Graphs read from correct locations

R/simulation_epigeopop.r

@@ -75,12 +75,13 @@ run_complete_simulation <- function(output_dir="data/Andorra/simulation_outputs"
   sir_plot <- create_sir_plot(df_long, display = TRUE)
   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))
 
-  plot_rt_curves("data/Andorra/simulation_outputs/secondary_infections.csv")
-
-  create_serial_interval_plot("data/Andorra/simulation_outputs/serial_intervals.csv", display = TRUE)
+  # 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 = "", si_plot = ""))
+  return(list(simulation = sim, data = df_long, sir_plot = sir_plot, rt_plot = rt_plot, si_plot = si_plot))
 }
 
 results <- run_complete_simulation()

R/simulation_toy.r

@@ -78,9 +78,11 @@ run_complete_simulation <- function(output_dir="data/toy/simulation_outputs",
   save_sir_plot(sir_plot, file.path(output_dir, sir_plot_file))
 
 
-  plot_rt_curves("data/simulation_outputs/secondary_infections.csv")
+  # Generate Rt plot
+  rt_plot <- plot_rt_curves(file.path(output_dir, "secondary_infections.csv"), display =TRUE,  location = file.path(output_dir, rt_plot_file))
 
-  create_serial_interval_plot("data/simulation_outputs/serial_intervals.csv", display = TRUE)
+  # 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 = "", si_plot = ""))
 }

R/wrapper.R

@@ -153,15 +153,6 @@ create_sir_plot <- function(df_long, title = "SIR Model Flow", display = TRUE) {
 }
 
 # Save plot
-save_sir_plot <- function(plot, filename, width = 10, height = 6, dpi = 300) {
-  ggsave(
-    filename = here(filename),
-    plot = plot,
-    width = width,
-    height = height,
-    dpi = dpi
-  )
-}
 
 save_sir_plot <- function(plot, filename, width = 10, height = 6, dpi = 300) {
   ggsave(
@@ -173,7 +164,7 @@ save_sir_plot <- function(plot, filename, width = 10, height = 6, dpi = 300) {
   )
 }
 
-plot_rt_curves <- function(file_path) {
+plot_rt_curves <- function(file_path, location) {
   # Check if file exists
   if (!file.exists(file_path)) {
     stop("The file does not exist. Please provide a valid file path.")
@@ -216,7 +207,7 @@ plot_rt_curves <- function(file_path) {
 }
 
 # Create serial interval plot
-create_serial_interval_plot <- function(file_path, title = "Serial Interval Distribution", display = TRUE) {
+create_serial_interval_plot <- function(file_path, title = "Serial Interval Distribution", display = TRUE, location) {
   # Read the CSV file and exclude the first row
   data <- read.csv(file_path, header = TRUE)[-1, ]
 
@@ -245,7 +236,7 @@ create_serial_interval_plot <- function(file_path, title = "Serial Interval Dist
   }
 
   # Save the plot
-  save_sir_plot(p, "data/simulation_outputs/serial_interval.png")
+  save_sir_plot(p, location)
 
   return(p)
 }