Graham Smith <myotis...@gmail.com> writes:
> Dan
>
> I have started a new thread so it has a propel babel string. I have
> also created a small file for testing.
>
Hi Graham,
> The colnames t works as expected, but how do I then see the variable
> names when using the summary command,
Just use :colnames t again for that.
> and str doesn't work at all
> (source block produced no output) . They appear OK in the R buffer.
OK, so Austin was right about the problem here. Remember that by
default, org-babel works in ':results value' mode -- i.e., it tries to
give you back an org table corresponding to the *value* of the last
expression in your code. But the R function str() simply *prints* out
some information about the object. You can see that it has no useful
value by doing this in the R buffer:
> str.value <- str(babeltest)
'data.frame': 10 obs. of 4 variables:
$ ID : int 1 2 3 4 5 6 7 8 9 10
$ var1: int 34 56 78 34 56 23 45 23 89 46
$ var2: int 1 4 3 5 6 7 5 6 7 4
$ var3: int 400 499 500 600 500 300 200 340 400 450
> str.value
NULL
What you need here is ':results output', which tells org-babel to give
you back whatever printed output there is. You'll need to use :results
output whenever you want to see the printed output from R as opposed to
the value of a data frame/table/vector etc.
I've pasted a working version of your example below.
Dan
>
> Orgmode+babel output below
>
> Graham
>
> #+srcname:babeltest
> #+begin_src R :colnames t
(This needs ':session babeltest' for your example to work, but I expect
that just accidentally got left out of your email)
> babeltest<-read.csv("/home/graham/Dropbox/myotis/Learn/learn/babeltest.csv",header=TRUE)
> #+end_src
-------------------------------------------------------------------------------
#+srcname:babeltest
#+begin_src R :colnames t :session babeltest
babeltest<-read.csv("/tmp/babeltest.csv",header=TRUE)
#+end_src
#+results: babeltest
| "ID" | "var1" | "var2" | "var3" |
|------+--------+--------+--------|
| 1 | 34 | 1 | 400 |
| 2 | 56 | 4 | 499 |
| 3 | 78 | 3 | 500 |
| 4 | 34 | 5 | 600 |
| 5 | 56 | 6 | 500 |
| 6 | 23 | 7 | 300 |
| 7 | 45 | 5 | 200 |
| 8 | 23 | 6 | 340 |
| 9 | 89 | 7 | 400 |
| 10 | 46 | 4 | 450 |
#+begin_src R :session babeltest :colnames t
summary(babeltest)
#+end_src
#+results:
| "ID" | "var1" | "var2" | "var3" |
|-----------------+----------------+---------------+-----------------|
| "Min. : 1.00" | "Min. :23.0" | "Min. :1.0" | "Min. :200.0" |
| "1st Qu.: 3.25" | "1st Qu.:34.0" | "1st Qu.:4.0" | "1st Qu.:355.0" |
| "Median : 5.50" | "Median :45.5" | "Median :5.0" | "Median :425.0" |
| "Mean : 5.50" | "Mean :48.4" | "Mean :4.8" | "Mean :418.9" |
| "3rd Qu.: 7.75" | "3rd Qu.:56.0" | "3rd Qu.:6.0" | "3rd Qu.:499.8" |
| "Max. :10.00" | "Max. :89.0" | "Max. :7.0" | "Max. :600.0" |
#+begin_src R :session babeltest :results output
str(babeltest)
#+end_src
#+results:
: 'data.frame': 10 obs. of 4 variables:
: $ ID : int 1 2 3 4 5 6 7 8 9 10
: $ var1: int 34 56 78 34 56 23 45 23 89 46
: $ var2: int 1 4 3 5 6 7 5 6 7 4
: $ var3: int 400 499 500 600 500 300 200 340 400 450
-------------------------------------------------------------------------------
>
> #+resname: babeltest
> | "ID" | "var1" | "var2" | "var3" |
> |------+--------+--------+--------|
> | 1 | 34 | 1 | 400 |
> | 2 | 56 | 4 | 499 |
> | 3 | 78 | 3 | 500 |
> | 4 | 34 | 5 | 600 |
> | 5 | 56 | 6 | 500 |
> | 6 | 23 | 7 | 300 |
> | 7 | 45 | 5 | 200 |
> | 8 | 23 | 6 | 340 |
> | 9 | 89 | 7 | 400 |
> | 10 | 46 | 4 | 450 |
>
>
>
> #+begin_src R :session babeltest
> summary(babeltest)
> #+end_src
>
> #+resname:
> | "Min. : 1.00" | "Min. :23.0" | "Min. :1.0" | "Min. :200.0" |
> | "1st Qu.: 3.25" | "1st Qu.:34.0" | "1st Qu.:4.0" | "1st Qu.:355.0" |
> | "Median : 5.50" | "Median :45.5" | "Median :5.0" | "Median :425.0" |
> | "Mean : 5.50" | "Mean :48.4" | "Mean :4.8" | "Mean :418.9" |
> | "3rd Qu.: 7.75" | "3rd Qu.:56.0" | "3rd Qu.:6.0" | "3rd Qu.:499.8" |
> | "Max. :10.00" | "Max. :89.0" | "Max. :7.0" | "Max. :600.0" |
>
> #+begin_src R :session babeltest
> str(babeltest)
> #+end_src
>
> #+resname:
>
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