fixed issues with global variables, paths, and makeing sure target ou…

…tputs update with new file paths

1- Run RVFV Simulations.R

@@ -398,7 +398,9 @@ vxp <- (unlist(param_vec["vax"])/(unlist(param_vec["muL"])+ unlist(param_vec["g"
 
   save.image(file = rdata_path)
 
-  return("RVFV Sim")
+  return_value <- paste("RVFV Sim:",run_path_target,sep = " ")
+
+  return(return_value)
 
 }
 

2_RVF_LHC_Sensitivity_Analysis.R

@@ -26,8 +26,8 @@
 # library(here)
 RVF_LHC_SA <- function(target, h = 4000){
 #Set scenario
-SA <- TRUE
-h <- h #Number of simulations to run in sensitivity anlaysis
+SA <<- TRUE
+h <<- h #Number of simulations to run in sensitivity analysis
 
 #Source data and code
 #Functions for setting the hatching switches the data
@@ -48,7 +48,7 @@ model_run_path <- target
 
 #Set timing
 start.time <- 0
-end.time <- nrow(All_Precip) 
+end.time <<- nrow(All_Precip) 
 timestep <- 1
 times <- seq(from = start.time, 
              to = end.time, 

3- Calculate and Plot_R0.R

@@ -109,7 +109,7 @@ pts$X <- R0params[x]
 if(!names(R0params[x])=="biteA"){
   stop()
 }
-plot.biteA <- ggplot()+#
+plot.biteA <<- ggplot()+#
   geom_line(data = df_plot, aes(x = Value, y = R0_both, col = "1B"), size = 1, alpha = .5, linetype = "dashed")  +
   geom_line(data = df_plot, aes(x = Value, y = R0_A, col = "2A"), size = 1, alpha = .5, linetype = "dashed")  +
   geom_line(data = df_plot, aes(x = Value, y = R0_C, col = "3C"), size = 1, alpha = .5, linetype = "dashed")  +
@@ -132,7 +132,7 @@ pts$X <- R0params[x]
 if(!names(R0params[x])=="q"){
   stop()
 }
-plot.q <- ggplot()+#
+plot.q <<- ggplot()+#
   geom_line(data = df_plot, aes(x = Value, y = R0_both, col = "1B"), size = 1, alpha = .5, linetype = "dashed")  +
   geom_line(data = df_plot, aes(x = Value, y = R0_A, col = "2A"), size = 1, alpha = .5, linetype = "dashed")  +
   geom_line(data = df_plot, aes(x = Value, y = R0_C, col = "3C"), size = 1, alpha = .5, linetype = "dashed")  +
@@ -155,7 +155,7 @@ pts$X <- R0params[x]
 if(!names(R0params[x])=="Tcsl"){
   stop()
 }
-plot.Tcsl <- ggplot()+#
+plot.Tcsl <<- ggplot()+#
   geom_line(data = df_plot, aes(x = Value, y = R0_both, col = "1B"), size = 1, alpha = .5, linetype = "dashed")  +
   geom_line(data = df_plot, aes(x = Value, y = R0_A, col = "2A"), size = 1, alpha = .5, linetype = "dashed")  +
   geom_line(data = df_plot, aes(x = Value, y = R0_C, col = "3C"), size = 1, alpha = .5, linetype = "dashed")  +
@@ -178,7 +178,7 @@ pts$X <- R0params[x]
 if(!names(R0params[x])=="muC"){
   stop()
 }
-plot.muC <- ggplot()+#
+plot.muC <<- ggplot()+#
   geom_line(data = df_plot, aes(x = Value, y = R0_both, col = "1B"), size = 1, alpha = .5, linetype = "dashed")  +
   geom_line(data = df_plot, aes(x = Value, y = R0_A, col = "2A"), size = 1, alpha = .5, linetype = "dashed")  +
   geom_line(data = df_plot, aes(x = Value, y = R0_C, col = "3C"), size = 1, alpha = .5, linetype = "dashed")  +
@@ -201,7 +201,7 @@ pts$X <- R0params[x]
 if(!names(R0params[x])=="biteC"){
   stop()
 }
-plot.biteC <- ggplot()+#
+plot.biteC <<- ggplot()+#
   geom_line(data = df_plot, aes(x = Value, y = R0_both, col = "1B"), size = 1, alpha = .5, linetype = "dashed")  +
   geom_line(data = df_plot, aes(x = Value, y = R0_A, col = "2A"), size = 1, alpha = .5, linetype = "dashed")  +
   geom_line(data = df_plot, aes(x = Value, y = R0_C, col = "3C"), size = 1, alpha = .5, linetype = "dashed")  +

Functions/Function 7 Manage model outputs.R

@@ -1,16 +1,16 @@
 ## create folder for outputs from hash of params vector
 
 
-get_run_id <- function(){
-  rlang::hash(Sys.time())
+get_run_id <- function(value = Sys.time()){
+  rlang::hash(value)
 }
 
 create_model_folders <- function(run_id,overwrite = FALSE){
   folder_path <- sprintf("%s/%s", "model_runs", run_id)
   dir.create(folder_path,recursive = TRUE)
 
   ## Create set of subfolders for different outputs ----  
-  sub_folders <- c("Publication_Figures/Draft_Figures","Data for sensistivity analysis" )
+  sub_folders <- c("Publication_Figures/Draft_Figures","Data for sensitivity analyses" )
 
   for(folder in sub_folders){
     sub_folder_path <- sprintf("%s/%s", folder_path, folder)
@@ -25,8 +25,8 @@ write_model_run_path <- function(folder_path){
   saveRDS(object = folder_path,"model_runs/current_run_path.RDS")
 }
 
-create_model_run_path <- function(){
-  run_id <- get_run_id()
+create_model_run_path <- function(value = Sys.time()){
+  run_id <- get_run_id(value)
   print(sprintf("Model run id: %s", run_id))
 
   folder_path <- create_model_folders(run_id)
@@ -47,10 +47,15 @@ read_model_run_path <- function(){
 
 delete_model_run_path <- function(target,...){
   dep_obj <- paste(target,...,collapse = ", ")
+  pathRemoved <- readRDS("model_runs/current_run_path.RDS")
   unlink("model_runs/current_run_path.RDS")
-  message("Current_run_path.RDS removed. 
+  message(glue::glue("Current_run_path.RDS removed.
+          Any outputs were saved in {pathRemoved}
+  
           Use set_model_run_path to interactively 
-          set the model run path")
+          set the model run path"))
+
+
   return("current_run_path.RDS removed")
 }
 

_targets.R

@@ -40,8 +40,8 @@ list(
   ),
   tar_target(
     name = b_LHC_SA,
-    command = RVF_LHC_SA(Create_Run_Path, h = 1),
-    cue = targets::tar_cue("never") ## takes around 100hrs on 8 core machine
+    command = RVF_LHC_SA(Create_Run_Path, h = 1)
+    #cue = targets::tar_cue("never") ## 4k sims takes around 100hrs on 8 core machine
   ),
   tar_target(
     name = c_Calc_Plot_R0,