Re: [Rd] [PATCH] show vector length in summary()
On 10 September 2013 at 10:32, Sam Steingold wrote:
| (summary.default): show the vector length in addition to quantiles
|
|
| diff -u -i -p -F '^(def' -b -w -B
/home/sds/src/R-3.0.1/src/library/base/R/summary.R.old
/home/sds/src/R-3.0.1/src/library/base/R/summary.R
| --- /home/sds/src/R-3.0.1/src/library/base/R/summary.R.old2013-03-05
18:02:33.0 -0500
| +++ /home/sds/src/R-3.0.1/src/library/base/R/summary.R2013-09-10
10:19:02.682946339 -0400
| @@ -39,6 +39,7 @@ summary.default <-
| qq <- stats::quantile(object)
| qq <- signif(c(qq[1L:3L], mean(object), qq[4L:5L]), digits)
| names(qq) <- c("Min.", "1st Qu.", "Median", "Mean", "3rd Qu.", "Max.")
| + qq <- c(qq,"Length" = length(object))
| if(any(nas))
| c(qq, "NA's" = sum(nas))
| else qq
|
| Diff finished. Tue Sep 10 10:19:40 2013
Base R functions are rarely modified; others may have expectations on
summary() returning the six values it returns.
Many alternatives are available, including describe in Hmisc which returns
the count you suggest, and a count of missingness.
R> set.seed(42)
R> describe(rnorm(100))
rnorm(100)
n missing uniqueMean .05 .10 .25 .50 .75 .90
.95
100 0 100 0.03251 -1.7641 -1.2117 -0.6167 0.0898 0.6616 1.3730
1.5116
lowest : -2.993 -2.656 -2.440 -2.414 -1.781, highest: 1.513 1.576 1.895
2.018 2.287
R>
Dirk
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[Rd] [PATCH] show vector length in summary()
(summary.default): show the vector length in addition to quantiles
diff -u -i -p -F '^(def' -b -w -B
/home/sds/src/R-3.0.1/src/library/base/R/summary.R.old
/home/sds/src/R-3.0.1/src/library/base/R/summary.R
--- /home/sds/src/R-3.0.1/src/library/base/R/summary.R.old 2013-03-05
18:02:33.0 -0500
+++ /home/sds/src/R-3.0.1/src/library/base/R/summary.R 2013-09-10
10:19:02.682946339 -0400
@@ -39,6 +39,7 @@ summary.default <-
qq <- stats::quantile(object)
qq <- signif(c(qq[1L:3L], mean(object), qq[4L:5L]), digits)
names(qq) <- c("Min.", "1st Qu.", "Median", "Mean", "3rd Qu.", "Max.")
+ qq <- c(qq,"Length" = length(object))
if(any(nas))
c(qq, "NA's" = sum(nas))
else qq
Diff finished. Tue Sep 10 10:19:40 2013
--
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Re: [Rd] R CMD config for R >= 3.0.1
I need to build R on a Centos machine where I have no admin privileges. Believe I have to build from source, but cannot find the configure script in the source bundle. Am I missing something? -- View this message in context: http://r.789695.n4.nabble.com/R-CMD-config-for-R-3-0-1-tp4667399p4675813.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD config for R >= 3.0.1
Also have no cooperation from the admin of the machine, so can't ask for a yum install. -- View this message in context: http://r.789695.n4.nabble.com/R-CMD-config-for-R-3-0-1-tp4667399p4675814.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD config for R >= 3.0.1
On Sep 10, 2013, at 5:30 PM, crunch wrote: > Also have no cooperation from the admin of the machine, so can't ask for a > yum install. > Please follow Brian's advice. If you don't have even Fortran on that machine, then you're really in a pickle: you can extract the gfortran rpm contents (and all dependencies you may need) by hand in any place that you have access to and adjust LD_LIBRARY_PATH for the runtime accordingly. However, it's not a trivial task - it particular if you're not very familiar with subtleties of Linux. (I had to do this fairly recently on a CentOS machine, so I know it's possible, but there are a few gotchas that may require a few symlinks created by hand). Cheers, Simon > > -- > View this message in context: > http://r.789695.n4.nabble.com/R-CMD-config-for-R-3-0-1-tp4667399p4675814.html > Sent from the R devel mailing list archive at Nabble.com. > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [PATCH] show vector length in summary()
On Sep 10, 2013, at 12:56 PM, Sam Steingold wrote:
>> * Dirk Eddelbuettel [2013-09-10 10:21:33 -0500]:
>>
>> On 10 September 2013 at 10:32, Sam Steingold wrote:
>> | (summary.default): show the vector length in addition to quantiles
>> |
>> |
>> | diff -u -i -p -F '^(def' -b -w -B
>> /home/sds/src/R-3.0.1/src/library/base/R/summary.R.old
>> /home/sds/src/R-3.0.1/src/library/base/R/summary.R
>> | --- /home/sds/src/R-3.0.1/src/library/base/R/summary.R.old 2013-03-05
>> 18:02:33.0 -0500
>> | +++ /home/sds/src/R-3.0.1/src/library/base/R/summary.R 2013-09-10
>> 10:19:02.682946339 -0400
>> | @@ -39,6 +39,7 @@ summary.default <-
>> |qq <- stats::quantile(object)
>> |qq <- signif(c(qq[1L:3L], mean(object), qq[4L:5L]), digits)
>> |names(qq) <- c("Min.", "1st Qu.", "Median", "Mean", "3rd Qu.", "Max.")
>> | + qq <- c(qq,"Length" = length(object))
>> |if(any(nas))
>> |c(qq, "NA's" = sum(nas))
>> |else qq
>> |
>> | Diff finished. Tue Sep 10 10:19:40 2013
>>
>> Base R functions are rarely modified; others may have expectations on
>> summary() returning the six values it returns.
>
> Note that summary sometimes returns 5 values (when there no "NA's").
> It is clearly wrong to rely on the details of the return value of a UI
> function.
>
.. except that summary() is not a UI function. It is used to create summary
*objects*, not some UI output. Although sometimes users like to print such
summary objects, that is not the task of summary(). There are quite common
programmatic uses of summary() -- one prominent one that comes to my mind is in
conjunction with connections.
(Not that any of this has anything to do with the original question ... )
>> Many alternatives are available, including describe in Hmisc which
>> returns the count you suggest, and a count of missingness.
>
> Such a minor issue hardly justifies installing a whole new package.
> (but thanks for the suggestion!)
>
> --
> Sam Steingold (http://sds.podval.org/) on Ubuntu 13.04 (raring) X
> 11.0.11303000
> http://www.childpsy.net/ http://www.memritv.org http://palestinefacts.org
> http://www.PetitionOnline.com/tap12009/ http://pmw.org.il http://dhimmi.com
> WHO ATE MY BREAKFAST PANTS?
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
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Re: [Rd] R CMD config for R >= 3.0.1
On 10/09/2013 22:24, crunch wrote: I need to build R on a Centos machine where I have no admin privileges. Believe I have to build from source, but cannot find the configure script in the source bundle. Am I missing something? Yes, as it is there. We can only guess that 'the source bundle' you have is not the correct file. As 3.0.2 is close, I would start with R-patched from ftp://ftp.stat.math.ethz.ch/Software/R/ (a link on the CRAN front page). It contains an installation manual, online at http://cran.r-project.org/doc/manuals/r-patched/R-admin.html [What may be more of a problem is installing the tools you need: does your box have a Fortran compiler, for example?] -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [PATCH] show vector length in summary()
> * Dirk Eddelbuettel [2013-09-10 10:21:33 -0500]:
>
> On 10 September 2013 at 10:32, Sam Steingold wrote:
> | (summary.default): show the vector length in addition to quantiles
> |
> |
> | diff -u -i -p -F '^(def' -b -w -B
> /home/sds/src/R-3.0.1/src/library/base/R/summary.R.old
> /home/sds/src/R-3.0.1/src/library/base/R/summary.R
> | --- /home/sds/src/R-3.0.1/src/library/base/R/summary.R.old 2013-03-05
> 18:02:33.0 -0500
> | +++ /home/sds/src/R-3.0.1/src/library/base/R/summary.R 2013-09-10
> 10:19:02.682946339 -0400
> | @@ -39,6 +39,7 @@ summary.default <-
> | qq <- stats::quantile(object)
> | qq <- signif(c(qq[1L:3L], mean(object), qq[4L:5L]), digits)
> | names(qq) <- c("Min.", "1st Qu.", "Median", "Mean", "3rd Qu.", "Max.")
> | + qq <- c(qq,"Length" = length(object))
> | if(any(nas))
> | c(qq, "NA's" = sum(nas))
> | else qq
> |
> | Diff finished. Tue Sep 10 10:19:40 2013
>
> Base R functions are rarely modified; others may have expectations on
> summary() returning the six values it returns.
Note that summary sometimes returns 5 values (when there no "NA's").
It is clearly wrong to rely on the details of the return value of a UI function.
> Many alternatives are available, including describe in Hmisc which
> returns the count you suggest, and a count of missingness.
Such a minor issue hardly justifies installing a whole new package.
(but thanks for the suggestion!)
--
Sam Steingold (http://sds.podval.org/) on Ubuntu 13.04 (raring) X 11.0.11303000
http://www.childpsy.net/ http://www.memritv.org http://palestinefacts.org
http://www.PetitionOnline.com/tap12009/ http://pmw.org.il http://dhimmi.com
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Re: [Rd] Package installation and path.package
Hi Simon, thank you for this comment! I will do it now the regular way - this is always the most reliable one. Best Simon On Sep 9, 2013, at 3:29 PM, Simon Urbanek wrote: > e you need something that the user has write-permissions for. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Package installation and path.package
Hi Dirk,
thanks for the help I take a more thorough look at it.
Best
Simon
On Sep 9, 2013, at 3:41 PM, Dirk Eddelbuettel wrote:
>
> On 9 September 2013 at 09:26, Simon Urbanek wrote:
> | On Sep 9, 2013, at 4:22 AM, Simon Zehnder wrote:
> | > I am writing right now my own package that makes use of 'tempfile' and
> | > there within with 'path.package'. When I install it, I get the error:
> Error
> | > in path.package("mypackage") : none of the packages are loaded. Here is
> the
> | > code, I use in my package:
> [...]
> | That path to your package is dynamic - in general it will not be know when
> | creating the lazy-load DB, so you really want to put that code in .onLoad()
> | where the path is known.
>
> And you may want to use system.file() rather than path.package(), at
> least if I understand the question right.
>
> Here is what I use to share the bibtex file for the Rcpp vignettes with other
> Rcpp* package vignettes:
>
> R> system.file(package="Rcpp", "doc", "Rcpp.bib")
> [1] "/usr/local/lib/R/site-library/Rcpp/doc/Rcpp.bib"
> R>
>
> Answer conditional on my particular Linux system, but the path is guaranteed
> to be valid as long as Rcpp is installed which one can ensure via Depends:
> from another package.
>
> Dirk
>
> --
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Re: [Rd] [PATCH] show vector length in summary()
On Sep 10, 2013, at 18:38, Simon Urbanek wrote:
>
> On Sep 10, 2013, at 12:56 PM, Sam Steingold wrote:
>
>>> * Dirk Eddelbuettel [2013-09-10 10:21:33 -0500]:
>>>
>>> On 10 September 2013 at 10:32, Sam Steingold wrote:
>>> | (summary.default): show the vector length in addition to quantiles
>>> |
>>> |
>>> | diff -u -i -p -F '^(def' -b -w -B
>>> /home/sds/src/R-3.0.1/src/library/base/R/summary.R.old
>>> /home/sds/src/R-3.0.1/src/library/base/R/summary.R
>>> | --- /home/sds/src/R-3.0.1/src/library/base/R/summary.R.old2013-03-05
>>> 18:02:33.0 -0500
>>> | +++ /home/sds/src/R-3.0.1/src/library/base/R/summary.R2013-09-10
>>> 10:19:02.682946339 -0400
>>> | @@ -39,6 +39,7 @@ summary.default <-
>>> | qq <- stats::quantile(object)
>>> | qq <- signif(c(qq[1L:3L], mean(object), qq[4L:5L]), digits)
>>> | names(qq) <- c("Min.", "1st Qu.", "Median", "Mean", "3rd Qu.",
>>> "Max.")
>>> | + qq <- c(qq,"Length" = length(object))
>>> | if(any(nas))
>>> | c(qq, "NA's" = sum(nas))
>>> | else qq
>>> |
>>> | Diff finished. Tue Sep 10 10:19:40 2013
>>>
>>> Base R functions are rarely modified; others may have expectations on
>>> summary() returning the six values it returns.
>>
>> Note that summary sometimes returns 5 values (when there no "NA's").
>> It is clearly wrong to rely on the details of the return value of a UI
>> function.
>
> .. except that summary() is not a UI function. It is used to create summary
> *objects*, not some UI output. Although sometimes users like to print such
> summary objects, that is not the task of summary(). There are quite common
> programmatic uses of summary() -- one prominent one that comes to my mind is
> in conjunction with connections.
> (Not that any of this has anything to do with the original question ... )
As Simon surely knows but others perhaps not:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-should-I-write-summary-methods_003f
MW
>
>
>>> Many alternatives are available, including describe in Hmisc which
>>> returns the count you suggest, and a count of missingness.
>>
>> Such a minor issue hardly justifies installing a whole new package.
>> (but thanks for the suggestion!)
>>
>> --
>> Sam Steingold (http://sds.podval.org/) on Ubuntu 13.04 (raring) X
>> 11.0.11303000
>> http://www.childpsy.net/ http://www.memritv.org http://palestinefacts.org
>> http://www.PetitionOnline.com/tap12009/ http://pmw.org.il http://dhimmi.com
>> WHO ATE MY BREAKFAST PANTS?
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> __
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Re: [Rd] R CMD config for R >= 3.0.1
As an alternative, you might consider installing a virtual machine in your user space and installing R from there. That way you don't have to do a bunch of one-off gymnastics to get R compiled. On Sep 11, 2013, at 1:40 AM, Simon Urbanek wrote: > On Sep 10, 2013, at 5:30 PM, crunch wrote: > >> Also have no cooperation from the admin of the machine, so can't ask for a >> yum install. > > Please follow Brian's advice. If you don't have even Fortran on that machine, > then you're really in a pickle: you can extract the gfortran rpm contents > (and all dependencies you may need) by hand in any place that you have access > to and adjust LD_LIBRARY_PATH for the runtime accordingly. However, it's not > a trivial task - it particular if you're not very familiar with subtleties of > Linux. (I had to do this fairly recently on a CentOS machine, so I know it's > possible, but there are a few gotchas that may require a few symlinks created > by hand). > > Cheers, > Simon > > >> >> -- >> View this message in context: >> http://r.789695.n4.nabble.com/R-CMD-config-for-R-3-0-1-tp4667399p4675814.html >> Sent from the R devel mailing list archive at Nabble.com. >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
