PEP R Training

R is a language for statistical computing as well as a general purpose programming language. R has become one of the primary languages used in data science and for data analysis across many of the natural sciences. This training workshop will provide attendees with the foundation for using R work with PEP reporting products.

Course objectives

This course is designed to expose you to the fundamentals of using R for working with the peptools R package developed for the Peconic Estuary Program. We will also cover the basics of using R if you are not familiar with the software. You will not be R experts by the end of the course, but you will have a solid foundation for continued learning. By the end of this course you will be able to or have the resources to find out how to:

  • Use R for basic data analysis
  • Use the peptools package to read, analyze, and plot water quality data
  • Use the peptools package to read, analyze, and plot pathogens data
  • Use the peptools package to read, analyze, and plot dissolved oxygen data


Please see this link for a live recording of the training.

Tuesday, February 23rd, 2021

Housekeeping day of training

There are a few housekeeping items we need to go over before we start the workshop.

  1. Please mute your microphones unless you have a question. You can also type a question in the chat, but I may not see it right away.

  2. Please use RStudio Cloud or your own installation of RStudio during this workshop. The setup instructions for RStudio Cloud are here and for RStudio installation here. You may use one or the other, but we recommend RStudio Cloud for the training.

  3. We have a live coding link that we’ll be using as we go through the lessons. If you get lost, you can copy/paste code from this link into RStudio.

  4. All training content is on this website. We will be covering the content directly on the website, so if you get lost you can view the agenda to see which lesson we’re covering and find where we’re at by scrolling through the content.

  5. Each lesson has it’s own R script that is linked at the top. If you are not using the live coding link, you can download the lesson R script and use that directly.

  6. Finally, if you are not using RStudio Cloud, please make sure to download the required datasets here and make sure you have the the tidyverse, mapview, remotes, and peptools packages installed. See the setup instructions for details.

All exercises and breaks will be timed to make sure that we stay on schedule. We’ll display a timer on the screen to track progress. Each lesson will also be recorded so you can review at a later date.

Software requirements

This training will use RStudio and R. Please make sure that you are ready to use the required software prior to the workshop. We will not be available for installation issues or questions on the day of training. There are two options for setup:

  1. Use RStudio Cloud to access from a web browser following the setup instructions.


  2. Install RStudio and R on your personal computer following the setup instructions.

Data and resources

Please view the Data and Resources page for data used in the training and additional links for R learning material. A live coding link is also available.


Marcus Beck ( - Marcus is the Program Scientist for the Tampa Bay Estuary Program and is developing data analysis and visualization methods for Bay health indicators. He received his BS in Zoology from the University of Florida in 2007 and his MSc and PhD in Conservation Biology from the University of Minnesota in 2009 and 2013. Marcus has experience researching environmental indicators and developing open science products to support environmental decision-making.

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