os_type == "windows") {
+    # Use parLapply for Windows
+    cl <- makeCluster(ncores)
+    on.exit(stopCluster(cl)) # Ensure the cluster is stopped after use
 
-  return(matrices)
-}
+    clusterExport(cl, varlist = c("theta", "n", "ndays", "seeds", "prepare_data"), envir = environment())
+    clusterEvalQ(cl, library(epiworldR)) # Load necessary libraries on workers
+
+    matrices <- parLapply(cl, 1:N, function(i) {
+      set.seed(seeds[i])
+      m <- epiworldR::ModelSIRCONN(
+        "mycon",
+        prevalence        = theta$preval[i],
+        contact_rate      = theta$crate[i],
+        transmission_rate = theta$ptran[i],
+        recovery_rate     = theta$prec[i],
+        n                 = n
+      )
+
+      verbose_off(m)
+      run(m, ndays = ndays)
+      ans <- prepare_data(m, max_days = ndays)
 
+      return(ans)
+    })
 
+  } else {
+    # Use mclapply for macOS/Linux
+    matrices <- mclapply(1:N, function(i) {
+      set.seed(seeds[i])
+      m <- epiworldR::ModelSIRCONN(
+        "mycon",
+        prevalence        = theta$preval[i],
+        contact_rate      = theta$crate[i],
+        transmission_rate = theta$ptran[i],
+        recovery_rate     = theta$prec[i],
+        n                 = n
+      )
 
-# run_simulations <- function(N, n, ndays, ncores, theta) {
-#   matrices <- parallel::mclapply(1:N, FUN = function(i) {
-#     fn <- sprintf("~/myfisrt.package/misc/simulated_data/sir-%06i.rds", i)
-#
-#     if (file.exists(fn))
-#       return(readRDS(fn))
-#     seeds <- sample.int(.Machine$integer.max, N, TRUE)
-#     set.seed(seeds[i])
-#
-#     m <- ModelSIRCONN(
-#       "mycon",
-#       prevalence        = theta$preval[i],
-#       contact_rate      = theta$crate[i],
-#       transmission_rate = theta$ptran[i],
-#       recovery_rate     = theta$prec[i],
-#       n                 = n
-#     )
-#
-#     verbose_off_and_run(m, ndays)
-#     ans <- prepare_data(m)
-#     saveRDS(ans, fn)
-#
-#     return(ans)
-#   }, mc.cores = ncores)
-#
-#   return(matrices)
-# }
-# run_simulations(2e4,5000,50,20,theta)
-#path="~/myfisrt.package/misc/simulated_data/sir-%06i.rds"
-# source("~/myfisrt.package/R/dataprep.R")
-# Input dataset as a vector
+      verbose_off(m)
+      run(m, ndays = ndays)
+      ans <- prepare_data(m, max_days = ndays)
 
+      return(ans)
+    }, mc.cores = ncores)
+  }
+
+  return(matrices)
+}
 
diff --git a/vignettes/calibrate.Rmd b/vignettes/calibrate.Rmd
index 5c7660f..7f81bdc 100644
--- a/vignettes/calibrate.Rmd
+++ b/vignettes/calibrate.Rmd
@@ -81,6 +81,8 @@ head(seeds,5)
 Next, the function runs the simulations for the SIR model using the generated parameters and seeds and using epiworldR package:
 
 ```{r}
+N=10
+n=5000
 ndays=50
 ncores=20
 matrices <- run_simulations(N, n, ndays, ncores, theta, seeds)