Re: [O] Babel: communicating irregular data to R source-code block

[Michael Hannon]

Greetings.  I'm sorry to belabor this, but I thought I had found a relatively
clean way to pass a "ragged" table to an R source-code block.  Simple answer:
add the "fill=TRUE" option to the read.table function.  Please see the
appended for the log of an R session that does what I want.

I then tried to do the same thing in an R source-code block:

    #+RESULTS: pascals_triangle
    | 1 |   |    |    |   |   |
    | 1 | 1 |    |    |   |   |
    | 1 | 2 |  1 |    |   |   |
    | 1 | 3 |  3 |  1 |   |   |
    | 1 | 4 |  6 |  4 | 1 |   |
    | 1 | 5 | 10 | 10 | 5 | 1 |
    
    
    #+NAME: sanity-check(sc_input=pascals_triangle)
    #+BEGIN_SRC R
    
    pt <- read.table(sc_input, fill=TRUE)
    rowSums(pt)
    
    #+END_SRC  

Unfortunately, this still results in the "error" that the first line did not
contain five elements:

<<<<<<<<<<
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
> : 
  line 1 did not have 5 elements

Enter a frame number, or 0 to exit   

1: read.table("/tmp/babel-3780tje/R-import-37801if", header = FALSE, row.names
= NULL, sep = "
2: scan(file = file, what = what, sep = sep, quote = quote, dec = dec, nmax =
nrows, skip = 0,
>>>>>>>>>>

I.e.,it seems that Org is going to do its own "read.table" before even
looking at the code in the source block.

Is there some way to get Org to use the "fill=TRUE" option on a case-by-case
basis?

Thanks.

-- Mike


Appendix: R code that correctly reads and processes a Pascal's triangle
=======================================================================


> system("cat pascal.dat")
1
1 1
1 2 1
1 3 3 1
1 4 6 4 1
> 
> x <- read.table("pascal.dat", fill=TRUE)
> 
> x
  V1 V2 V3 V4 V5
1  1 NA NA NA NA
2  1  1 NA NA NA
3  1  2  1 NA NA
4  1  3  3  1 NA
5  1  4  6  4  1
> 
> y <- as.matrix(x)
> 
> y
     V1 V2 V3 V4 V5
[1,]  1 NA NA NA NA
[2,]  1  1 NA NA NA
[3,]  1  2  1 NA NA
[4,]  1  3  3  1 NA
[5,]  1  4  6  4  1
> 
> y[is.na(y)] <- 0
> 
> y
     V1 V2 V3 V4 V5
[1,]  1  0  0  0  0
[2,]  1  1  0  0  0
[3,]  1  2  1  0  0
[4,]  1  3  3  1  0
[5,]  1  4  6  4  1
> 
> dimnames(y)[[2]]=NULL  #### cosmetic change
> 
> y
     [,1] [,2] [,3] [,4] [,5]
[1,]    1    0    0    0    0
[2,]    1    1    0    0    0
[3,]    1    2    1    0    0
[4,]    1    3    3    1    0
[5,]    1    4    6    4    1
>