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---
title: "Practical R Workflow for Scientists June-July 2021"
---
<img style="float: right;" src="images/tools-logo-transparent.png" width=30%>
These short sessions (45min to 1hr) will be focused on tools and practices for NMFS scientists to help you be **faster, more efficient and organized** in your coding and in merging reports with code. The focus of these workshops is practical skills and tools. Each session will be stand-alone. While the sessions will be introductory, I will give you links to my GitHub repositories that illustrate more complex examples (and that you can copy and build on).
**Target audience**: You already code in R, maybe use RStudio too, but want to learn some tips about being more efficient from a seasoned R programmer who does the kind of coding and work that you do.
**About me**: I am a modeler/applied mathematician and I am immersed in R. I develop R packages for public use. I teach time-series analysis at the University of Washington (using R) and I teach workshops on R and reproducible research.
## Set-up for the workshop
Before the workshops, go to [Set-up](set-up.html) for instructions. Unless you will only be listening, you'll need a [GitHub](https://github.com/) account. To actively participate in the activities, you'll want either R, RStudio and GitHub Desktop installed on your computer or you can use [RStudio Cloud](https://rstudio.cloud/). If you do the latter, you don't need to install any software.
## Video and GitHub Organization links for the sessions
Please email Eli ([email protected]) from your NOAA email, and I will send you the WebEx links and link to the GitHub Classroom. It is the same link for each session.
## Topics
* [Week 1](week1.html) Introduction to workflow using RStudio and Git/GitHub. The session video will be posted June 2nd but the link has my lectures notes and short videos of the skills. [Lecture notes and video links](week1.html)
* [Week 2](week2.html). More Git skills. The 3 key Git skills. These 3 basic skills are all you need for 95% of your work with Git repositories. [The lecture notes, discussion and videos](week2.html)
* [Week 3](week3.html). GitHub skills. We'll learn how to use issues and releases on GitHub to be more efficient either working alone or in a team. I'll show you how I use organizations to organize my repositories and some of the nice 'landing page' features of GitHub. For those curious about GitHub Actions, I give you a short demo on that too. [The lecture notes and discussion](week3.html)
* [Week 4](week4.html). Rmarkdown for reports. Let's make a report that updates when our data change and post that to GitHub.
* Week 5. Making plots with ggplot2. Learning ggplot2 will make it much easier to make plots from the big and complex datasets that you deal with on a daily basis.
* Week 6. Creating a R package. I show you how to make basic data and code packages that allows you to version and document your data and code.
* Week 7. Documentation for R packages using Roxygen.
* Week 8. Creating landing pages using RStudio/R Markdown/GitHub and R packages landing pages using pkgdown.
## Video only
I will make videos of this material.
* Handy clustering tools in R
* Making raster plots with the raster and tmap packages. Working with spatial data is a huge area. We are going to start gently by making raster plots and using the tmap package. You'll see how easy it easy to make maps of data on a grid.
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<div style="text-align: center">
<i class="fas fa-cubes"></i> NWFSC Math Bio Program <i class="fas fa-cubes"></i>
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