From: Rainer M Krug <Rainer@krugs.de>
To: "Charles C. Berry" <ccberry@ucsd.edu>
Cc: emacs-orgmode@gnu.org, Eric Schulte <schulte.eric@gmail.com>
Subject: Re: [PATCH] -for review- Tangling with variable transfer of variables
Date: Tue, 24 Jun 2014 14:08:36 +0200 [thread overview]
Message-ID: <m21tueldbv.fsf@krugs.de> (raw)
In-Reply-To: <alpine.OSX.2.00.1406231020550.341@charles-berrys-macbook.local> (Charles C. Berry's message of "Mon, 23 Jun 2014 10:56:05 -0700")
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"Charles C. Berry" <ccberry@ucsd.edu> writes:
> On Mon, 23 Jun 2014, Rainer M Krug wrote:
>
>> One more question concerning the variable transfer of tables:
>>
>> ,----
>> | (let ((file (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
>> | (header (if (or (eq (nth 1 value) 'hline) colnames-p)
>> | "TRUE" "FALSE"))
>> | (row-names (if rownames-p "1" "NULL")))
>> | (if (= max min)
>> | (format "%s <- local({
>> | con <- textConnection(
>> | %S
>> | )
>> | res <- read.table(
>> | con,
>> | header = %s,
>> | row.names = %s,
>> | sep = \"\\t\",
>> | as.is = TRUE
>> | )
>> | close(con)
>> | res
>> | })" name file header row-names)
>> | (format "%s <- local({
>> | con <- textConnection(
>> | %S
>> | )
>> | res <- read.table(
>> | con,
>> | header = %s,
>> | row.names = %s,
>> | sep = \"\\t\",
>> | as.is = TRUE,
>> | fill = TRUE,
>> | col.names = paste(\"V\", seq_len(%d), sep =\"\")
>> | )
>> | close(con)
>> | res
>> | })" name file header row-names max))))
>> `----
>>
>> It seems that the two variable transfer routines only differ slightly:
>>
>> 1. routine: =header= is present (TRUE) and defined in table when passed
>> as =colnames= while
>>
>> 2. routine: =header= is not present (FALSE) and =colnames= is generated
>> as V1 .. Vn
>>
>> This generation is actually not needed as this is the R default value
>> which is used when =colnames= is not supplied.
>>
>> Also: I do not undestand why the argument =fill= is TRUE in the second
>> routine. From R:
>>
>> ,----
>> | fill: logical. If ‘TRUE’ then in case the rows have unequal length,
>> | blank fields are implicitly added. See ‘Details’.
>> `----
>>
>> If I understands tables in org correctly, this is not needed as the rows
>> always have equal length?
>>
>> so if I am not mistaken the following lines could be deleted:
>>
>> ,----
>> | row.names = %s,
>> | sep = \"\\t\",
>> | as.is = TRUE,
>> | - fill = TRUE,
>> | - col.names = paste(\"V\", seq_len(%d), sep =\"\")
>> `----
>>
>> Or am I missing something here?
>
> You need not pass a table - this
>
> #+BEGIN_SRC R :var x='(1 2 3)(4 5))
I always forget that there are other objects wich can be passed from org
to R.
>
> will produce a data.frame with two rows with is.na(x[2,2]) being TRUE.
>
>
> Re col.names, from help("read.table")
>
> The number of data columns is determined by looking at the first
> five lines of input (or the whole file if it has less than five
> lines), or from the length of 'col.names' if it is specified and
> is longer. This could conceivably be wrong if 'fill' or
> 'blank.lines.skip' are true, so specify 'col.names' if necessary
> (as in the 'Examples').
>
>
> This block
>
> #+BEGIN_SRC R :var x=(append (make-vector 10 '(1 2)) '((1 2 3)))
> x
> #+END_SRC
>
> makes an 11 by 3 data.frame with all(is.na(x[,1:10]))
>
> but taking away the col.names arg will cause it to make a 12 by 2
> data.frame with x[12,1]==3 and is.na(x[12,2]).
>
> so leave the col.names as is, I think.
I will - promised.
>
> Without fill, read.table will throw an error in that block
This is true for these cases - I was only thinking about tables which
can be passed to R
Thanks,
Rainer
>
> Chuck
>
> [rest deleted]
>
--
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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next prev parent reply other threads:[~2014-06-24 12:08 UTC|newest]
Thread overview: 16+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-06-19 20:19 [PATCH] -for review- Tangling with variable transfer of variables Rainer M Krug
2014-06-19 21:09 ` Aaron Ecay
2014-06-19 23:23 ` Charles Berry
2014-06-20 13:15 ` Rainer M Krug
2014-06-20 20:34 ` Rainer M Krug
2014-06-21 19:44 ` Charles C. Berry
2014-06-22 3:39 ` Aaron Ecay
2014-06-23 10:46 ` Rainer M Krug
2014-06-23 8:57 ` Rainer M Krug
2014-06-23 9:14 ` Rainer M Krug
2014-06-23 17:56 ` Charles C. Berry
2014-06-24 12:08 ` Rainer M Krug [this message]
2014-06-23 10:45 ` Rainer M Krug
2014-06-23 18:25 ` Charles C. Berry
2014-06-24 12:28 ` Rainer M Krug
2014-06-20 13:07 ` Rainer M Krug
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