Links to the Lecture 2 Slides and Emacs quick reference guide might be helpful (in other windows!)
This lab was initially done on a Linux system. Modifications might be necessary to make it work under other systems. I will willingly accept corrections and additions which will make it work, but short of being asked to give a similar course again, do not have time to make it work on different platforms. The necessary files, Sweave-Example.Rnw, SweaveMakefile, and Sweave.sh are available. Note that Sweave.sh is a shell script which needs to be made executable.
Note that you need to have ESS and R installed to do this lab.
Commands to type are generally in parens, i.e. (type this) means to
type "type this", not "(type this)")!
1. Using PUTTY or a similar Windows SSH shell, log in
to ?? or Lannerfalk.kubism.ku.dk
2. Change into the Lab2 directory (cd Lab2)
3. First example: try starting an R session using
emacs -f R
4. Now, we are going to load in the first example Sweave file,
(C-x C-f Sweave-Example.Rnw)
5. However, it isn't going to be in the right mode by default, so we
need to get it there:
(M-x noweb-mode)
(M-x noweb-set-code-mode R-mode)
6. Look at the file, change the author to you, and evaluate it
(M-x compile {ret} make -k -f SweaveMakefile)
You will have to add the "-f SweaveMakefile" to the compile
command!
7. To view the results, you will have to make a WWW directory;
(mkdir ~/public_html)
and copy the files you'd like to view (the final PDF file!) there
(cp Sweave-Example.pdf ~/public_html)
Now you can use your local WWW browser to display:
http://www.biostat.ku.dk/~bsguest1/Sweave-Example.pdf
but you might need to change bsguest1 to the account that you are
using!
8. Now, move the cursor into the Sweave-Example.Rnw
file. You might need to use (C-x b) to switch back to it.
9. We will now step through the R code to evaluate it. That should
be possible within the noweb code chunks; you might get prompted
as to the process to use when changing the code chunks. Step
through them using (C-c C-n) (which will only work if the file is
in the right (ESS[R]) mode. Always check modes, if there is a
problem, let Tony know -- Emacs sometimes gets confused).
It might be hard for the plots, but the text output should
respond.
8. If you have gotten to this point, talk with Tony about the options
for finishing off this Lab (I'm not sure how long this will take).
There are three other templates to look at:
EuroVac.Rnw, HVTNScenarios.Rnw, esApply.Rnw
(and corresponding makefiles exist, as well).
9. The last part of the exercise is to use the code in Part 1 (the
ToothGrowth data, with a linear models fit) and the
Sweave-Example.Rnw template to create a new data analysis.
10. (C-x C-r ../Lab1/Lab1-2.R) to open the old R file read-only.
11. Cut-and-Paste is done via C-{space} to set mark, moving the
cursor, and C-w to cut, ESC-w to copy, and C-y to paste.
12. (C-x C-f Lab2.Rnw ) to load in an empty buffer
13. (C-x i Sweave-Example.Rnw ) to insert the Sweave Example into
the Lab2.Rnw buffer (and save, C-x C-s)
14. Produce a quick data analysis report, using the old file. Add a
bit of text to make it "real".
15. (C-x C-f Makefile ) to open up the makefile
16. Insert SweaveMakefile into it. Edit the line (SOURCE=) to be
SOURCE=Lab2
17. Save the buffer
18. Now, you should be able to (M-x compile) the Lab2 Sweave report.
19. if it works, cp Lab2.pdf ~/public_html/
20. View by going to the URL:
http://www.biostat.ku.dk/~bsguest1/Lab2.pdf
(replacing bsguest1 with your account (2,3,4) if needed).
9. See you Friday morning!
10. The End.