Merge branch 'main' into new_inference

HopkinsIDD · Apr 26, 2024 · 2b720f3 · 2b720f3
2 parents 4431f8f + 40207b7
commit 2b720f3
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Showing 4 changed files with 12 additions and 4 deletions.
diff --git a/datasetup/build_US_setup.R b/datasetup/build_US_setup.R
@@ -153,6 +153,9 @@ if (length(config$subpop_setup$geodata) > 0) {
 # manually remove PR
 census_data <- census_data %>% filter(USPS != "PR")
 
+
+if(!dir.exists(dirname(config$subpop_setup$geodata))){
+  dir.create(dirname(config$subpop_setup$geodata))}
 write.csv(file = file.path(geodata_file), census_data, row.names=FALSE)
 print(paste("Wrote geodata file:", file.path(geodata_file)))
 
@@ -162,13 +165,13 @@ print(paste("Wrote geodata file:", file.path(geodata_file)))
 # MOBILITY DATA (COMMUTER DATA) ------------------------------------------------------------
 
 
-if(state_level & !file.exists(paste0(config$data_path, "/", config$subpop_setup$mobility))){
+if(state_level & !file.exists(paste0(config$subpop_setup$mobility))){
 
   warning(paste("State-level mobility files must be created manually because `build_US_setup.R` does not generate a state-level mobility file automatically. No valid mobility file named", paste0(config$data_path, "/", config$subpop_setup$mobility), "(specified in the config) currently exists. Please check again."))
 
-} else if(state_level & file.exists(paste0(config$data_path, "/", config$subpop_setup$mobility))){
+} else if(state_level & file.exists(paste0(config$subpop_setup$mobility))){
 
-  warning(paste("Using existing state-level mobility file named", paste0(config$data_path, "/", config$subpop_setup$mobility)))
+  warning(paste("Using existing state-level mobility file named", paste0(config$subpop_setup$mobility)))
 
 } else{
 

diff --git a/datasetup/build_covid_data.R b/datasetup/build_covid_data.R
@@ -389,7 +389,8 @@ us_data <- us_data %>%
     # mutate(across(starts_with("incid"), ~ replace_na(.x, 0))) %>%
     mutate(across(starts_with("incid"), ~ as.numeric(.x)))
 
-
+if(!dir.exists(dirname(config$inference$gt_data_path))){
+  dir.create(dirname(config$inference$gt_data_path))}
 # Save
 write_csv(us_data, config$inference$gt_data_path)
 

diff --git a/datasetup/build_flu_data.R b/datasetup/build_flu_data.R
@@ -80,6 +80,8 @@ us_data <- us_data %>%
     filter(date >= lubridate::as_date(config$start_date) & date <= lubridate::as_date(end_date_)) %>%
     filter(!is.na(source))
 
+if(!dir.exists(dirname(config$inference$gt_data_path))){
+  dir.create(dirname(config$inference$gt_data_path))}
 write_csv(us_data, config$inference$gt_data_path)
 
 

diff --git a/datasetup/build_nonUS_setup.R b/datasetup/build_nonUS_setup.R
@@ -103,6 +103,8 @@ if(opt$w){
 }
 
 # Save population geodata
+if(!dir.exists(dirname(config$subpop_setup$geodata))){
+  dir.create(dirname(config$subpop_setup$geodata))}
 names(census_data) <- c("subpop","admin2","admin0","pop")
 write.csv(file = file.path('geodata.csv'), census_data,row.names=FALSE)