changed config$outcomes$scenarios to config$outcomes_modifiers$scenar…

…ios to match new simplified config format
HopkinsIDD · Oct 11, 2023 · 10d118b · 10d118b
1 parent c051cc0
commit 10d118b
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Showing 11 changed files with 20 additions and 22 deletions.
diff --git a/flepimop/R_packages/flepicommon/R/config_test_new.R b/flepimop/R_packages/flepicommon/R/config_test_new.R
@@ -526,7 +526,7 @@ validation_list$outcomes$settings<-function(value, full_config,config_name){
   if(is.null(value)){
     print("No outcome settings mentioned default assigned") #Assign Default
   }
-  for (scenario in full_config$outcomes$scenarios){
+  for (scenario in full_config$outcomes_modifiers$scenarios){
     if(!(scenario %in% names(value))){
       print(paste0("No details mentioned about scenario ",scenario," in outcomes"))
       return(FALSE)

diff --git a/flepimop/main_scripts/inference_main.R b/flepimop/main_scripts/inference_main.R
@@ -43,9 +43,9 @@ config <- flepicommon::load_config(opt$config)
 ##If outcome scenarios are specified check their existence
 outcome_modifiers_scenarios <- opt$outcome_modifiers_scenarios
 if (all(outcome_modifiers_scenarios == "all")) {
-  outcome_modifiers_scenarios <- config$outcomes$scenarios
-} else if (!(outcome_modifiers_scenarios %in% config$outcomes$scenarios)){
-  message(paste("Invalid outcome scenario argument:[",paste(setdiff(outcome_modifiers_scenarios, config$outcome$scenarios)), "]did not match any of the named args in", paste(config$outcomes$scenarios, collapse = ", "), "\n"))
+  outcome_modifiers_scenarios <- config$outcomes_modifiers$scenarios
+} else if (!(outcome_modifiers_scenarios %in% config$outcomes_modifiers$scenarios)){
+  message(paste("Invalid outcome scenario argument:[",paste(setdiff(outcome_modifiers_scenarios, config$outcome$scenarios)), "] did not match any of the named args in", paste(config$outcomes_modifiers$scenarios, collapse = ", "), "\n"))
   quit("yes", status=1)
 }
 

diff --git a/flepimop/main_scripts/inference_slot.R b/flepimop/main_scripts/inference_slot.R
@@ -137,9 +137,9 @@ if (!dir.exists(data_dir)){
 ##If outcome scenarios are specified check their existence
 outcome_modifiers_scenarios <- opt$outcome_modifiers_scenarios
 if(all(outcome_modifiers_scenarios == "all")) {
-    outcome_modifiers_scenarios <- config$outcomes$scenarios
-} else if (!(outcome_modifiers_scenarios %in% config$outcomes$scenarios)){
-    message(paste("Invalid outcome scenario argument:[",paste(setdiff(outcome_modifiers_scenarios, config$outcome$scenarios)), "]did not match any of the named args in", paste(config$outcomes$scenarios, collapse = ", "), "\n"))
+    outcome_modifiers_scenarios <- config$outcomes_modifiers$scenarios
+} else if (!(outcome_modifiers_scenarios %in% config$outcomes_modifiers$scenarios)){
+    message(paste("Invalid outcome scenario argument:[",paste(setdiff(outcome_modifiers_scenarios, config$outcome$scenarios)), "] did not match any of the named args in", paste(config$outcomes_modifiers$scenarios, collapse = ", "), "\n"))
     quit("yes", status=1)
 }
 
@@ -148,20 +148,20 @@ seir_modifiers_scenarios <- opt$seir_modifiers_scenarios
 if (all(seir_modifiers_scenarios == "all")){
     seir_modifiers_scenarios <- config$seir_modifiers$scenarios
 } else if (!all(seir_modifiers_scenarios %in% config$seir_modifiers$scenarios)) {
-    message(paste("Invalid intervention scenario arguments: [",paste(setdiff(seir_modifiers_scenarios, config$seir_modifiers$scenarios)), "] did not match any of the named args in ", paste(config$seir_modifiers$scenarios, collapse = ", "), "\n"))
+    message(paste("Invalid intervention scenario arguments: [", paste(setdiff(seir_modifiers_scenarios, config$seir_modifiers$scenarios)), "] did not match any of the named args in ", paste(config$seir_modifiers$scenarios, collapse = ", "), "\n"))
     quit("yes", status=1)
 }
 
 ##Creat heirarchical stats object if specified
 hierarchical_stats <- list()
-if ("hierarchical_stats_geo"%in%names(config$inference)) {
+if ("hierarchical_stats_geo" %in% names(config$inference)) {
     hierarchical_stats <- config$inference$hierarchical_stats_geo
 }
 
 
 ##Create priors if specified
 defined_priors <- list()
-if ("priors"%in%names(config$inference)) {
+if ("priors" %in% names(config$inference)) {
     defined_priors <- config$inference$priors
 }
 

diff --git a/postprocessing/model_output_notebook.Rmd b/postprocessing/model_output_notebook.Rmd
@@ -66,7 +66,7 @@ import_model_outputs <-
       "/",
       config$interventions$scenarios,
       "/",
-      config$outcomes$scenarios
+      config$outcomes_modifiers$scenarios
     )
     subdir_ <- paste0(dir_, "/", list.files(dir_),
                       "/",
@@ -280,8 +280,7 @@ Here are the results from your outcomes model. If you ran more than one simulati
 ## add something so that if it doesn't exist, it prints some 'no output' message
 
 # get all outcome variables
-scns <- config$outcomes$scenarios
-list_of_vars_config <- paste0("config$outcomes$settings$", scns)
+list_of_vars_config <- "config$outcomes$outcomes"
 outcomes <- eval(parse(text = list_of_vars_config))
 outcome_vars <- names(outcomes)
 
@@ -494,8 +493,7 @@ In your inference method you specified that your model be fit to `r names(config
 ```{r hosp_trajectories_inference_aggregate, fig.dim = c(10,10), results='asis'}
 if(inference){
   # get all outcome variables
-  scns <- config$outcomes$scenarios
-  list_of_vars_config <- paste0("config$outcomes$settings$", scns)
+  list_of_vars_config <- "config$outcomes$outcomes"
   outcomes <- eval(parse(text = list_of_vars_config))
   outcome_vars <- names(outcomes)
   fit_stats <- names(config$inference$statistics)

diff --git a/postprocessing/postprocess_snapshot.R b/postprocessing/postprocess_snapshot.R
@@ -82,7 +82,7 @@ import_model_outputs <- function(scn_dir, outcome, global_opt, final_opt,
                  outcome, "/",
                  config$name, "/",
                  config$interventions$scenarios, "/",
-                 config$outcomes$scenarios)
+                 config$outcomes_modifiers$scenarios)
   subdir_ <- paste0(dir_, "/", list.files(dir_),
                     "/",
                     global_opt,

diff --git a/postprocessing/processing_diagnostics.R b/postprocessing/processing_diagnostics.R
@@ -77,7 +77,7 @@ import_s3_outcome <- function(scn_dir, outcome, global_opt, final_opt){
                  outcome, "/",
                  config$name, "/",
                  config$interventions$scenarios, "/",
-                 config$outcomes$scenarios)
+                 config$outcomes_modifiers$scenarios)
   subdir_ <- paste0(dir_, "/", list.files(dir_),
                     "/",
                     global_opt,

diff --git a/postprocessing/processing_diagnostics_AWS.R b/postprocessing/processing_diagnostics_AWS.R
@@ -77,7 +77,7 @@ import_s3_outcome <- function(scn_dir, outcome, global_opt, final_opt){
                  outcome, "/",
                  config$name, "/",
                  config$interventions$scenarios, "/",
-                 config$outcomes$scenarios)
+                 config$outcomes_modifiers$scenarios)
   subdir_ <- paste0(dir_, "/", list.files(dir_),
                     "/",
                     global_opt,

diff --git a/postprocessing/processing_diagnostics_SLURM.R b/postprocessing/processing_diagnostics_SLURM.R
@@ -23,7 +23,7 @@ import_s3_outcome <- function(scn_dir, outcome, global_opt, final_opt){
                  outcome, "/",
                  config$name, "/",
                  config$interventions$scenarios, "/",
-                 config$outcomes$scenarios)
+                 config$outcomes_modifiers$scenarios)
   subdir_ <- paste0(dir_, "/", list.files(dir_),
                     "/",
                     global_opt,

diff --git a/postprocessing/run_sim_processing_FluSightExample.R b/postprocessing/run_sim_processing_FluSightExample.R
@@ -368,7 +368,7 @@ peak_ram_ <- peakRAM::peakRAM({
                                  plot_samp = plot_samp,
                                  gt_data = gt_data,
                                  geodata_file = geodata_file_path,
-                                 death_filter = config$outcomes$scenarios,
+                                 death_filter = config$outcomes_modifiers$scenarios,
                                  summarize_peaks = (smh_or_fch == "smh"),
                                  save_reps = save_reps)
         tmp_out <- list(tmp_out, tmp_out_)

diff --git a/postprocessing/run_sim_processing_SLURM.R b/postprocessing/run_sim_processing_SLURM.R
@@ -382,7 +382,7 @@ tmp_out <- process_sims(scenario_num = scenario_num,
                         plot_samp = plot_samp,
                         gt_data = gt_data,
                         geodata_file = geodata_file_path,
-                        death_filter = config$outcomes$scenarios,
+                        death_filter = config$outcomes_modifiers$scenarios,
                         summarize_peaks = (smh_or_fch == "smh"),
                         save_reps = save_reps)
 

diff --git a/postprocessing/run_sim_processing_TEMPLATE.R b/postprocessing/run_sim_processing_TEMPLATE.R
@@ -368,7 +368,7 @@ peak_ram_ <- peakRAM::peakRAM({
                                  plot_samp = plot_samp,
                                  gt_data = gt_data,
                                  geodata_file = geodata_file_path,
-                                 death_filter = config$outcomes$scenarios,
+                                 death_filter = config$outcomes_modifiers$scenarios,
                                  summarize_peaks = (smh_or_fch == "smh"),
                                  save_reps = save_reps)
         tmp_out <- list(tmp_out, tmp_out_)