diff --git a/.DS_Store b/.DS_Store
new file mode 100644
index 0000000..6727c55
Binary files /dev/null and b/.DS_Store differ
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/lint.yaml b/.github/workflows/lint.yaml
index 3943132..1d81280 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -40,9 +40,6 @@ jobs:
           remotes::install_cran("lintr")
         shell: Rscript {0}
 
-      - name: Install package
-        run: R CMD INSTALL .
-
       - name: Lint
         run: lintr::lint_package()
         shell: Rscript {0}
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/.gitignore b/.gitignore
index e75435c..0cb361a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,12 +12,18 @@
 # Example code in package build process
 *-Ex.R
 
+# Input parameters to simulation
+*.json
+
 # Output files from R CMD build
 /*.tar.gz
 
 # Output files from R CMD check
 /*.Rcheck/
 
+# Output from simulation
+*.csv
+
 # RStudio files
 .Rproj.user/
 
diff --git a/DESCRIPTION b/DESCRIPTION
index 19446b1..a84cef2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,25 +1,34 @@
 Package: rEpiabm
 Type: Package
-Title: R-wrapper of Epiabm
+Title: R-Wrapper of Epiabm
 Version: 0.0.2
 Authors@R: c(
-    person('Anita', 'Applegarth', role = c('aut', 'cre', 'cph'), email = 'anita.applegarth@ox.ac.uk'), 
-    person('Kingley', 'Oguma', role = 'aut', email = "kemukperuo@gmail.com"))
-Description: Wraps the epiabm Python module. R users can...
+    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.
 License: BSD_3_clause
 Encoding: UTF-8
 Archs: x64
 SystemRequirements: Python (>= 2.7.0)
-Suggests: 
-    tinytest
-Depends:
-    reticulate (>= 1.14),
-    R (>= 3.3.0)
+Suggests: tinytest
+Imports: 
+    ggplot2,
+    here,
+    tidyr,
+    reticulate (>= 1.14)
+Depends: R (>= 3.3.0)
 Config/reticulate:
-  list(
-    packages = list(
-      list(package = "numpy", pip = TRUE),
-      list(package = "matplotlib", pip = TRUE)
+    list(
+        packages = list(
+            list(package = "numpy", pip = TRUE),
+            list(package = "pandas", pip = TRUE),
+            list(package = "matplotlib", pip = TRUE),
+            list(
+                package = "pyEpiabm",
+                pip = TRUE,
+                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/.DS_Store b/R/.DS_Store
new file mode 100644
index 0000000..c1bb6e3
Binary files /dev/null and b/R/.DS_Store differ
diff --git a/R/blank.R b/R/blank.R
deleted file mode 100644
index 8b13789..0000000
--- a/R/blank.R
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/R/simulation_flow_check.R b/R/simulation_flow_check.R
new file mode 100644
index 0000000..3a61840
--- /dev/null
+++ b/R/simulation_flow_check.R
@@ -0,0 +1,157 @@
+#
+# Example simulation script with data output
+#
+
+# Import dependencies
+source("R/zzz.R")
+initialize_python_env()
+check_python_env()
+
+library(reticulate)
+library(here)
+library(tidyr)
+
+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()
+
+# Set config file for Parameters
+pe$Parameters$set_file(here("data", "simple_parameters.json"))
+
+# Method to set the seed at the start of the simulation, for reproducibility
+pe$routine$Simulation$set_random_seed(seed = as.integer(42))
+
+# Pop_params are used to configure the population structure being used in this
+# simulation.
+pop_params <- list(
+  population_size = as.integer(100),
+  cell_number = as.integer(2),
+  microcell_number = as.integer(2),
+  household_number = as.integer(5),
+  place_number = as.integer(2)
+)
+
+# Create a population based on the parameters given.
+population <- pe$routine$ToyPopulationFactory()$make_pop(pop_params)
+
+# sim_params
+sim_params <- list(
+  simulation_start_time = as.integer(0),
+  simulation_end_time = as.integer(60),
+  initial_infected_number = as.integer(10),
+  include_waning = TRUE
+)
+
+# file_params
+file_params <- list(
+  output_file = "output.csv",
+  output_dir = here("simulation_outputs"),
+  spatial_output = FALSE,
+  age_stratified = FALSE
+)
+
+# dem_file_params
+dem_file_params <- list(
+  output_dir = here("simulation_outputs"),
+  spatial_output = FALSE,
+  age_output = FALSE
+)
+
+# inf_history_params
+inf_history_params <- list(
+  output_dir = here("simulation_outputs"),
+  status_output = TRUE,
+  infectiousness_output = TRUE,
+  compress = FALSE  # Set to TRUE if compression desired
+)
+
+# Create a simulation object
+sim <- pe$routine$Simulation()
+
+# Configure the simulation with parameters
+sim$configure(
+  population,
+  list(
+    pe$sweep$InitialInfectedSweep(),
+    pe$sweep$InitialDemographicsSweep(dem_file_params)
+  ),
+  list(
+    pe$sweep$HouseholdSweep(),
+    pe$sweep$QueueSweep(),
+    pe$sweep$HostProgressionSweep()
+  ),
+  sim_params,
+  file_params,
+  inf_history_params
+)
+
+# Run the simulation
+sim$run_sweeps()
+sim$compress_csv()
+
+# Create dataframe for plots
+filename <- here("simulation_outputs", "output.csv")
+df <- read.csv(filename)
+
+library(ggplot2)
+
+# Reshape the data from wide to long format using base R
+status_columns <- c(
+  "InfectionStatus.Susceptible",
+  "InfectionStatus.InfectMild",
+  "InfectionStatus.Recovered",
+  "InfectionStatus.Dead"
+)
+
+df_long <- pivot_longer(
+  df,
+  cols = all_of(status_columns),
+  names_to = "Status",
+  values_to = "Count"
+)
+
+df_long$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)) +
+  geom_line() +
+  scale_color_manual(
+    values = c(
+      "Susceptible" = "blue",
+      "Infected" = "red",
+      "Recovered" = "green",
+      "Dead" = "black"
+    )
+  ) +
+  theme_minimal() +
+  labs(
+    title = "SIR Model Flow",
+    x = "Time",
+    y = "Count"
+  ) +
+  theme(
+    legend.position = "right",
+    plot.title = element_text(hjust = 0.5),
+    panel.grid.minor = element_blank()
+  )
+
+# Display the plot
+print(p)
+
+# Save the plot
+ggsave(
+  filename = here("simulation_outputs", "simulation_flow_SIR_plot.png"),
+  plot = p,
+  width = 10,
+  height = 6,
+  dpi = 300
+)
diff --git a/R/zzz.R b/R/zzz.R
new file mode 100644
index 0000000..69a1b5d
--- /dev/null
+++ b/R/zzz.R
@@ -0,0 +1,183 @@
+# 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")
+  }
+}
diff --git a/data/simple_parameters.json b/data/simple_parameters.json
new file mode 100644
index 0000000..9a2c6eb
--- /dev/null
+++ b/data/simple_parameters.json
@@ -0,0 +1,429 @@
+{
+    "basic_reproduction_num": 2.8,
+    "latent_period": 4.59,
+    "asympt_infect_period": 14,
+    "mean_mild_to_recov": 7,
+    "mean_gp_to_recov": 7,
+    "mean_gp_to_hosp": 5,
+    "mean_gp_to_death": 7,
+    "mean_hosp_to_recov": 1,
+    "mean_hosp_to_icu": 1,
+    "mean_hosp_to_death": 1,
+    "mean_icu_to_icurecov": 1,
+    "mean_icu_to_death": 1,
+    "mean_icurecov_to_recov": 1,
+    "mean_recov_to_susc": 0,
+    "time_steps_per_day": 1,
+    "prob_symptomatic": 0.66,
+    "sympt_infectiousness": 1.5,
+    "asympt_infectiousness": 1.0,
+    "latent_to_sympt_delay": 0.5,
+    "household_transmission": 0.1,
+    "false_positive_rate": 0,
+    "place_transmission": 0.1,
+    "use_ages": 0,
+    "use_waning_immunity": 1,
+    "note1": "Mainly change values above this",
+    "age_contact": [0.6, 0.7, 0.75, 1, 1, 1, 1, 1,
+        1, 1, 1, 1, 1, 1, 1, 0.75, 0.5],
+        "household_size_distribution": [0.283708848, 0.345103011, 0.150677793,
+            0.12764915, 0.057777709, 0.022624223,
+            0.007151747, 0.002988208, 0.001179132,
+            0.001140178],
+    "max_household_size": 10,
+    "household_age_params": {
+        "mean_child_age_gap": 2,
+        "min_adult_age": 19,
+        "max_MF_partner_age_gap": 5,
+        "min_parent_age_gap": 19,
+        "max_FM_partner_age_gap": 5,
+        "max_parent_age_gap": 44,
+        "max_child_age": 20,
+        "one_child_two_pers_prob": 0.08,
+        "two_child_three_pers_prob": 0.11,
+        "one_pers_house_prob_old": 0.5,
+        "two_pers_house_prob_old": 0.5,
+        "one_pers_house_prob_young": 0.23,
+        "two_pers_house_prob_young": 0.23,
+        "one_child_prob_youngest_child_under_five": 0.5,
+        "two_children_prob_youngest_under_five": 0.0,
+        "prob_youngest_child_under_five": 0.0,
+        "zero_child_three_pers_prob": 0.25,
+        "one_child_four_pers_prob": 0.2,
+        "young_and_single_slope": 0.7,
+        "young_and_single": 36,
+        "no_child_pers_age": 44,
+        "old_pers_age": 60,
+        "three_child_five_pers_prob": 0.5,
+        "older_gen_gap": 19,
+        "prop_other_parent_away": 0.0
+    },
+    "note2": "Don't change parameters below this",
+    "CDF_RES": 20,
+"latent_period_iCDF": [
+    0,
+    0.098616903,
+    0.171170649,
+    0.239705594,
+    0.307516598,
+    0.376194441,
+    0.446827262,
+    0.520343677,
+    0.597665592,
+    0.679808341,
+    0.767974922,
+    0.863671993,
+    0.968878064,
+    1.086313899,
+    1.219915022,
+    1.37573215,
+    1.563841395,
+    1.803041398,
+    2.135346254,
+    2.694118208,
+    3.964172493
+],
+"asympt_infect_icdf": [
+    0,
+    0.171566836,
+    0.424943468,
+    0.464725594,
+    0.50866631,
+    0.55773764,
+    0.613298069,
+    0.67732916,
+    0.752886568,
+    0.843151261,
+    0.895791527,
+    0.955973422,
+    1.026225109,
+    1.110607115,
+    1.216272375,
+    1.336349102,
+    1.487791911,
+    1.701882384,
+    1.865779085,
+    2.126940581,
+    2.524164972
+],
+"mild_to_recov_icdf": [
+    0,
+    0.341579599,
+    0.436192391,
+    0.509774887,
+    0.574196702,
+    0.633830053,
+    0.690927761,
+    0.74691114,
+    0.802830695,
+    0.859578883,
+    0.918015187,
+    0.97906363,
+    1.043815683,
+    1.113669859,
+    1.190557274,
+    1.277356871,
+    1.378761429,
+    1.50338422,
+    1.670195767,
+    1.938414132,
+    2.511279379
+],
+"gp_to_recov_icdf": [
+    0,
+    0.341579599,
+    0.436192391,
+    0.509774887,
+    0.574196702,
+    0.633830053,
+    0.690927761,
+    0.74691114,
+    0.802830695,
+    0.859578883,
+    0.918015187,
+    0.97906363,
+    1.043815683,
+    1.113669859,
+    1.190557274,
+    1.277356871,
+    1.378761429,
+    1.50338422,
+    1.670195767,
+    1.938414132,
+    2.511279379
+],
+"gp_to_hosp_icdf": [
+    0,
+    0.341579599,
+    0.436192391,
+    0.509774887,
+    0.574196702,
+    0.633830053,
+    0.690927761,
+    0.74691114,
+    0.802830695,
+    0.859578883,
+    0.918015187,
+    0.97906363,
+    1.043815683,
+    1.113669859,
+    1.190557274,
+    1.277356871,
+    1.378761429,
+    1.50338422,
+    1.670195767,
+    1.938414132,
+    2.511279379
+],
+"gp_to_death_icdf": [
+    0,
+    2.257735908,
+    3.171065856,
+    3.924183798,
+    4.608738224,
+    5.260437017,
+    5.898728066,
+    6.53669783,
+    7.184755068,
+    7.852438367,
+    8.549591424,
+    9.287408763,
+    10.07967529,
+    10.94457146,
+    11.90769274,
+    13.00769447,
+    14.3081531,
+    15.92655201,
+    18.12320384,
+    21.71626849,
+    29.58154704
+],
+"hosp_to_recov_icdf": [
+    0,
+    0.634736097,
+    1.217461548,
+    1.805695261,
+    2.41206761,
+    3.044551205,
+    3.71010552,
+    4.415905623,
+    5.170067405,
+    5.982314035,
+    6.864787504,
+    7.833196704,
+    8.908589322,
+    10.12027655,
+    11.51100029,
+    13.14682956,
+    15.13821107,
+    17.69183155,
+    21.27093904,
+    27.35083955,
+    41.35442157
+],
+"hosp_to_icu_icdf": [
+    0,
+    0.108407687,
+    0.220267228,
+    0.337653773,
+    0.46159365,
+    0.593106462,
+    0.733343356,
+    0.88367093,
+    1.045760001,
+    1.221701998,
+    1.414175806,
+    1.62669998,
+    1.864032461,
+    2.132837436,
+    2.442868902,
+    2.809242289,
+    3.257272257,
+    3.834402667,
+    4.647120033,
+    6.035113821,
+    9.253953212
+],
+"hosp_to_death_icdf": [
+    0,
+    1.703470233,
+    2.39742257,
+    2.970367222,
+    3.491567676,
+    3.988046604,
+    4.474541783,
+    4.960985883,
+    5.455292802,
+    5.964726999,
+    6.496796075,
+    7.06004732,
+    7.665014091,
+    8.325595834,
+    9.061367792,
+    9.901900127,
+    10.8958347,
+    12.133068,
+    13.81280888,
+    16.56124574,
+    22.5803431
+],
+"icu_to_icurecov_icdf": [
+    0,
+    1.308310071,
+    1.87022015,
+    2.338694632,
+    2.76749788,
+    3.177830401,
+    3.581381361,
+    3.986127838,
+    4.398512135,
+    4.824525291,
+    5.270427517,
+    5.743406075,
+    6.252370864,
+    6.809125902,
+    7.430338867,
+    8.141231404,
+    8.983341913,
+    10.03350866,
+    11.46214198,
+    13.80540164,
+    18.95469153
+],
+"icu_to_death_icdf": [
+    0,
+    1.60649128,
+    2.291051747,
+    2.860938008,
+    3.382077741,
+    3.880425012,
+    4.37026577,
+    4.861330415,
+    5.361460943,
+    5.877935626,
+    6.4183471,
+    6.991401405,
+    7.607881726,
+    8.282065409,
+    9.034104744,
+    9.894486491,
+    10.91341144,
+    12.18372915,
+    13.9113346,
+    16.74394356,
+    22.96541429
+],
+"icurecov_to_recov": [
+    0,
+    0.133993315,
+    0.265922775,
+    0.402188416,
+    0.544657341,
+    0.694774487,
+    0.853984373,
+    1.023901078,
+    1.206436504,
+    1.403942719,
+    1.619402771,
+    1.856711876,
+    2.121118605,
+    2.419957988,
+    2.763950408,
+    3.169692564,
+    3.664959893,
+    4.301777536,
+    5.196849239,
+    6.7222126,
+    10.24997697
+],
+"recov_to_susc_icdf": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+        0, 0, 0, 0, 0, 0, 0, 0],
+"infectiousness_prof": [0.487464241, 1, 1.229764827, 1.312453175,
+        1.307955665, 1.251658756, 1.166040358, 1.065716869,
+        0.960199498, 0.855580145, 0.755628835, 0.662534099,
+        0.577412896, 0.500665739, 0.432225141, 0.371729322,
+        0.318643018, 0.272340645, 0.232162632, 0.19745264,
+        0.167581252, 0.141960133, 0.120049578, 0.101361532,
+        0.085459603, 0.071957123, 0.060514046, 0.050833195,
+        0.04265624, 0.035759641, 0.029950735, 0.025064045,
+        0.02095788, 0.017511251, 0.014621091, 0.012199802,
+        0.010173075, 0.008477992, 0.007061366, 0.005878301,
+        0.00489096, 0.004067488, 0.003381102, 0.00280931,
+        0.002333237, 0.001937064, 0.001607543, 0.001333589,
+        0.001105933, 0.00091683, 0.000759816, 0.000629496,
+        0.000521372, 0.000431695, 0.000357344, 0.000295719,
+        0.000244659],
+"age_proportions": [6.2, 5.6, 5.8, 6.3, 6.8, 6.8, 6.5, 6.6,
+        7.3, 7.3, 6.5, 5.7, 6, 4.8, 3.9, 3.2, 4.7],
+"host_progression_lists": {
+    "prob_gp_to_hosp": [0.001896, 0.001616, 0.002981, 0.006083,
+                        0.013513, 0.025793, 0.040294, 0.057278,
+                        0.070361, 0.092402, 0.13409, 0.164461,
+                        0.220964, 0.248858, 0.298479, 0.346454,
+                        0.351508],
+    "prob_gp_to_recov": [0.998104, 0.998384, 0.997019, 0.993917,
+                            0.986487, 0.974207, 0.959706, 0.942722,
+                            0.929639, 0.907598, 0.86591, 0.835539,
+                            0.779036, 0.751142, 0.701521, 0.653546,
+                            0.648492],
+    
+    "prob_exposed_to_asympt": [0.34, 0.34, 0.34, 0.34, 0.34, 0.34,
+                                0.34, 0.34, 0.34, 0.34, 0.34, 0.34,
+                                0.34, 0.34, 0.34, 0.34, 0.34],
+    "prob_exposed_to_gp": [0.220278, 0.220237, 0.220438, 0.220896,
+                            0.222, 0.223849, 0.226073, 0.228734,
+                            0.230827, 0.234442, 0.241597, 0.247091,
+                            0.258007, 0.263759, 0.274652, 0.286074,
+                            0.287333],
+    "prob_exposed_to_mild": [0.439722, 0.439763, 0.439562, 0.43910,
+                                0.438, 0.436151, 0.433927, 0.431266,
+                                0.429173, 0.425558, 0.418403, 0.41291,
+                                0.401993, 0.396241, 0.385348,
+                                0.373926, 0.372667],
+    
+    "prob_hosp_to_death": [0.110981, 0.108089, 0.119602, 0.134584,
+                            0.153656, 0.171186, 0.184562, 0.196264,
+                            0.203616, 0.212462, 0.219792, 0.207716,
+                            0.171205, 0.107889, 0.344512, 0.423204,
+                            0.473935],
+    "prob_hosp_to_recov": [0.770565, 0.773457, 0.761945, 0.746962,
+                            0.72789, 0.710361, 0.696984, 0.678225,
+                            0.655474, 0.611583, 0.535832, 0.43985,
+                            0.301002, 0.168066, 0.473511, 0.522406,
+                            0.509332],
+    "prob_hosp_to_icu": [0.118454, 0.118454, 0.118453, 0.118454,
+                            0.118454, 0.118454, 0.118454, 0.125511,
+                            0.14091, 0.175955, 0.244376, 0.352435,
+                            0.527792, 0.724045, 0.181977, 0.054391,
+                            0.016733],
+    
+    "prob_icu_to_death": [0.52349, 0.52349, 0.52349, 0.52349,
+                            0.52349, 0.52349, 0.52349, 0.52349,
+                            0.52349, 0.52349, 0.52349, 0.52349,
+                            0.52349, 0.52349, 0.52349, 0.52349,
+                            0.52349],
+    "prob_icu_to_icurecov": [0.47651, 0.47651, 0.47651, 0.47651,
+                                0.47651, 0.47651, 0.47651, 0.47651,
+                                0.47651, 0.47651, 0.47651, 0.47651,
+                                0.47651, 0.47651, 0.47651, 0.47651,
+                                0.47651]
+    },
+"rate_multiplier_params": {
+    "gp_to_hosp": [0.25, 0.421052632],
+    "gp_to_death": [0.25, 0.421052632],
+
+    "exposed_to_infect": [0.75, 0.842105263],
+
+    "hosp_to_death": [0.9, 1],
+    "hosp_to_icu": [0.9, 1],
+
+    "icu_to_death": [0.9, 1]
+    },
+"antibody_level_params": {
+    "igg_peak_at_age_41": 4.26,
+    "igg_half_life_at_age_41": 85.38,
+    "peak_change_per_10_yrs_age": 0.21,
+    "half_life_diff_per_10_yrs_age": 4.07,
+    "days_positive_pcr_to_max_igg": 24
+    }
+}
\ 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/counts.csv b/simulation_outputs/counts.csv
new file mode 100644
index 0000000..319bb8a
--- /dev/null
+++ b/simulation_outputs/counts.csv
@@ -0,0 +1,3 @@
+Cell,Age group 0
+0,56
+1,44
diff --git a/simulation_outputs/demographics.csv b/simulation_outputs/demographics.csv
new file mode 100644
index 0000000..4b9f31d
--- /dev/null
+++ b/simulation_outputs/demographics.csv
@@ -0,0 +1,101 @@
+id,kw_or_chr
+0.0.0.0,X
+0.0.0.1,X
+0.0.0.2,X
+0.0.0.3,X
+0.0.0.4,X
+0.0.1.0,X
+0.0.1.1,X
+0.0.1.2,X
+0.0.2.0,X
+0.0.2.1,X
+0.0.2.2,X
+0.0.3.0,X
+0.0.3.1,X
+0.0.3.2,X
+0.0.3.3,X
+0.0.4.0,X
+0.0.4.1,X
+0.0.4.2,X
+0.0.4.3,X
+0.0.4.4,X
+0.0.4.5,X
+0.0.4.6,X
+0.0.4.7,X
+0.0.4.8,X
+0.1.0.0,X
+0.1.0.1,X
+0.1.0.2,X
+0.1.0.3,X
+0.1.0.4,X
+0.1.0.5,X
+0.1.0.6,X
+0.1.0.7,X
+0.1.0.8,X
+0.1.1.0,X
+0.1.1.1,X
+0.1.1.2,X
+0.1.1.3,X
+0.1.1.4,X
+0.1.1.5,X
+0.1.2.0,X
+0.1.2.1,X
+0.1.2.2,X
+0.1.2.3,X
+0.1.2.4,X
+0.1.2.5,X
+0.1.2.6,X
+0.1.3.0,X
+0.1.3.1,X
+0.1.4.0,X
+0.1.4.1,X
+0.1.4.2,X
+0.1.4.3,X
+0.1.4.4,X
+0.1.4.5,X
+0.1.4.6,X
+0.1.4.7,X
+1.0.0.0,X
+1.0.0.1,X
+1.0.0.2,X
+1.0.0.3,X
+1.0.0.4,X
+1.0.0.5,X
+1.0.0.6,X
+1.0.0.7,X
+1.0.0.8,X
+1.0.1.0,X
+1.0.1.1,X
+1.0.1.2,X
+1.0.1.3,X
+1.0.1.4,X
+1.0.2.0,X
+1.0.2.1,X
+1.0.3.0,X
+1.0.3.1,X
+1.0.3.2,X
+1.0.4.0,X
+1.0.4.1,X
+1.0.4.2,X
+1.0.4.3,X
+1.0.4.4,X
+1.1.0.0,X
+1.1.0.1,X
+1.1.1.0,X
+1.1.1.1,X
+1.1.1.2,X
+1.1.2.0,X
+1.1.2.1,X
+1.1.2.2,X
+1.1.2.3,X
+1.1.2.4,X
+1.1.3.0,X
+1.1.3.1,X
+1.1.3.2,X
+1.1.3.3,X
+1.1.3.4,X
+1.1.4.0,X
+1.1.4.1,X
+1.1.4.2,X
+1.1.4.3,X
+1.1.4.4,X
diff --git a/simulation_outputs/inf_status_history.csv b/simulation_outputs/inf_status_history.csv
new file mode 100644
index 0000000..564b8ca
--- /dev/null
+++ b/simulation_outputs/inf_status_history.csv
@@ -0,0 +1,62 @@
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diff --git a/simulation_outputs/infectiousness_history.csv b/simulation_outputs/infectiousness_history.csv
new file mode 100644
index 0000000..66edf4f
--- /dev/null
+++ b/simulation_outputs/infectiousness_history.csv
@@ -0,0 +1,62 @@
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diff --git a/simulation_outputs/output.csv b/simulation_outputs/output.csv
new file mode 100644
index 0000000..6fdc45f
--- /dev/null
+++ b/simulation_outputs/output.csv
@@ -0,0 +1,62 @@
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diff --git a/simulation_outputs/simulation_flow_SIR_plot.png b/simulation_outputs/simulation_flow_SIR_plot.png
new file mode 100644
index 0000000..5f43b63
Binary files /dev/null and b/simulation_outputs/simulation_flow_SIR_plot.png differ
diff --git a/tests/test.R b/tests/test.R
index 8b13789..e69de29 100644
--- a/tests/test.R
+++ b/tests/test.R
@@ -1 +0,0 @@
-