Gents:
I would add that:
1) attach() should probably no longer be used in R, for all the
reasons (and more) cited,
2) The preferred alternative these days is to use lists, including
data frames, as containers and make liberal use of the ?with and
?within functions. Environments can also be useful, but are more
complicated as their semantics differ. S4 classes and objects are
probably also relevant.
Comments, criticisms, links, additions, and subtractions welcome, as
this issue comes up regularly here and it would be nice to have
consensus wisdom to refer to.
Cheers,
Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374
"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
H. Gilbert Welch
On Tue, Dec 31, 2013 at 2:14 AM, Berwin A Turlach
<berwin.turl...@gmail.com> wrote:
> G'day David,
>
> On Mon, 30 Dec 2013 20:42:53 -0500
> David Parkhurst <parkh...@indiana.edu> wrote:
>
> Some wild guesses in the absence of a reproducible example.
>
>> I have several variables in a data frame that aren't listed by ls()
>> after I attach that data frame.
>
> ls() list the objects in the global environment. If you attach a data
> frame it is attached to the search path, typically after the global
> environment.
>
> Type 'search()' to see your search path.
>
> ls() list the global environment, the first entry in the list and
> called ".GlobalEnv". Your data frame should be listed as an object in
> that environment.
>
> Assuming the name of your data frame is 'foo', then there should be the
> name 'foo' somewhere in the list of names returned by 'search()'.
> Assuming 'foo' is listed in the second position, then 'ls(2)' should
> list all the objects found at that location of the search path, i.e.
> all the variables in your data frame.
>
>> Where did they go,
>
> See above.
>
>> and how can I stop the hidden ones from masking the local ones?
>
> Do you mean with "local ones" those in the global environment and by
> "hidden ones" those that you couldn't find? I.e. is there an object
> "bar" listed by 'ls()' but also an object "bar" listed by 'ls(2)' (i.e.
> your data frame 'foo' contained a variable with name 'bar')? Then it is
> the other way round, the local ones are hiding the hidden ones.
>
> For that reason attaching data frames has its dangers. It allows to
> easily access the variables in the data frame, but any changes to a
> variable creates a local copy. Thus, any change *will* not propagate
> back to the data frame!
>
> Hopefully the commands below will clarify further.
>
> Cheers,
>
> Berwin
>
>
> R> foo <- data.frame(bar=rnorm(2), fubar=runif(2))
> R> ls()
> [1] "foo"
> R> attach(foo)
> R> search()
> [1] ".GlobalEnv" "foo" "package:stats"
> [4] "package:graphics" "package:grDevices" "package:utils"
> [7] "package:datasets" "package:methods" "Autoloads"
> [10] "package:base"
> R> ls(2)
> [1] "bar" "fubar"
> R> bar
> [1] -0.07741633 1.05804653
> R> fubar
> [1] 0.08516929 0.82718383
> R> bar <- "what now"
> R> ls()
> [1] "bar" "foo"
> R> bar
> [1] "what now"
> R> ls(2)
> [1] "bar" "fubar"
> R> get("bar", pos=2)
> [1] -0.07741633 1.05804653
> R> foo
> bar fubar
> 1 -0.07741633 0.08516929
> 2 1.05804653 0.82718383
> R> detach(2)
> R> bar
> [1] "what now"
> R> fubar
> Error: object 'fubar' not found
> R> foo
> bar fubar
> 1 -0.07741633 0.08516929
> 2 1.05804653 0.82718383
> R> attach(foo)
> The following object is masked _by_ .GlobalEnv:
>
> bar
> R> bar
> [1] "what now"
> R> fubar
> [1] 0.08516929 0.82718383
> R> detach(2)
> R> bar
> [1] "what now"
> R> fubar
> Error: object 'fubar' not found
> R> foo
> bar fubar
> 1 -0.07741633 0.08516929
> 2 1.05804653 0.82718383
>
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