Re: [Orgmode] [Babel] - importing a data file- missing header row

[Thomas S. Dye]

Hi Graham,

On Dec 8, 2009, at 6:41 AM, Graham Smith wrote:

I need a bit of help importing a data file into orgmode/babel.

The import doesn't seem to know about having a header row

#+srcname:woodland
#+begin_src R
read.table("/home/graham/Dropbox/College/BY4001/WoodlandData/BY4001WoodlandDataFinal.txt",header=TRUE)
#+end_src

#+resname: woodland
| "V1.1"  | "v" | 0 | 0 | 0 |  0 | 0 |  0 |  0 |  0 |  0 |  0 |  0 |
0 |  0 |  0 | 0 |  0 | 0 |  0 |  0 |  0 |  0 | 0 |  0 | 0 | 0 |  0 |
0 |  0 | 0 |  0 |  5 |  0 |  0 | 10 |  0 | 0 |  0 | 100 |  0 |  3 | B


But strangely if I change the command and run the names(woodland)
after the import, I get a table of variable names but no data. I'm not
sure if the data is there but hidden as I can't get any commands to
work on the woodland object.

* Woodland Data
#+srcname:woodland
#+begin_src R
woodland<-read.table("/home/graham/Dropbox/College/BY4001/WoodlandData/BY4001WoodlandDataFinal.txt",header=TRUE)
names(woodland)
#+end_src

#+resname: woodland
| "ID"           |
| "wood"         |
| "Ajug.Rept"    |
| "Ange.sylv"    |
| "Brac.sylv"    |
| "Brom.ramo"    |
| "Care.pend"    |
| "Care.remo"    |
| "Care.sylv"    |
| "Cirs.palu"    |
| "Cory.avel"    |
| "Desc.caes"    |
| "Dryo.fili"    |
| "Endy.non"     |
| "Euph.amyg"    |

So it seems I already need some more help.

Graham

One solution would be to use a :session.  Variables created in R will persist in the session and can be shared by source code blocks assigned to the :session.

I don't have access to your data, but the following source code blocks should work for you.  I've chosen to name the session 'woodland' but you can name it whatever you'd like, or not name it and use the default session.

* Woodland Data

- Create a variable woodland and populate it with BY4001WoodlandDataFinal.txt

#+srcname:woodland
#+begin_src R :session woodland
woodland<-read.table("/home/graham/Dropbox/College/BY4001/WoodlandData/BY4001WoodlandDataFinal.txt",header=TRUE)
#+end_src

- Run some summary commands to see if the woodland variable looks right

#+begin_src R :session woodland

names(woodland)

str(woodland)

summary(woodland)

#+end_src

- Show the woodland data

#+begin_src R :session woodland

woodland

#+end_src

I like this approach because I don't have to save a bunch of R objects when I'm done.  I just re-create them when I need them again, because the R code that I've already tested is saved with my org file.

HTH,

Tom