Open source tools at Utah DWQ

Jake Vander Laan (jvander@utah.gov)

Elise Hinman (ehinman@utah.gov)

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What is open source?

Source code made publicly available for use and modification.

Why use open source?

Transparency
Repeatability
Efficiency
Flexibility
Ownership

What do we use open source tools for?

Querying/downloading data
Water quality assessments
Data visualization
Documenting & communicating analyses

Our general approach

Reusable, generalizable functions with flexible inputs
Use arguments to modify functions, instead of re-programming
Link functions in series to perform analyses
Document functions and analyses
Use interactive figures and applications to enhance user understanding

What platforms do we use?

R

R is an open source statistical program and coding language.
r-project.org

Robust user community of coders & problem solvers.
Fully customizable.

R

Functions & packages

Function:
A block of code that performs a particular task or set of tasks. A function has a name, arguments, a body (code), and a return value.
Argument:
Change-able inputs to a function.
Package:
A portable collection of R functions.

R documentation

Help files
Package manuals

Markdown

Text formatting syntax that allows conversion of plain text to rich text HTML, PDF, and other document types including tables, figures, and code.

Documents (package rmarkdown)
Chapters & books (package bookdown)
Presentations
Dashboards
Websites

Markdown - Bookdown

Compile documents into books. Document complex processes & user build guides.

Example: Utah IR R tools user guide

Data portals & web services

Water quality data portal
waterqualitydata.us/portal

Data portals & web services

Web service capabilities

Data portals & web services

two_site_nr=readWQP(type="narrowresult",
                    siteid=c("UTAHDWQ_WQX-4900440","UTAHDWQ_WQX-4900470"), 
                    start_date="01/01/2016", end_date="12/31/2018")

utah_lake_nr=readWQP(type="narrowresult",
                     auid=c('UT-L-16020201-004_01', 'UT-L-16020201-004_02'),
                     start_date="01/01/2016", end_date="12/31/2018",
                     siteType="Lake, Reservoir, Impoundment")

Data portals & web services

ECHO

Data portals & web services

ECHO

UT0021717_tp_001=readECHO_ec(p_id="UT0021717", 
    parameter_code="00665", outfall="001", print=F)
UT0021717_tp_001_effluent=subset(UT0021717_tp_001, 
    monitoring_location_desc=="Effluent Gross")

Permit ID	Date	Parameter	Result	Units	Stat
UT0021717	12/31/2019	Phosphorus, total [as P]	2.50	mg/L	30DA AVG
UT0021717	11/30/2019	Phosphorus, total [as P]	2.61	mg/L	30DA AVG
UT0021717	10/31/2019	Phosphorus, total [as P]	2.40	mg/L	30DA AVG
UT0021717	09/30/2019	Phosphorus, total [as P]	2.60	mg/L	30DA AVG
UT0021717	08/31/2019	Phosphorus, total [as P]	2.40	mg/L	30DA AVG
UT0021717	07/31/2019	Phosphorus, total [as P]	2.48	mg/L	30DA AVG

GitHub

Collaborative code writing, versioning, & sharing platform.
Individuals, organizations, teams, and repositories.

GitHub

DWQ GitHub organization
A location for DWQ staff to store, collaborate, and share repositories.
github.com/utah-dwq

DWQ R packages
DWQ has two packages in current development. These can be viewed and installed via GitHub.

R-Shiny

Shiny is an R package for building interactive web applications to visualize and analyze data and communicate analytical results.

Examples

Querying & processing data

Full page

Salinity in Great Salt Lake

An analysis of changes in salinity in Great Salt Lake in response to changes to in hydrologic connectivity through a railroad causeway that bisects the lake.