G18 Data Workshop

Workshop: “Doing the most with your data: Processing, products, metadata and web applications"

Organized by Corinna Gries & Hilary Dugan

Objectives

• Use R to download data from the LTER data repository, the CUAHSI data center, and the GLEON DataONE member node.

• Learn the basics of Metadata

• Use the R package EML do develop metadata formatted in the Ecological Metadata Language

• Upload data and metadata to the GLEON DataONE member node (demonstration only, due to current log-in changes in DataONE)

• Aggregate data the easy way, using dplyr and tidyr

• Become familiar with R package Lake Metabolizer. Contains a variety of methods for calculating lake metabolism from buoy data.

• Build a Shiny App. Shiny is a web application framework for R, which you can use to turn your R code an interactive application.

  • Example: http://poseidon.limnology.wisc.edu:3838/metviewer/

Tasks to be completed prior to arriving at G18

1. Download and install R.

This is achieved using a CRAN mirror, such as: http://cran.stat.sfu.ca/

-Or-

Update R, if you are using an R version < 3.2.4

2. Download and install RStudio

We will be using RStudio for all examples/demonstrations. Please have the RStudio application on your laptop.

https://www.rstudio.com/products/rstudio/download/

3. Install R packages

The following packages should be installed on your computer. To install packages in R, use the following code:

install.packages(‘shiny’)

Please install:

• LakeMetabolizer

• rLakeAnalyzer

• shiny

• dataone

• devtools

• rmarkdown (this will install several other packages)

• tidyr

• dplyr

• lubridate

• readr

• WaterML

Some packages are not yet available on CRAN. You can install packages directly from github using the devtools package. We will be using the EML package (this is installed from github, which means that you’ll need to install devtools first and then issue the command:

devtools::install_github("ropensci/EML")

Instructions are at: https://github.com/ropensci/EML

4. Download Data for the Workshop

Sparkling Lake, Wisconsin, 1-minute buoy data. We will be working with these during the workshop. 

• Sparkling Lake Water Temperature 2014 (200MB)
• Sparkling Lake DO, PAR, AirTemp, RH, Windspeed 2014 (14MB)

Sparkling Lake, Wisconsin, hourly buoy data. These are for reference. We will be making these during the workshop.

• Sparkling Lake Water Temperature 2014 - Hourly (1MB)
• Sparkling Lake DO, PAR, AirTemp, RH, Windspeed 2014 - Hourly (0.4MB)

Shiny template files. Please download. 

• Shiny Template Files (2kb)

5. Workshop material - Coding vignettes, presentation

• Vignette: Aggregating buoy data from minute to hourly (pdf)
• Vignette: R code for metabolism estimates (pdf)
• Vignette: R code for creating EML metadata (pdf)
• Presentation: Metadata presentation (pdf)
• Material: Create EML (zip)
• Material: Data Download example scripts (zip)
• Shiny code available on github

Additional Resources

• Shiny Tutorial: http://shiny.rstudio.com/tutorial/

• Shiny App Gallery: http://shiny.rstudio.com/gallery/

• Data wrangling cheatshet: https://www.rstudio.com/wp-content/uploads/2015/02/data-wrangling-cheatsheet.pdf

• Data processing with tidyr and dplyr https://rpubs.com/bradleyboehmke/data_wrangling

Schedule, July 4th, 2016