R help - Jun 2011 - Reshape:cast; error using "..." in formula expression.

Whenever I use "..." in the formula of the cast function, from the
reshape
package, I get the following error:

Error in `[.data.frame`(data, , variables, drop = FALSE) : 
  undefined columns selected


For example:

data(french_fries) #available in the reshape package
> head(french_fries)
   time treatment subject rep potato buttery grassy rancid painty
61    1         1       3   1    2.9     0.0    0.0    0.0    5.5
25    1         1       3   2   14.0     0.0    0.0    1.1    0.0
62    1         1      10   1   11.0     6.4    0.0    0.0    0.0
26    1         1      10   2    9.9     5.9    2.9    2.2    0.0
63    1         1      15   1    1.2     0.1    0.0    1.1    5.1
27    1         1      15   2    8.8     3.0    3.6    1.5    2.3
>cast(french_fries, ...~ subject)
Using painty as value column.  Use the value argument to cast to override
this choice
Error in `[.data.frame`(data, , variables, drop = FALSE) : 
  undefined columns selected


 

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Hi:

Short answer: use one dot, not three:
> cast(french_fries, . ~ subject)
Using painty as value column.  Use the value argument to cast to
override this choice
Aggregation requires fun.aggregate: length used as default
  value  3 10 15 16 19 31 51 52 63 78 79 86
1 (all) 54 60 60 60 60 54 60 60 60 60 54 54

Long answer:
It's the same as using . in a model formula. The ... construct is used
as a formal argument in a function *definition* to allow passage of
needed arguments in a function call that are not part of the list of
formal arguments. I noticed
> args(cast)
function (data, formula = ... ~ variable, fun.aggregate = NULL,
    ..., margins = FALSE, subset = TRUE, df = FALSE, fill = NULL,
    add.missing = FALSE, value = guess_value(data))

so I can see where you may have gotten confused. Here's an example
using the same data frame where the ... argument comes into play:

# melt the response variables (the sensory attributes) into
# a factor variable for the attributes themselves and a value
# variable for their corresponding values.

ffm <- melt(french_fries, id = c('subject', 'time',
'treatment', 'rep'))
head(ffm)

# Recast the data so that the average score per subject/treatment
score is produced.
# However, there are NAs in the data frame, so we need to pass na.rm = TRUE:

cast(ffm, subject + treatment  ~ variable, value_var = 'value',
        fun.aggregate = 'mean', na.rm = TRUE)

# To average over all subjects, treatments, times and reps,
cast(ffm, . ~ variable, value_var = 'value', fun.aggregate =
'mean',
         na.rm = TRUE)
  value   potato  buttery    grassy  rancid   painty
1 (all) 6.952518 1.823699 0.6641727 3.85223 2.521758

na.rm  is not part of the formal argument list to cast(), but because
the ... construct is present, we can pass na.rm = TRUE to the mean()
function used to aggregate the data in the actual call. Observe that
> args(mean.default)
function (x, trim = 0, na.rm = FALSE, ...)

so the na.rm = TRUE argument in the call to cast() is actually passed to mean().
 [To understand how this works, you need to do some study about
function writing; the R Language Definition manual is one place where
this is described in detail. The formal arguments to mean.default()
are x, trim, na.rm and ...; trim and na.rm have default values 0 and
FALSE than can be overridden in an actual call to that function.]

You should never need to use ... in an actual function call; in a
formula, use of . on one side of ~ means to use all variables in the
data frame except those used on the other side (the side where one or
more  variables are specified). For example, in a linear regression
context,

lm(y ~ ., data = mydata)

would use all variables in mydata except y as covariates in the model.

HTH,
Dennis



On Thu, Jun 9, 2011 at 12:10 AM, misterbray <misterbray at gmail.com>
wrote:
> Whenever I use "..." in the formula of the cast function, from
the reshape
> package, I get the following error:
>
> Error in `[.data.frame`(data, , variables, drop = FALSE) :
> ?undefined columns selected
>
>
> For example:
>
> data(french_fries) #available in the reshape package
>> head(french_fries)
> ? time treatment subject rep potato buttery grassy rancid painty
> 61 ? ?1 ? ? ? ? 1 ? ? ? 3 ? 1 ? ?2.9 ? ? 0.0 ? ?0.0 ? ?0.0 ? ?5.5
> 25 ? ?1 ? ? ? ? 1 ? ? ? 3 ? 2 ? 14.0 ? ? 0.0 ? ?0.0 ? ?1.1 ? ?0.0
> 62 ? ?1 ? ? ? ? 1 ? ? ?10 ? 1 ? 11.0 ? ? 6.4 ? ?0.0 ? ?0.0 ? ?0.0
> 26 ? ?1 ? ? ? ? 1 ? ? ?10 ? 2 ? ?9.9 ? ? 5.9 ? ?2.9 ? ?2.2 ? ?0.0
> 63 ? ?1 ? ? ? ? 1 ? ? ?15 ? 1 ? ?1.2 ? ? 0.1 ? ?0.0 ? ?1.1 ? ?5.1
> 27 ? ?1 ? ? ? ? 1 ? ? ?15 ? 2 ? ?8.8 ? ? 3.0 ? ?3.6 ? ?1.5 ? ?2.3
>
>>cast(french_fries, ...~ subject)
> Using painty as value column. ?Use the value argument to cast to override
> this choice
> Error in `[.data.frame`(data, , variables, drop = FALSE) :
> ?undefined columns selected
>
>
>
>
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> View this message in context:
http://r.789695.n4.nabble.com/Reshape-cast-error-using-in-formula-expression-tp3584721p3584721.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Yes, the basic problem is that you forgot to melt the data before
trying to cast it.

Hadley

On Thursday, June 9, 2011, misterbray <misterbray at gmail.com>
wrote:
> Dennis, doing some more research, and it seems you actually can include the
> ... term directly in the formula: cf. page 8 of
> http://www.had.co.nz/reshape/introduction.pdf (that article also explains
> why you might want to do so). It seems including the ... term only works,
> however, when your value column actually has the name "value"
(e.g. using
> the value="my.val" option yields the error). This was the
"bug" that was
> catching me up yesterday.
>
> Thank you again Dennis,
> Yours,
> Rob
>
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> View this message in context:
http://r.789695.n4.nabble.com/Reshape-cast-error-using-in-formula-expression-tp3584721p3586597.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org?mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/