Merge pull request #8 from SABS-R3-Epidemiology/anita_testing

Updated Coverage files and README

.covrignore

@@ -0,0 +1,9 @@
+# Files to ignore
+R/zzz.R
+R/simulation_epigeopop.r
+R/simulation_toy.r
+data
+images
+man
+tests
+walk_through

.github/workflows/coverage.yml

@@ -3,7 +3,7 @@ name: "Coverage"
 on:
   push:
     branches:
-      - main
+      - '**'
   pull_request:
     branches:
       - '**'
@@ -62,3 +62,4 @@ jobs:
         run: |
           covr::codecov()
         shell: Rscript {0}
+

DESCRIPTION

@@ -15,6 +15,7 @@ Suggests: tinytest
 Imports: 
     ggplot2,
     here,
+    testthat,
     tidyr,
     reticulate (>= 1.14)
 Depends: R (>= 3.3.0)

R/simulation_epigeopop.r

@@ -1,13 +1,13 @@
 source("R/wrapper.R")
 # Example usage:
 # Run complete simulation
-run_complete_simulation <- function(country="Andorra",
+run_complete_simulation <- function(country = "Andorra",
                                     output_file = "output.csv",
                                     sir_plot_file = "SIR_plot.png",
                                     rt_plot_file = "Rt_plot.png",
                                     si_plot_file = "SerialInterval_plot.png",
                                     simulation_duration = 60,
-                                    initial_infected = 100) { 
+                                    initial_infected = 100) {
   output_dir <- paste0("data/", country, "/simulation_outputs")
 
   # Initialize environment
@@ -51,17 +51,17 @@ run_complete_simulation <- function(country="Andorra",
     generation_time_output = TRUE,
     serial_interval_output = TRUE
   )
-
 
   # Use Andorra population data
-  population <- create_epigeopop_population(pe, 
-  paste0("data/", country, "/inputs/", country, 
-  "_microcells.csv"))
+  population <- create_epigeopop_population(pe,
+    paste0("data/", country, "/inputs/", country, "_microcells.csv")
+  )
 
   # Run simulation
-  sim <- run_geopop_sim(pe, sim_params, 
-  file_params, dem_file_params, population, 
-  inf_history_params, seed)
+  sim <- run_geopop_sim(pe, sim_params,
+    file_params, dem_file_params, population,
+    inf_history_params, seed
+  )
 
   # Process data
   df_long <- process_simulation_data(file.path(output_dir, output_file))
@@ -74,16 +74,19 @@ run_complete_simulation <- function(country="Andorra",
   save_sir_plot(sir_plot, file.path(output_dir, sir_plot_file))
 
   # Generate Rt plot
-  rt_plot <- plot_rt_curves(file.path(output_dir, "secondary_infections.csv"), 
-  location = file.path(output_dir, rt_plot_file))
+  rt_plot <- plot_rt_curves(file.path(output_dir, "secondary_infections.csv"),
+    location = file.path(output_dir, rt_plot_file)
+  )
 
   # Generate Serial Interval plot
-  si_plot <- create_serial_interval_plot(file.path(output_dir, 
-  "serial_intervals.csv"), display = TRUE, 
-  location = file.path(output_dir, si_plot_file))
-
-  return(list(simulation = sim, data = df_long, 
-  sir_plot = sir_plot, rt_plot = rt_plot, si_plot = si_plot))
+  si_plot <- create_serial_interval_plot(file.path
+    (output_dir, "serial_intervals.csv"), display = TRUE,
+    location = file.path(output_dir, si_plot_file)
+  )
+
+  return(list(simulation = sim, data = df_long, sir_plot = sir_plot,
+              rt_plot = rt_plot, si_plot = si_plot)
+  )
 }
 
 results <- run_complete_simulation()

README.md

@@ -1,3 +1,4 @@
+[![codecov](https://codecov.io/gh/SABS-R3-Epidemiology/rEpiabm/graph/badge.svg?token=YXS3D0IDBV)](https://codecov.io/gh/SABS-R3-Epidemiology/rEpiabm)
 ADD BADGES
 # rEpiabm
 rEpiabm enables users familiar with R to use [Epiabm](https://github.com/SABS-R3-Epidemiology/epiabm). Epiabm is a simulation tool that models the progress of an epidemic across a specified region of interest within a specific timeframe. It has been developed in python (PyEpiabm) for small-scale implementations and C++ (cEpiabm) for fast, large-scale simulations. PyEpiabm has a modular design, with many options to configure specific requirements.

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(rEpiabm)
+
+test_check("rEpiabm")  # Run all tests in the testthat directory