Lab manual for the Thornton lab at UC Irvine
KT strongly recommends using R
markdown over Jupyter
notebooks.
The main reasons for this recommendation are:
R
and Python
.git
-friendly.RStudio
.As always, there are exceptions to this rule!
KT likes Jupyter
notebooks, and they are the best/only game in town for generating interactive Python
graphics.
R Markdown is a “flavor” of markdown
.
The way most people use R markdown
is within RStudio.
Rstudio
is an “integrated development environment”, or IDE
for the R
programming language.
It differs from “vanilla” markdown
is that you can execute R
code display graphics generated via R
.
With the reticulate package installed, you may also do the same with Python
code.
More info on R markdown
can be found in the section Generating content with R markdown
on the main page.
R markdown
document is plain text, making it git
-friendly.R
and Python
HTML
and PDF
.RStudio
makes a nice “one stop shop” for a project using R
.RStudio
has git
integration!R markdown
format can be the basis of slides, manuscripts, or books.R markdown
used for slides, books, etc., can have subtly different ways of doing specific things.markdown
to the output format from top to bottom.
Thus, it can take some time to reprocess a large document.RStudio
is not straightforward to set up for remote work.Jupyter lab is a browser-based notebook application that supports many different languages, including R
and Python
.
Its language agnosticism means that it is not an IDE
for any language.
Rather, it is a nice application for entering text and code and making reports, slides, etc..
R
and Python
HTML
and PDF
.git
/GitHub
.
There are workarounds for this problem, but they aren’t as good as plain text.