* Re: [babel] Babel - importing a data file- missing header row
2009-12-08 16:41 Babel - importing a data file- missing header row Graham Smith
@ 2009-12-08 17:46 ` Dan Davison
2009-12-08 18:08 ` Graham Smith
0 siblings, 1 reply; 3+ messages in thread
From: Dan Davison @ 2009-12-08 17:46 UTC (permalink / raw)
To: Graham Smith; +Cc: emacs-orgmode
Graham Smith <myotisone@gmail.com> writes:
> 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
>
Hi Graham,
Could you post the first few lines of your data file, or a small example
with the same format, as I don't completely understand the output you
are getting.
But try using the ':colnames t' header argument. For example, if I have
this data file (space-separated, header line has same num entries as
data rows).
-----------------------------
ID wood A.reptans E.amygdaloides
a wood1 5 10
b wood2 1 0
-----------------------------
Then I get
#+srcname:woodland
#+begin_src R
read.table("/tmp/woodlands.txt",header=TRUE)
#+end_src
#+results: woodland
| "a" | "wood1" | 5 | 10 |
| "b" | "wood2" | 1 | 0 |
And if I use the colnames header argument I get
#+srcname:woodland
#+begin_src R :colnames t
read.table("/tmp/woodlands.txt",header=TRUE)
#+end_src
#+results: woodland
| "ID" | "wood" | "A.reptans" | "E.amygdaloides" |
|------+---------+-------------+------------------|
| "a" | "wood1" | 5 | 10 |
| "b" | "wood2" | 1 | 0 |
Also, I recommend working with the :session header argument. Then after
you evaluate an org-babel block, you can go to the ESS session and
examine the R objects it has created. You'd need to save the data frame
to a variable of course, so something like this
#+srcname:woodland
#+begin_src R :colnames t :session
woodlands <- read.table("/tmp/woodlands.txt",header=TRUE)
woodlands
#+end_src
Now if I switch to the *R* buffer, I can see what it has done:
First you'll see some lines like this; these reflect what org-babel did
-----------------------------------------------------------------------------------------------------------
>
woodlands <- read.table("/tmp/woodlands.txt",header=TRUE)
write.table(.Last.value, file="/tmp/org-babel-R6645iE0", sep="\t", na="nil",row.names=FALSE, col.names=TRUE, quote=FALSE)
'org_babel_R_eoe'
> woodlands <- read.table("/tmp/woodlands.txt",header=TRUE)
> write.table(.Last.value, file="/tmp/org-babel-R6645iE0", sep="\t", na="nil",row.names=FALSE, col.names=TRUE, quote=FALSE)
> 'org_babel_R_eoe'
[1] "org_babel_R_eoe"
-----------------------------------------------------------------------------------------------------------\
Ignore the org_babel_R_eoe stuff, that's to do with org-babel internals.
Now you can check that your variable looks sensible:
-----------------------------------------------------------------------------------------------------------\
> woodlands
ID wood A.reptans E.amygdaloides
1 a wood1 5 10
2 b wood2 1 0
>
-----------------------------------------------------------------------------------------------------------\
Dan
p.s. Please include the string "[babel]" in the subject line!
> #+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
>
>
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