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Building the book on your local machine (optional)

To build the book using Rstudio:

  • Make sure you have the most recent version of R and R Studio
    • Check that pandoc is installed and functioning on your machine (library(rmarkdown); pandoc_available() should return TRUE)
  • Start a new project in R Studio using version control
  • Fork or clone the GitHub repository from this url: https://github.com/ioos/bio_data_guide.git
  • Install all the required packages: specifically bookdown and others as required
  • In the Build tab, click 'Build Book' or in the console run rmarkdown::render_site(encoding = 'UTF-8')
  • Commit and push changes to all modified files using the git pane in R Studio

To build the book using R Console:

install.packages(c("librarian", "rgdal", "rmarkdown", "vroom", "xfun", "tinytex"), type = "binary");
librarian::shelf(bookdown, dm, here, lubridate, , rmarkdown, tidyverse, worms);
remotes::install_github("iobis/obistools", upgrade="never");
tinytex::install_tinytex()
  • To build the book:
setwd("bio-data-guide/")
options(knitr.duplicate.label = "allow")
bookdown::render_book("index.Rmd")
  • OR, make a PDF of the book:
options(knitr.duplicate.label = "allow")
bookdown::render_book("index.Rmd", "bookdown::pdf_book")
  • The markdown and pdf will be saved in the local bio-data-guide/docs directory.

Building and publishing the book through GitHub on your fork

  • Create a fork of this repo under your ownership
  • create an empty gh-pages branch in your fork (see here).
  • Host GitHub Pages
    • In your GitHub repository, go to Settings -> Pages
    • Select the gh-pages branch and the /(root) directory.
    • Select Save
  • You need to make a change (any change) to the repository to initiate the GitHub Action to build the website in the gh-pages branch.
    • Make a minor edit to one of the markdown files in bio-data-guide.
    • When you commit the change the GitHub action will build the webpage.
    • Once the GitHub action finishes, you should be able to view the document at [username].github.io/bio_data_guide
      • [username] is your GitHub username.