Index

0.1 Things to add

Signe recommended students run a live tutorial in swirl

0.2 Documentation for Author

0.3 Andrew’s Resources

These resources are not relevant for students but they are to me.

0.3.1 Styling your docx template

0.4 Andrew’s Notes / Ramblings

  • It might be easier to consider making this a website. There’s a really nice example using Hugo which would allow me to embed presentations. I’m not sure how I feel about it. I really like Google Slides because they are so easy to create but it might be a way to embed YouTube videos along with presentations and learnR modules all in one place. I have it forked on my GitHub

To render the book used the following code, you must do this before knitting the GitBook (webpage)

bookdown::render_book("index.Rmd", "bookdown::gitbook")
bookdown::render_book("index.Rmd", "bookdown::pdf_book", encoding="UTF-8")
bookdown::render_book("index.Rmd", "bookdown::epub_book")

# after previewing the book 
#Which is done by running these lines

bookdown::serve_book()

# To stop the process run (or you can restart your session)
servr::daemon_stop("981593464")

The _output.yml contains the header arguments. I would but them here so its cleaner and easier to read the code.

0.5 To Do

  • Is there a way I can have matlab code syntax highlighted properly? Maybe here

  • Make a logo

  • Get Camera to take nice pictures

  • Create example datasets that I can run through

  • Can I export this to github.io? The GitHub Repository for this guidebook can be found here

  • Add highlight arg to _output.yml

  • There should be a section on general access to your df. How to manipulate it effectively (perhaps in the data wrangling section) This would include things like using df$colname to access a column

  • Implement Open Review which will allow people to make comments. An example can be seen here

  • Finish my changes

  • Push my commits to GitHub

  • Open a pull request

  • Cleaned the main directory to make it easier to interpret for beginners

  • Look into adding content from both the Workshop and Data Battles there is useful slides in both. In DataBattles I show a breakdown of functions which might be useful for new users.

  • I also have content from a mixed model workshop I hosted (the one Ashley asked me to run)

For Chapter 5

  • steal logo from here. It would be great to have a logo here that was cowboy themed
  • These animations would be great at explaining some key concepts

0.6 Title word cloud

Titles: inquiry-based R for researchers in a hurry Reproducible science. Reproducible science for the busy researcher.

0.7 Copy from Chapter 1 Example

You can label chapter and section titles using {#label} after them, e.g., we can reference Chapter \@ref(intro). If you do not manually label them, there will be automatic labels anyway, e.g., Chapter \@ref(methods).

Figures and tables with captions will be placed in figure and table environments, respectively.

par(mar = c(4, 4, .1, .1))
plot(pressure, type = 'b', pch = 19)

Reference a figure by its code chunk label with the fig: prefix, e.g., see Figure \@ref(fig:nice-fig). Similarly, you can reference tables generated from knitr::kable(), e.g., see Table \@ref(tab:nice-tab).

knitr::kable(
  head(iris, 20), caption = 'Here is a nice table!',
  booktabs = TRUE
)

You can write citations, too. For example, we are using the bookdown package in this sample book, which was built on top of R Markdown and knitr .

0.8 MATLAB Highlighting

% This is a comment in MATLAB
function y = average(x)
if ~isvector(x)
   error('Input must be a vector')
end
y = sum(x)/length(x); 
end

So could this

0.9 CSS / Templates

https://bookdown.org/yihui/bookdown/templates.html https://rstudio4edu.github.io/rstudio4edu-book/book-dress.html github.com/hebrewseniorlife/bookdownThemeEditor

In the terminal I ran

git config –global user.name ‘alapo’ git config –global user.email ‘

git config –global user.name ‘Jane Doe’ git config –global user.email ‘

0.10 Teaching RStudio

learnr guide

I created this course to work backwards from traditional methods.

Students will learn the basics of RMarkdown first and then learn how to insert chunks within it. I do this for a few reasons

  1. They are able to see the end result immediately
  2. Most students are going to be using another program while taking this course, so its a start
  3. We can use static images and datasets to insert figures and tables into our RMarkdown document

0.11 Misc code/data

gitbook(fig_caption = TRUE, number_sections = TRUE, self_contained = FALSE, 
   lib_dir = "libs", pandoc_args = NULL, ..., template = "default", 
   split_by = c("chapter", "chapter+number", "section", "section+number", 
       "rmd", "none"), split_bib = TRUE, config = list(), table_css = TRUE)

0.12 Other Resources

Book called Just Enough R

An example on how to use GitHub with student projects. Really nice breakdown that is worth a read.

Allison Horst on Twitter has some amazing images that I may want to use

This is a course outline similar to what I want