Overview

This website is the starting point for the free 8-week webinar training series on Reproducible Reporting with R (R³) for marine ecological indicators, sponsored by the Working Group on the Northwest Atlantic Regional Sea (WGNARS) and open to all.

Materials will be populated into the Schedule below and menu above. Please consult the Setup to have accounts created and software installed.

Webinar

Please join the WebEx meeting here Mondays 2-3:30 pm Eastern time:

Webex: Open Sci Short Course, hosted by NEFSC

The first hour will be a presentation and the last half hour for discussion and exercise completion time. All webinars will be recorded and posted to this website for future reference.

Schedule

1. June 14: Collaborate
   Use Github to share and version code, as well as handle basic project management with issues and project boards. The RStudio development environment will be introduced to interface with git and Github. Use of Github Pages to host knitted Rmarkdown documents will enable sharing of online reports.
   Video, Slides, Lesson
   
   
2. June 21: Manipulate
   Use the latest “tidyverse” of R packages (readr, dplyr, tidyr, stringr, lubridate) for wrangling data and sequencing operations with the pipe (%>%) operator.
   Video, Slides, Lesson
   
   
3. June 28: Visualize
   Use principles of the “grammar of graphics” to develop static plots in the R package ggplot2. Make these interactive with plotly. Develop dedicated time series plots with dygraphs.
   Video, Slides, Lesson
   
   
4. July 12: Map
   Read and write vector data (points, lines, polygons) using the spatial features sf R package in conjuction with dplyr to wrangle and summarize. Use the raster R package for gridded data. Generate interactive maps with leaflet.
   Video, Slides, Lesson
   
   
5. July 19: Report
   Dive into Rmarkdown for for knitting formatted text (markdown) with chunks of evaluated R code into html, pdf and docx formats. Use Rmarkdown for single page reports, bookdown for reports with chapters, flexdashboard for dashboards and Rmarkdown websites for simple websites with shared navigation. Automatically render with Github Actions.
   Video, Slides, Lesson
   
   
6. July 26: Infographics
   Use a custom infographiq Javascript library to intelligently link icons of ecosystem elements to pop-up windows containing data figures, which could be static images or interactive visualizations.
   Video, Slides, Lesson
   
   
7. August 2: Applications
   Use the Shiny framework to develop online interactive applications accepting user input to render outputs from arbitrary R functions. Server requirements differentiating from simpler Rmarkdown renderings will be reviewed as well as use of Crosstalk to gain similar functionality with Rmarkdown with simple data.
   Video, Slides, Lesson
   
   
8. August 9: Packages
   An R package is a documented set of functions that can act as building blocks for data ingestion, analysis, visualization and reporting. We’ll go over the basics of creating an R package and documenting functions within.
   Slides, Lesson