harmonize_wq:

Standardize, clean, and wrangle Water Quality Portal data into more analytic-ready formats

Useful links: Code Repository | Issues

Overview

US EPA’s Water Quality Portal (WQP) aggregates water quality, biological, and physical data provided by many organizations and has become an essential resource with tools to query and retrieve data using python or R. Given the variety of data and data originators, using the data in analysis often requires cleaning to ensure it meets required quality standards and wrangling to get it in a more analytic-ready format. Recognizing the definition of analysis-ready varies depending on the analysis, the harmonize_wq package is intended to be a flexible water quality specific framework to help:

• Identify differences in data units (including speciation and basis)

• Identify differences in sampling or analytic methods

• Resolve data errors using transparent assumptions

• Transform data from long to wide format

Domain experts must decide what data meets their quality standards for data comparability and any thresholds for acceptance or rejection.

Getting Started

• Overview
• Installing harmonize_wq
  • Install harmonize_wq using pip:
  • Install the latest development version of harmonize_wq using pip:
• Example Workflow
  • dataretrieval Query for a GeoJSON
  • Harmonize results
  • Clean results
  • Transform results from long to wide format

Tutorial Notebooks

• Pensacola Bay FL - Simple workflow
• Pensacola Bay FL - Detailed step-by-step
• Tampa Bay, FL - Simple workflow
• Tampa Bay, FL - Detailed step-by-step
• Cape Cod - Simple workflow
• Cape Cod - Detailed step-by-step
• Gulf of Mexico Estuaries - Try the example workflow in other estuaries

To instead run tutorials directly in ipython notebooks or using R, see: demos

Reference Documentation

• harmonize_wq

Indices and tables

• Index

• Module Index

• Search Page

Disclaimer

The United States Environmental Protection Agency (EPA) GitHub project code is provided on an “as is” basis and the user assumes responsibility for its use. EPA has relinquished control of the information and no longer has responsibility to protect the integrity , confidentiality, or availability of the information. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by EPA. The EPA seal and logo shall not be used in any manner to imply endorsement of any commercial product or activity by EPA or the United States Government.