R for Data Analysis & Visualization in Science
This is the repository for website used to teach the quarter-long graduate seminar course, R-DAVIS. Course content integrates and builds on Data Carpentry Ecology lessons, and is taught as part of the curriculum for students in the Graduate Group in Ecology at the University of California, Davis, USA.
Because much of the varied content found in the lessons, there are a number of package dependencies to be aware of. This list may not be complete, but before building the site locally, these packages should be installed:
c("tidyverse", "ggplot2", "tidyr", "readr", "dplyr", "purrr", "emojifont","BrailleR","sonify","seewave", "viridis", "mapdata", "maps", "mapview", "measurements", "gapminder", "broom", "gutenbergr", "tidytext", "patchwork", "cowplot", "hexbin", "geosphere", "ggmap", "ggthemes", "magrittr", "leaflet", "plotly", "knitr", "rio")
To get an updated list of packages for the website, navigate to the repo on the command line, then try one of these commands:
grep -horE 'library\(.*?\)' . | sed 's/library//g; s/[()]//g; s/"//g' | sed "s/\'//g" | grep -Eo '^\w+' | sort | uniq
or
grep -horE 'library\(.*?\)' . | sed 's/library//g; s/[()]//g; s/"//g' | grep -Eo '^\w+' | sort | uniq
The course website can be rebuilt locally by using the "Build" tab in RStudio. Assuming the above packages are installed on your machine:
- Open the R-DAVIS project in RStudio. Click on the
Buildtab, and "More", select "Clean All". - Then select
Build Website. This process make take a few minutes.
You can also clean and build the website from the command line by navigating to the repo and running R -e 'rmarkdown::clean_site()' or R -e 'rmarkdown::render_site()'.
If you only need to rebuild one lesson or one page, you can run rmarkdown::render_site(input = "path_to_page_from_project_directory").
See the Releases tab in this repo to find the completed version for a given year. We expect further development of the website for future iterations as the course improves in the future.