Wrong results from R source block when returning a list

Wrong results from R source block when returning a list

[Rainer M Krug]

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Hi

The following code block returns a wrong table / list:


#+begin_src R :results value list
list(1:10, 1:5)
#+end_src

#+RESULTS:
- (1 1)
- (2 2)
- (3 3)
- (4 4)
- (5 5)
- (6 1)
- (7 2)
- (8 3)
- (9 4)
- (10 5)

The result is actually in R:

#+begin_src R :results output
list(1:10, 1:5)
#+end_src

#+RESULTS:
: [[1]]
:  [1]  1  2  3  4  5  6  7  8  9 10
: 
: [[2]]
: [1] 1 2 3 4 5

This is likely caused by the recycling rules in R, but it is actually
wrong in the org context:

The shown result is:

#+begin_src R :results table
list(1:10, 1:5)
#+end_src

#+RESULTS:
|  1 | 1 |
|  2 | 2 |
|  3 | 3 |
|  4 | 4 |
|  5 | 5 |
|  6 | 1 |
|  7 | 2 |
|  8 | 3 |
|  9 | 4 |
| 10 | 5 |


Whil;e I would expect:

#+RESULTS:
|  1 | 1 |
|  2 | 2 |
|  3 | 3 |
|  4 | 4 |
|  5 | 5 |
|  6 |   |
|  7 |   |
|  8 |   |
|  9 |   |
| 10 |   |

I have no idea if this is a bug or wrong result due to incompatible
types (R list and org table)?

Is this mentioned in the manual?

Rainer

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug

PGP: 0x0F52F982

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Re: Wrong results from R source block when returning a list

[Charles C. Berry]

On Tue, 3 Nov 2015, Rainer M Krug wrote:

> Hi
>
> The following code block returns a wrong table / list:
>
>
> #+begin_src R :results value list
> list(1:10, 1:5)
> #+end_src
>
> #+RESULTS:
> - (1 1)
> - (2 2)
> - (3 3)
> - (4 4)
> - (5 5)
> - (6 1)
> - (7 2)
> - (8 3)
> - (9 4)
> - (10 5)
>
> The result is actually in R:


In particular in `org-babel-R-write-object-command' which uses 
write.table() which uses as.data.frame() which dispatches to 
as.data.frame.list() which calls data.frame() where the recycling occurs.

[snip]

> I have no idea if this is a bug or wrong result due to incompatible
> types (R list and org table)?

If you can't coerce a non-atomic R object to a data.frame and get a 
pleasing result, you need to craft your own solution.

>
> Is this mentioned in the manual?

Not that I know of. A comment in `Results Types' in ob-doc-R -

http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html#orgheadline6

- might be helpful.

Chuck

Re: Wrong results from R source block when returning a list

[Rainer M Krug]

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"Charles C. Berry" <ccberry@ucsd.edu> writes:

> On Tue, 3 Nov 2015, Rainer M Krug wrote:
>
>> Hi
>>
>> The following code block returns a wrong table / list:
>>
>>
>> #+begin_src R :results value list
>> list(1:10, 1:5)
>> #+end_src
>>
>> #+RESULTS:
>> - (1 1)
>> - (2 2)
>> - (3 3)
>> - (4 4)
>> - (5 5)
>> - (6 1)
>> - (7 2)
>> - (8 3)
>> - (9 4)
>> - (10 5)
>>
>> The result is actually in R:
>
>
> In particular in `org-babel-R-write-object-command' which uses
> write.table() which uses as.data.frame() which dispatches to
> as.data.frame.list() which calls data.frame() where the recycling
> occurs.

Thanks for this info - I thought something along these lines, but this
makes it clear why.

>
> [snip]
>
>> I have no idea if this is a bug or wrong result due to incompatible
>> types (R list and org table)?
>
> If you can't coerce a non-atomic R object to a data.frame and get a
> pleasing result, you need to craft your own solution.

Yup - I did it in R

>
>>
>> Is this mentioned in the manual?
>
> Not that I know of. A comment in `Results Types' in ob-doc-R -
>
> http://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html#orgheadline6
>
> - might be helpful.

Yes - thanks,

Rainer

>
> Chuck

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug

PGP: 0x0F52F982

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