diff --git a/.Rbuildignore b/.Rbuildignore
new file mode 100644
index 0000000..0107785
--- /dev/null
+++ b/.Rbuildignore
@@ -0,0 +1,12 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.travis\.yml$
+^codecov\.yml$
+^CRAN-RELEASE$
+^cran-comments\.md$
+^\.github$
+^doc$
+^Meta$
+^windows\\i386\*
+^i386\.*$
+.lintr
\ No newline at end of file
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 41633c1..63d525f 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -2,7 +2,11 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: 
+      - '**'
+  pull_request:
+    branches:
+      - '**'
   release:
     types: [published]
   workflow_dispatch:
@@ -28,9 +32,16 @@ jobs:
           extra-packages: any::pkgdown, local::., any::XML
           needs: website
 
-      - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.9'
+
+      - name: Setup r-reticulate env
+        run: reticulate::virtualenv_create("r-reticulate", Sys.which("python"))
         shell: Rscript {0}
+
+      - name: Build site
+        run: Rscript -e "pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)"
         
       - name: Deploy to GitHub pages
         if: github.event_name != 'pull_request'
diff --git a/.github/workflows/test_macos.yml b/.github/workflows/test_macos.yml
index 40cab78..3816760 100644
--- a/.github/workflows/test_macos.yml
+++ b/.github/workflows/test_macos.yml
@@ -3,7 +3,7 @@ name: "Unit tests: macOS"
 on:
   push:
     branches:
-      - main
+      - '**'
   pull_request:
     branches:
       - '**'
@@ -22,6 +22,10 @@ jobs:
 
       - name: Checkout repository
         uses: actions/checkout@v2
+      
+      - name: Install build dependencies
+        run: |
+          brew install curl
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
@@ -49,6 +53,7 @@ jobs:
           install.packages(c("devtools"))
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
+          reticulate::install_python(version = "3.9:latest")
         shell: Rscript {0}
 
       - name: Check
@@ -62,4 +67,4 @@ jobs:
       - name: Show testthat output
         if: always()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+        shell: bash
\ No newline at end of file
diff --git a/.github/workflows/test_ubuntu.yml b/.github/workflows/test_ubuntu.yml
index cc6209c..b8d90be 100644
--- a/.github/workflows/test_ubuntu.yml
+++ b/.github/workflows/test_ubuntu.yml
@@ -3,7 +3,7 @@ name: "Unit tests: Ubuntu"
 on:
   push:
     branches:
-      - main
+      - '**'
   pull_request:
     branches:
       - '**'
diff --git a/.github/workflows/test_windows.yml b/.github/workflows/test_windows.yml
index 3656a2c..c2ad3d6 100644
--- a/.github/workflows/test_windows.yml
+++ b/.github/workflows/test_windows.yml
@@ -3,13 +3,12 @@ name: "Unit tests: Windows"
 on:
   push:
     branches:
-      - main
+      - '**'
   pull_request:
     branches:
       - '**'
 
 jobs:
-
   test:
     name: tests on Windows with R ${{ matrix.R }}
     runs-on: windows-latest
@@ -19,6 +18,13 @@ jobs:
         R: [ '4.1.0' ]
 
     steps:
+      - name: Check Windows architecture
+        run: |
+          if (-not [Environment]::Is64BitOperatingSystem) { throw "Not 64-bit Windows" }
+          Write-Host "OS Architecture: $([Environment]::Is64BitOperatingSystem)"
+          Write-Host "Process Architecture: $([Environment]::Is64BitProcess)"
+          systeminfo | findstr /B /C:"OS Name" /C:"OS Version" /C:"System Type"
+        shell: pwsh
 
       - name: Checkout repository
         uses: actions/checkout@v2
@@ -28,14 +34,23 @@ jobs:
         with:
           r-version: ${{ matrix.R }}
           Ncpus: 2
-          
+          r-arch: 'x64'
+
+      - name: Verify R architecture
+        run: |
+          Rscript -e "if(R.version$arch != 'x64') stop('R architecture is not 64-bit!')"
+          Rscript -e "cat('R Architecture:', R.version$arch, '\n')"
+          Rscript -e "cat('.Machine$sizeof.pointer:', .Machine$sizeof.pointer, '\n')"
+          Rscript -e "cat('Using R at:', R.home(), '\n')"
+        shell: cmd
+
       - name: Query dependencies
         run: |
           install.packages('remotes')
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
         
-      - name: cache R installed packages
+      - name: Cache R packages
         uses: actions/cache@v2.1.7
         id: cache
         with:
@@ -43,7 +58,7 @@ jobs:
             ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-R${{ matrix.R }}-2-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ runner.os }}-R${{ matrix.R }}-2-
-      
+
       - name: Install packages
         run: |
           install.packages(c("devtools"))
@@ -56,10 +71,10 @@ jobs:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
         run: |
           options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran" ,'--no-multiarch'), error_on = "error", check_dir = "check")
         shell: Rscript {0}
 
       - name: Show testthat output
         if: always()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+        shell: bash
\ No newline at end of file
diff --git a/DESCRIPTION b/DESCRIPTION
index 8f4073c..a84cef2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: R-Wrapper of Epiabm
 Version: 0.0.2
 Authors@R: c(
-    person('Anita', 'Applegarth', role = c('aut', 'cre', 'cph'), email = 'anita.applegarth@reub.ox.ac.uk'),
+    person('Anita', 'Applegarth', role = c('aut', 'cre', 'cph'), email = 'anita.applegarth@reuben.ox.ac.uk'),
     person('Kingsley', 'Oguma', role = 'aut', email = "kemukperuo@gmail.com")
     )
 Description: Wraps the epiabm Python module in R.
@@ -12,20 +12,23 @@ Encoding: UTF-8
 Archs: x64
 SystemRequirements: Python (>= 2.7.0)
 Suggests: tinytest
-Imports: ggplot2, here
-Depends: 
-    reticulate (>= 1.14),
-    R (>= 3.3.0)
+Imports: 
+    ggplot2,
+    here,
+    tidyr,
+    reticulate (>= 1.14)
+Depends: R (>= 3.3.0)
 Config/reticulate:
     list(
         packages = list(
             list(package = "numpy", pip = TRUE),
-	    list(package = "pandas", pip = TRUE),
+            list(package = "pandas", pip = TRUE),
             list(package = "matplotlib", pip = TRUE),
             list(
                 package = "pyEpiabm",
                 pip = TRUE,
-                pip_options = "--index-url git+https://github.com/SABS-R3-Epidemiology/epiabm.git@main#egg=pyEpiabm&subdirectory=pyEpiabm"
+                pip_options = "--extra-index-url https://github.com/SABS-R3-Epidemiology/epiabm.git@main#egg=pyEpiabm&subdirectory=pyEpiabm"
             )
         )
     )
+RoxygenNote: 7.3.2
diff --git a/NAMESPACE b/NAMESPACE
index c950c17..d9e4281 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1 +1,4 @@
-import(reticulate)
+# Generated by roxygen2: do not edit by hand
+
+export(check_python_env)
+export(initialize_python_env)
diff --git a/R/simulation_flow_check.R b/R/simulation_flow_check.R
index e0ee6a1..4990237 100644
--- a/R/simulation_flow_check.R
+++ b/R/simulation_flow_check.R
@@ -2,15 +2,20 @@
 # Example simulation script with data output
 #
 # Import dependencies
+source("R/zzz.R")
+initialize_python_env()
+check_python_env()
 
 library(reticulate)
+#library(rEpiabm)
 library(here)
+library(tidyr)
 
-os <- import("os")
-logging <- import("logging")
-pd <- import("pandas")
-plt <- import("matplotlib.pyplot")
-pe <- import("pyEpiabm")
+os <- import("os", delay_load = TRUE)
+logging <- import("logging", delay_load = TRUE)
+pd <- import("pandas", delay_load = TRUE)
+plt <- import("matplotlib.pyplot", delay_load = TRUE)
+pe <- import("pyEpiabm", delay_load = TRUE)
 
 # Set working directory for relative directory references
 base_dir <- here()
@@ -91,12 +96,8 @@ sim$compress_csv()
 
 # Create dataframe for plots
 filename <- here("simulation_outputs", "output.csv")
-df <- pd$read_csv(filename)
+df <- read.csv(filename)
 
-# Convert pandas dataframe to R dataframe
-df_r <- as.data.frame(df)
-
-# Load library for plotting
 library(ggplot2)
 
 # Reshape the data from wide to long format using base R
@@ -105,13 +106,15 @@ status_columns <- c("InfectionStatus.Susceptible",
                     "InfectionStatus.Recovered",
                     "InfectionStatus.Dead")
 
-df_long <- data.frame(
-  time = rep(df_r$time, length(status_columns)),
-  Status = factor(rep(status_columns, each = nrow(df_r)),
-                  levels = status_columns,
-                  labels = c("Susceptible", "Infected", "Recovered", "Dead")),
-  Count = unlist(df_r[status_columns])
+df_long <- pivot_longer(
+  df,
+  cols = all_of(status_columns),
+  names_to = "Status",
+  values_to = "Count"
 )
+df_long$Status <- factor(df_long$Status,
+                        levels = status_columns,
+                        labels = c("Susceptible", "Infected", "Recovered", "Dead"))
 
 # Create the plot
 p <- ggplot(df_long, aes(x = time, y = Count, color = Status)) +
diff --git a/R/zzz.R b/R/zzz.R
new file mode 100644
index 0000000..bd741c7
--- /dev/null
+++ b/R/zzz.R
@@ -0,0 +1,189 @@
+# Environment setup and management functions for R package
+local <- new.env()
+
+#' Create and configure Python environment
+#' @param env_name Character. Name of the virtual environment to create
+#' @param python_version Character. Python version to use (e.g., "3.8")
+#' @return Logical indicating success
+#' @keywords internal
+create_python_env <- function(env_name = "r-reticulate", python_version = "3.9") {
+  tryCatch({
+    # Check if virtualenv package is available
+    if (!reticulate::virtualenv_exists(env_name)) {
+      message(sprintf("Creating new Python virtual environment: %s", env_name))
+      
+      # Create virtual environment with system site packages to help with SSL
+      reticulate::virtualenv_create(
+        envname = env_name,
+        version = python_version,
+        packages = "pip",
+        system_site_packages = TRUE
+      )
+    }
+    
+    # Activate the environment
+    reticulate::use_virtualenv(env_name, required = TRUE)
+    return(TRUE)
+  }, error = function(e) {
+    warning(sprintf("Failed to create/activate Python environment: %s", e$message))
+    return(FALSE)
+  })
+}
+
+.onLoad <- function(libname, pkgname) {
+  # Create and activate Python environment
+  env_success <- create_python_env()
+  
+  if (!env_success) {
+    warning("Failed to set up Python environment. Some functionality may be limited.")
+    return()
+  }
+  
+  # Configure reticulate to use the package's environment
+  reticulate::configure_environment(pkgname)
+  
+  # Install required packages if not present
+  ensure_python_dependencies()
+  
+  # Import dependencies with error handling
+  tryCatch({
+    load_python_modules()
+  }, error = function(e) {
+    warning(sprintf("Error loading Python dependencies: %s\nPlease run check_python_env() to diagnose issues.", e$message))
+  })
+}
+
+#' Ensure all required Python dependencies are installed
+#' @keywords internal
+ensure_python_dependencies <- function() {
+  # Upgrade pip
+  reticulate::py_run_string("
+import sys
+import subprocess
+subprocess.check_call([sys.executable, '-m', 'pip', 'install', '--upgrade', 'pip'])
+  ")
+  
+  # Install required packages
+  reticulate::py_run_string("
+import sys
+import subprocess
+
+# Install basic packages
+packages = ['numpy', 'pandas', 'matplotlib']
+for package in packages:
+    subprocess.check_call([sys.executable, '-m', 'pip', 'install', '--upgrade', package])
+
+# Install pyEpiabm from GitHub
+subprocess.check_call([
+    sys.executable, '-m', 'pip', 'install', '--upgrade',
+    'git+https://github.com/SABS-R3-Epidemiology/epiabm.git@main#egg=pyEpiabm&subdirectory=pyEpiabm'
+])
+  ")
+  
+  # Verify installations
+  result <- reticulate::py_run_string("
+import importlib.util
+
+packages = ['numpy', 'pandas', 'matplotlib', 'pyEpiabm']
+missing = []
+
+for package in packages:
+    if importlib.util.find_spec(package) is None:
+        missing.append(package)
+        
+print('Missing packages:', missing if missing else 'None')
+  ")
+  
+  if (length(result$missing) > 0) {
+    stop("Failed to install required packages: ", paste(result$missing, collapse = ", "))
+  }
+  
+  message("All required packages installed successfully")
+}
+
+#' Load Python modules into package environment
+#' @keywords internal
+load_python_modules <- function() {
+  # Define modules to load
+  modules <- list(
+    os = "os",
+    logging = "logging",
+    pd = "pandas",
+    plt = "matplotlib.pyplot",
+    pe = "pyEpiabm"
+  )
+  
+  # Import each module
+  for (var_name in names(modules)) {
+    module_name <- modules[[var_name]]
+    tryCatch({
+      module <- reticulate::import(module_name, delay_load = TRUE)
+      assign(var_name, module, envir = parent.env(local))
+    }, error = function(e) {
+      warning(sprintf("Failed to load module %s: %s", module_name, e$message))
+    })
+  }
+}
+
+#' Check Python environment and package availability
+#' @export
+check_python_env <- function() {
+  # Get Python configuration
+  python_config <- reticulate::py_config()
+  
+  # Print Python information
+  cat(sprintf("Python version: %s\n", reticulate::py_version()))
+  cat(sprintf("Python path: %s\n", python_config$python))
+  cat(sprintf("virtualenv: %s\n", if(is.null(python_config$virtualenv)) "None" else python_config$virtualenv))
+  
+  # Check required packages
+  required_packages <- c("numpy", "pandas", "matplotlib", "pyEpiabm")
+  
+  cat("\nPackage Status:\n")
+  pkg_status <- list()
+  
+  for (pkg in required_packages) {
+    if (reticulate::py_module_available(pkg)) {
+      # Try to get version information
+      tryCatch({
+        version <- reticulate::py_eval(sprintf("__import__('%s').__version__", pkg))
+        cat(sprintf("✓ %s (version %s)\n", pkg, version))
+        pkg_status[[pkg]] <- TRUE
+      }, error = function(e) {
+        cat(sprintf("✓ %s (version unknown)\n", pkg))
+        pkg_status[[pkg]] <- TRUE
+      })
+    } else {
+      cat(sprintf("✗ %s is not available\n", pkg))
+      pkg_status[[pkg]] <- FALSE
+    }
+  }
+  
+  # Return invisibly whether all packages are available
+  invisible(all(unlist(pkg_status)))
+}
+
+#' Initialize or repair Python environment
+#' @param force Logical. If TRUE, recreates the environment even if it exists
+#' @export
+initialize_python_env <- function(force = FALSE) {
+  env_name <- "r-py-env"
+  
+  if (force && reticulate::virtualenv_exists(env_name)) {
+    message("Removing existing Python environment...")
+    reticulate::virtualenv_remove(env_name)
+  }
+  
+  # Create and activate environment
+  if (create_python_env(env_name)) {
+    message("Python environment successfully created/activated")
+    
+    # Install dependencies
+    ensure_python_dependencies()
+    
+    # Check environment
+    check_python_env()
+  } else {
+    stop("Failed to initialize Python environment")
+  }
+}
\ No newline at end of file
diff --git a/man/check_python_env.Rd b/man/check_python_env.Rd
new file mode 100644
index 0000000..abb0efc
--- /dev/null
+++ b/man/check_python_env.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/zzz.R
+\name{check_python_env}
+\alias{check_python_env}
+\title{Check Python environment and package availability}
+\usage{
+check_python_env()
+}
+\description{
+Check Python environment and package availability
+}
diff --git a/man/create_python_env.Rd b/man/create_python_env.Rd
new file mode 100644
index 0000000..d8c0399
--- /dev/null
+++ b/man/create_python_env.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/zzz.R
+\name{create_python_env}
+\alias{create_python_env}
+\title{Create and configure Python environment}
+\usage{
+create_python_env(env_name = "r-py-env", python_version = "3.9")
+}
+\arguments{
+\item{env_name}{Character. Name of the virtual environment to create}
+
+\item{python_version}{Character. Python version to use (e.g., "3.8")}
+}
+\value{
+Logical indicating success
+}
+\description{
+Create and configure Python environment
+}
+\keyword{internal}
diff --git a/man/ensure_python_dependencies.Rd b/man/ensure_python_dependencies.Rd
new file mode 100644
index 0000000..20f0563
--- /dev/null
+++ b/man/ensure_python_dependencies.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/zzz.R
+\name{ensure_python_dependencies}
+\alias{ensure_python_dependencies}
+\title{Ensure all required Python dependencies are installed}
+\usage{
+ensure_python_dependencies()
+}
+\description{
+Ensure all required Python dependencies are installed
+}
+\keyword{internal}
diff --git a/man/initialize_python_env.Rd b/man/initialize_python_env.Rd
new file mode 100644
index 0000000..55918ab
--- /dev/null
+++ b/man/initialize_python_env.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/zzz.R
+\name{initialize_python_env}
+\alias{initialize_python_env}
+\title{Initialize or repair Python environment}
+\usage{
+initialize_python_env(force = FALSE)
+}
+\arguments{
+\item{force}{Logical. If TRUE, recreates the environment even if it exists}
+}
+\description{
+Initialize or repair Python environment
+}
diff --git a/man/load_python_modules.Rd b/man/load_python_modules.Rd
new file mode 100644
index 0000000..ec34d09
--- /dev/null
+++ b/man/load_python_modules.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/zzz.R
+\name{load_python_modules}
+\alias{load_python_modules}
+\title{Load Python modules into package environment}
+\usage{
+load_python_modules()
+}
+\description{
+Load Python modules into package environment
+}
+\keyword{internal}
diff --git a/rEpiabm.Rproj b/rEpiabm.Rproj
new file mode 100644
index 0000000..21a4da0
--- /dev/null
+++ b/rEpiabm.Rproj
@@ -0,0 +1,17 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
diff --git a/simulation_outputs/simulation_flow_SIR_plot.png b/simulation_outputs/simulation_flow_SIR_plot.png
index 9975830..5f43b63 100644
Binary files a/simulation_outputs/simulation_flow_SIR_plot.png and b/simulation_outputs/simulation_flow_SIR_plot.png differ