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 -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[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 -- Sam Steingold (http://sds.podval.org/) on Ubuntu 13.04 (raring) X 11.0.11303000 http://www.childpsy.net/ http://dhimmi.com http://openvotingconsortium.org http://thereligionofpeace.com http://www.memritv.org http://camera.org Between grand theft and a legal fee, there only stands a law degree. __ 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
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 > > __ 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 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 WHO ATE MY BREAKFAST PANTS? __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
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 > > -- > Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com __ 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 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 > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel [[alternative HTML version deleted]] __ 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
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