🔬 XRF Data Parsing Tool for OLYMPUS VANTA pXRF Chemistry Datasets

This Shiny application is designed to streamline the analysis of XRF datasets exported from the OLYMPUS VANTA pXRF device using the Geo Chem method. It simplifies complex raw data into a clean, normalized, and insightful format for geochemical analysis.

---

⚙️ Requirements & Data Setup

Prerequisites

To use this application, you must have the following:

• OLYMPUS VANTA pXRF device for data acquisition.
• Data must be exported using the Geo Chem export method.

Data Preparation

Ensure your CSV or XLSX export strictly adheres to the Geo Chem format Specifically:

• The Item Notes column must be consistently labeled as LAB_ID.
• The LAB_ID values should contain both letters and numbers (e.g., S-101, A-2B) for string-value compatibility and optimal parsing.
• If The file is XLSX make sure that the data read is on Sheet 1

---

✨ Features & Workflow

This tool is specifically tailored to parse OLYMPUS VANTA pXRF Geo Chem databases, focusing on selectively retaining element compositions and item IDs for downstream analysis.

How to Use: Tab-by-Tab Workflow

The application guides you through a sequential data processing workflow across four main tabs:

1. Raw Data 📥

This is your initial loading and pre-filter stage.

• Load Data: Use the input feature to upload your Geo Chem CSV file.
• Initial Filtering: Apply basic filters by Sample Name and the Analysis Method used to narrow down the dataset.

2. Subset Data 🧼

This tab presents a cleaned and refined dataset ready for analysis.

• Automatic Cleanup: Only the essential LAB_IDs and element concentration columns are retained.
• Processing Switches (Sidebar): Use the switches in the sidebar to:
  • Drop Zero Columns: Automatically remove element columns where the sum of readings is 0 (i.e., elements that were not detected).
  • Normalize Data: Apply normalization to the remaining element readings for comparative analysis.
• Manual Element Removal: You can remove additional unwanted element columns by deselecting them from the Input Selection in the sidebar.

3. Analytics 📈

This is the individual sample inspection stage.

• Individual Item Filtering: Select individual LAB_ID items from the dropdown to view their specific readings and analytics.
• Interactive Visualizations: Review table showing the composition for the selected sample(s).

4. Summary & Export 💾

This final tab aggregates your key findings and handles data output.

• Aggregated Results: Displays a summary of the LAB_ID items and their analytics that you selected and finalized in the Analytics tab.
• Analytics Selection (Sidebar): Choose the specific type of analytics (e.g., summary statistics, specific ratios) you wish to include in the final report via the Input Select tab in the sidebar.
• Saving Data: When the Save button is clicked, the application exports a compilation of:
  • The final, processed reading values.
  • The selected analytics results.
  • The original Raw Data table.
  • The cleaned Subset Data table.

---

🌳 Contribution & Versioning

This repository utilizes two main branches:

• master: This is the stable branch currently used for critical lab work. Do not push directly to this branch.
• experimental: Please push all new features, bug fixes, and development changes to the experimental branch. Pull requests will be reviewed and merged into master after validation.