These informations were gathered and first demonstrated in my [[https://github.com/alegrand/RR_webinars/blob/master/1_replicable_article_laboratory_notebook/index.org][First
webinar on reproducible research: litterate programming]].
***** Emacs shortcuts
Here are a few convenient emacs shortcuts for those that have never
used emacs. In all of the emacs shortcuts, =C=Ctrl=, =M=Alt/Esc= and
=S=Shift=. Note that you may want to use two hours to follow the emacs
tutorial (=C-h t=). In the configuration file CUA keys have been
activated and allow you to use classical copy/paste (=C-c/C-v=)
shortcuts. This can be changed from the Options menu.
- =C-x C-c= exit
- =C-x C-s= save buffer
- =C-g= panic mode ;) type this whenever you want to exit an awful
series of shortcuts
- =C-Space= start selection marker although selection with shift and
arrows should work as well
- =C-l= reposition the screen
- =C-_= (or =C-z= if CUA keys have been activated)
- =C-s= search
- =M-%= replace
- =C-x C-h= get the list of emacs shortcuts
- =C-c C-h= get the list of emacs shortcuts considering the mode you are
currently using (e.g., C, Lisp, org, ...)
There are a bunch of cheatsheets also available out there (e.g.,
[[http://www.shortcutworld.com/en/linux/Emacs_23.2.1.html][this one for emacs]] and [[http://orgmode.org/orgcard.txt][this one for org-mode]] or this [[http://sachachua.com/blog/wp-content/uploads/2013/05/How-to-Learn-Emacs-v2-Large.png][graphical one]]).
***** Org-mode
Many emacs shortcuts start by =C-x=. Org-mode's shortcuts generaly
start with =C-c=.
- =Tab= fold/unfold
- =C-c c= capture (finish capturing with =C-c C-c=, this is explained on
the top of the buffer that just opened)
- =C-c C-c= do something useful here (tag, execute, ...)
- =C-c C-o= open link
- =C-c C-t= switch todo
- =C-c C-e= export
- =M-Enter= new item/section
- =C-c a= agenda (try the =L= option)
- =C-c C-a= attach files
- =C-c C-d= set a deadl1ine (use =S-arrows= to navigate in the dates)
- =A-arrows= move subtree (add shift for the whole subtree)
***** Org-mode Babel (for literate programming)
- =<s + tab= template for source bloc. You can easily adapt it to get
this:
#+BEGIN_EXAMPLE
#+begin_src shell
ls
#+end_src
#+END_EXAMPLE
Now if you =C-c C-c=, it will execute the block.
#+BEGIN_EXAMPLE
#+RESULTS:
| #journal.org# |
| journal.html |
| journal.org |
| journal.org~ |
#+END_EXAMPLE
- Source blocks have many options (formatting, arguments, names,
sessions,...), which is why I have my own shortcuts =<b + tab= bash
block (or =B= for sessions).
#+BEGIN_EXAMPLE
#+begin_src shell :results output :exports both
ls /tmp/*201*.pdf
#+end_src
#+RESULTS:
: /tmp/2015_02_bordeaux_otl_tutorial.pdf
: /tmp/2015-ASPLOS.pdf
: /tmp/2015-Europar-Threadmap.pdf
: /tmp/europar2016-1.pdf
: /tmp/europar2016.pdf
: /tmp/M2-PDES-planning-examens-janvier2016.pdf
#+END_EXAMPLE
- I have defined many such templates in my configuration. You can
give a try to =<r=, =<R=, =<RR=, =<g=, =<p=, =<P=, =<m= ...
- Some of these templates are not specific to babel: e.g., =<h=, =<l=,
- [[#rstudio-and-gitgithubgitlab][Rstudio and git/github/gitlab]]
- [[#cheat-sheets][Cheat Sheets]]
* Installing Rstudio
** Linux (debian, ubuntu)
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
for other distributions (e.g.n redhat, fedora).
Today, the stable versions of the most common distributions provide
recent enough versions of emacs and org-mode:
- Debian (stretch) ships with [[https://packages.debian.org/stretch/r-base][R 3.3.3-1]], [[https://packages.debian.org/stretch/r-cran-knitr][knitr 1.15.1]], and [[https://packages.debian.org/stretch/r-cran-ggplot2][ggplot 2.2.1]]
- Ubuntu (bionic 18.04) ships with [[https://packages.ubuntu.com/bionic/r-base][R 3.4.4]], and [[https://packages.ubuntu.com/bionic/r-cran-knitr][knitr 1.17]], and [[https://packages.ubuntu.com/bionic/r-cran-ggplot2][ggplot 2.2.1]]
- Ubuntu (artful 17.04) ships with [[https://packages.ubuntu.com/artful/r-base][R 3.4.2]], and [[https://packages.ubuntu.com/artful/r-cran-knitr][knitr 1.15]], and [[https://packages.ubuntu.com/artful/r-cran-ggplot2][ggplot 2.2.1]]
If your distribution is older than this, well, it may be a good time
for upgrading...
*** Installing R
Beforehand, you need to install the R language and convenient packages
Some instructions on installing R and knitr must be missing. This
should be tested and improved.
#+END_QUOTE
Download and install rstudio from the [[https://www.rstudio.com/products/rstudio/download/#download][Rstudio webpage]] by choosing the
right operating system.
Then open Rstudio and type the following commands in the console to
install knitr and ggplot2:
#+BEGIN_SRC R
install.packages("knitr")
install.packages("ggplot2")
#+END_SRC
* Installing Git
** Linux (debian, ubuntu)
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
for other distributions (e.g.n redhat, fedora).
Run (as root):
#+begin_src sh :results output :exports both
apt-get update ; apt-get install git
#+end_src
** Mac OSX and Windows
- Download and install Git from the [[https://git-scm.com/downloads][Git website]].
- Optional Git clients (should not be needed if you work within
Rstudio):
- [[https://www.sourcetreeapp.com/][SourceTree]]
- [[github desktop][GitHub Desktop]]
#+BEGIN_QUOTE
[[https://github.com/desktop/desktop/issues/852][Apparently]], this works with gitlab and https.
#+END_QUOTE
* Rstudio and git/github/gitlab
#+BEGIN_QUOTE
We may want to redo a screencast in French for this
#+END_QUOTE
- [[https://www.rstudio.com/resources/webinars/rstudio-essentials-webinar-series-managing-part-2/][This video on using git/githugb/gitlab from Rstudio]] (starting at time 9:09)
