[R] How to see how a function is written

[Sergey Goriatchev]

Maybe I have to much stuff loaded in the workspace, Gavin, you are right:

> sessionInfo()
R version 2.10.1 (2009-12-14)
i386-pc-mingw32

locale:
[1] LC_COLLATE=German_Switzerland.1252
LC_CTYPE=German_Switzerland.1252
LC_MONETARY=German_Switzerland.1252
[4] LC_NUMERIC=C                        LC_TIME=German_Switzerland.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] PerformanceAnalytics_1.0.0 quantmod_0.3-13            TTR_0.20-1
               Defaults_1.1-1             xts_0.7-0
 [6] fPortfolio_2100.78         Rglpk_0.3-5                slam_0.1-9
               fAssets_2100.78            fCopulae_2110.78
[11] sn_0.4-14                  mnormt_1.3-3
fBasics_2110.79            timeSeries_2110.87         timeDate_2110.87
[16] robustbase_0.5-0-1         quadprog_1.4-12            MASS_7.3-5
               fEcofin_290.76             foreach_1.3.0
[21] codetools_0.2-2            iterators_1.0.3            zoo_1.6-3

loaded via a namespace (and not attached):
[1] grid_2.10.1    lattice_0.18-3 tools_2.10.1


On Tue, Jun 15, 2010 at 14:56, Gavin Simpson <gavin.simpson at ucl.ac.uk> wrote:
> On Tue, 2010-06-15 at 14:38 +0200, Sergey Goriatchev wrote:
>> Erik, I see the following when I type "apply" at the prompt:
>>
>> > apply
>> standardGeneric for "apply" defined from package "base"
>
> Looks like you have something loaded in your workspace (or have created
> something) that has altered the usual definition of apply(). Most likely
> is a package has made the base apply() function an S4 method.
>
> Send the output of sessionInfo() to the list so we can help if you
> interest is in the S4 method version of apply() (myself I'm not too
> familiar with S4 methods just yet).
>
> If you start R in a clean session, you should see the normal definition
> of apply
>
> R --vanilla
> apply
>
> On Windows you may need to add that option to the shortcut you use to
> start R.
>
> You could also try
>
> base:::apply
>
> to see the version in the base R namespace (at least I think that should
> work).
>
>>
>> function (X, MARGIN, FUN, ...)
>> standardGeneric("apply")
>> <environment: 0x03cad7d0>
>> Methods may be defined for arguments: X, MARGIN, FUN
>> Use  showMethods("apply")  for currently available ones.
>>
>> Also, whether I type "mean" at the prompt, or I type "edit(mean)", I
>> do not see the underlying code for function "mean". How would I be
>> able to see it?
>
> The info I sent in my previous email should help you with the mean
> function --- as long as that hasn't been overwritten by anything.
>
>> methods(mean)
> [1] mean.data.frame mean.Date       mean.default    mean.difftime
> [5] mean.POSIXct    mean.POSIXlt
>> getS3method("mean", "default")
> function (x, trim = 0, na.rm = FALSE, ...)
> {
>    if (!is.numeric(x) && !is.complex(x) && !is.logical(x)) {
>        warning("argument is not numeric or logical: returning NA")
>        return(NA_real_)
>    }
>    if (na.rm)
>        x <- x[!is.na(x)]
>    if (!is.numeric(trim) || length(trim) != 1L)
>        stop("'trim' must be numeric of length one")
>    n <- length(x)
>    if (trim > 0 && n) {
>        if (is.complex(x))
>            stop("trimmed means are not defined for complex data")
>        if (any(is.na(x)))
>            return(NA_real_)
>        if (trim >= 0.5)
>            return(stats::median(x, na.rm = FALSE))
>        lo <- floor(n * trim) + 1
>        hi <- n + 1 - lo
>        x <- sort.int(x, partial = unique(c(lo, hi)))[lo:hi]
>    }
>    .Internal(mean(x))
> }
> <environment: namespace:base>
>
> Although here, none of the mean methods are hidden so you could just
> type their names directly.
>
> The meaning of the .Internal(   ) bit is that this calls internal C
> code. Uwe Ligges article discusses what to do at this point.
>
> HTH
>
> G
>
>>
>> ---
>> My machine:
>> platform       i386-pc-mingw32
>> arch           i386
>> os             mingw32
>> system         i386, mingw32
>> status
>> major          2
>> minor          10.1
>> year           2009
>> month          12
>> day            14
>> svn rev        50720
>> language       R
>> version.string R version 2.10.1 (2009-12-14)
>>
>>
>>
>>
>>
>>
>>
>> On Tue, Jun 15, 2010 at 14:26, Erik Iverson <eriki at ccbr.umn.edu> wrote:
>> > Sergey Goriatchev wrote:
>> >>
>> >> Hello,
>> >>
>> >> If I want to see how, say, apply function is written, how would I be
>> >> able to do that?
>> >> Just typing "apply" at the prompt does not work.
>> >>
>> >
>> > Well, it is supposed to work, and it works for me.  So you need to tell us
>> > what "does not work" means, and all the info the posting guide requests, OS,
>> > versions, etc.
>> >
>>
>>
>>
>
> --
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>  Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
>  ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
>  Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
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>
>



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