Image updates and position adjustments

- Minor updates to run_pipeline.R including new screenshots
- Adjust library positioning in provided_files.R

Author: SWi1

provided_files.R

@@ -3,11 +3,13 @@
 # Polyphenol Estimator
 # DII Calculation
 # Built by: Stephanie Wilson
-# Date: November 2025
+# Date: February 2026
 # ==============================
 
 # PROVIDED FILES================
-# Unless moved, you do not have to change these
+# Unless moved, you do not have to change any file paths
+Local_R_packages = "local_library"
+dir.create(Local_R_packages, showWarnings = FALSE)
 
 # Files for Polyphenol Estimator
 # FDA-FDD Database Version 3.1

run_pipeline.R

@@ -1,26 +1,23 @@
 # ============================================================
 # Run Polyphenol Estimator
 # Built by: Stephanie Wilson
-# Date: November 2025
+# Date: February 2026
 # ============================================================
 
 # SET WORKING DIRECTORY
 setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
 
-# SOURCE FUNCTIONS
-# ------------------------------------------------------------
-source('functions/estimate_polyphenols.R')
-source('functions/calculate_DII.R')
-
 # RUN POLYPHENOL ESTIMATOR
 # ------------------------------------------------------------
 # diet_input_file = 'user_inputs/UPDATE_THIS_PATH.csv'
 # type, specify "ASA24" or "NHANES"
 # report, specify "none", "html", or "md" for your reports
+source('functions/estimate_polyphenols.R') # loads function
 estimate_polyphenols(diet_input_file = 'user_inputs/VVKAJ_Items.csv',
-                     type = "ASA24", report = "none") 
+                     type = "ASA24",  report = "none") 
 
 # CALCULATE DIETARY INFLAMMATORY INDEX
 # ------------------------------------------------------------
 # report, specify "none", "html", or "md" for your reports
+source('functions/calculate_DII.R') # loads function
 calculate_DII(report = "none")