search for: radfordn

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2013 Jun 22
1
Announcing pqR - a faster version of R
...tive thread. It also implements a true reference counting scheme to reduce the amount of unnecessary duplication of objects. There are also substantial speed ups in general interpretive overhead, and in particular operations. Readers of r-devel can try out pqR by downloading a source tarball from radfordneal.github.io/pqR (only tested on Linux/Unix so far). The source repository is github.com/radfordneal/pqR - look in the MODS file to see how the changes from R-2.15.0 are organized. The R Core Team may wish to look at the list of bugs fixed in pqR, in the NEWS file, since many of them are present i...
2015 Jul 14
3
Two bugs showing up mostly on SPARC systems
In testing pqR on Solaris SPARC systems, I have found two bugs that are also present in recent R Core versions. You can see the bugs and fixes at the following URLs: https://github.com/radfordneal/pqR/commit/739a4960a4d8f3a3b20cfc311518369576689f37 https://github.com/radfordneal/pqR/commit/339b7286c7b43dcc6b00e51515772f1d7dce7858 The first bug, in nls, is most likely to occur on a 64-bit big-endian system, but will occur with low probability on most platforms. The second bug, in re...
2018 Nov 27
1
Subsetting row in single column matrix drops names in resulting vector
...vector. In fact > it returns named vector when number of columns is > 1. > Same issue applicable to single row matrix. Is it a bug? looks very > counterintuitive. This and related issues are addressed in pqR, in the new release of 2018-11-18. (See pqR-project.org, and my blog post at radfordneal.wordpress.com) The behaviour of a[1,] is unchanged, for backwards compatibility reasons. But in pqR one can explicitly mark an argument as missing using "_". When an array subscript is missing in this way, the names will not be dropped in this context even if there is only one of th...
2015 Jan 20
1
[PATCH] Makefile: add support for git svn clones
Fellipe, CXXR development has moved to github, and we haven't fixed up the build for using git yet. Could you send a pull request with your change to the repo at https://github.com/cxxr-devel/cxxr/? Also, this patch may be useful for pqR too. https://github.com/radfordneal/pqR Thanks On Mon, Jan 19, 2015 at 2:35 PM, Dirk Eddelbuettel <edd at debian.org> wrote: > > On 19 January 2015 at 17:11, Duncan Murdoch wrote: > | The people who would have to maintain the patch can't test it. > > I don't understand this. > > The patch, as...
2015 Jul 14
0
Two bugs showing up mostly on SPARC systems
On 14/07/2015 6:08 PM, Radford Neal wrote: > In testing pqR on Solaris SPARC systems, I have found two bugs that > are also present in recent R Core versions. You can see the bugs and > fixes at the following URLs: > > https://github.com/radfordneal/pqR/commit/739a4960a4d8f3a3b20cfc311518369576689f37 Thanks for the report. Just one followup on this one: There are two sections of code that are really similar. Your patch applies to the code in port_nlsb(), but there's a very similar test in port_nlminb(), which is called from nlminb()...
2015 Aug 24
0
Problem with psignal.c for Windows builds
...sigmask(signal_Index) ((sigset_t)1<<(signal_Index-1)) /* This must be a macro, since we want setjmp working in the But the definition of sigset_t may also need to change, as discussed in my previous message. You can see the pqR versions at the following URLs: https://github.com/radfordneal/pqR/blob/44/src/gnuwin32/psignal.c https://github.com/radfordneal/pqR/blob/44/src/gnuwin32/fixed/h/psignal.h
2014 Mar 22
2
Varying results of package checks due to random seed
...using random number generation without setting the random numbers seed, in which case the seed is set based on the current time and process id, with an obvious possibility of results varying from run to run. In the current development version of pqR (in branch 19-mods, found at https://github.com/radfordneal/pqR/tree/19-mods), I have implemented a change so that if the R_SEED environment variable is set, the random seed is initialized to its value, rather than from the time and process id. This was motivated by exactly this problem - I can now just set R_SEED to something before running all the pac...
2015 Sep 18
2
is R syntax closed?
hi, i'm new to R and i discovered that for years people are complaining about lacking of very basic and hopefully simple things, like multiline comment, some marker for 'command doesn't end at this line' etc. so my question is why some of those things are still not implemented? is it because of compatibility/policy reasons? is R syntax done and any extensions are forbidden?
2015 Jul 15
1
Two bugs showing up mostly on SPARC systems
...rdoch wrote: > On 14/07/2015 6:08 PM, Radford Neal wrote: > > In testing pqR on Solaris SPARC systems, I have found two bugs that > > are also present in recent R Core versions. You can see the bugs and > > fixes at the following URLs: > > > > https://github.com/radfordneal/pqR/commit/739a4960a4d8f3a3b20cfc311518369576689f37 > > Thanks for the report. Just one followup on this one: > > There are two sections of code that are really similar. Your patch > applies to the code in port_nlsb(), but there's a very similar test in > port_nlminb(),...
2015 Mar 01
2
iterated lapply
...no meaning if you haven't looked at the source code for apply (and which doesn't tell you which element led to the error even if you know what "i" does). I've implemented this in the development version of pqR, on the development branch 31-apply-fix, at https://github.com/radfordneal/pqR/tree/31-apply-fix The changes are in src/main/apply.R, src/main/envir.R, and src/library/base/R/apply.R, plus a new test in tests/apply.R. You can compare to branch 31 to see what's changed. (Note rapply seems to not have had a problem, and that other apply functions just use these, s...
2015 Sep 19
0
is R syntax closed?
...repository and doesn't support pull requests in the same way git does. Since R is free in the GNU sense you can always define your own local version, see e.g. [2]. > i'm new to R welcome, and have fun! best, Mark [1] https://www.r-project.org/contributors.html [2] https://github.com/radfordneal/pqR Op za 19 sep. 2015 om 04:02 schreef Piotr Turski <piotr.turski at gmail.com>: > hi, > > i'm new to R and i discovered that for years people are complaining > about lacking of very basic and hopefully simple things, like multiline > comment, some marker for 'c...
2017 Jan 09
0
accelerating matrix multiply
...of NaN checks has been incorporated into my pqR version of R (see pqR-project.org). The documentation on this approach can be found with help("%*%") if you're running pqR, or you can just look at the source for this help file in the pqR source code repository, at https://github.com/radfordneal/pqR/blob/Release-2016-10-24/src/library/base/man/matmult.Rd Radford
2017 Mar 07
0
length(unclass(x)) without unclass(x)?
...he comparison. Unfortunately, assigning unclass(x) to a variable does result in a copy being made (this might often be avoided in future). These performance improvements are implemented using pqR's "variant result" mechanism, which also allows many other optimizations. See https://radfordneal.wordpress.com/2013/06/30/how-pqr-makes-programs-faster-by-not-doing-things/ for some explanation. There is no particular reason this mechanism couldn't be incorporated into R Core's implementation of R. Radford Neal
2019 Feb 23
0
Bug: time complexity of substring is quadratic
...elapsed 0.318 0.071 0.388 > system.time(for (i in 1:10) x<-substring(r,1:N,1:N)) user system elapsed 0.041 0.000 0.041 Some of this may be due to pqR's faster garbage collector - R Core implementatons have a particular GC problem with strings, as explained at https://radfordneal.wordpress.com/2018/11/29/faster-garbage-collection-in-pqr/ But there are also some specific improvements to string operations that you might want to have a look at. Radford Neal
2015 Mar 01
0
iterated lapply
...ooked > at the source code for apply (and which doesn't tell you which element > led to the error even if you know what "i" does). > > I've implemented this in the development version of pqR, on the > development branch 31-apply-fix, at > > https://github.com/radfordneal/pqR/tree/31-apply-fix > > The changes are in src/main/apply.R, src/main/envir.R, and > src/library/base/R/apply.R, plus a new test in tests/apply.R. You can > compare to branch 31 to see what's changed. (Note rapply seems to not > have had a problem, and that other apply fun...
2010 Jul 18
2
NA preserved in logical call - I don't understand this behavior because NA is not equal to 0
I am confused by the behavior of the below piece of code. The NAs are making it past the logical call ==0. I am sure that I am missing something. I just don't understand this behavior. Thanks for your help in advance. ########code####################################################### left <- (structure(list(measurment_num = c(2, 2.2, 2.4, 2.6, 2.8, 2.82, 3, NA, NA, NA),
2017 Oct 18
1
uniform sampling without replacement algorithm
...e a faster hashing scheme, but it is enabled by default only for very large n, since it produces a different result from the old, simple algorithm, and so (for example) re-running an old analysis might give different results if it were enabled. The development version of pqR (at https://github.com/radfordneal/pqR with the latest development branch being "73") implements a fast hashing scheme that produces the same result as the old method, and so is always enabled (when it would seem advantageous). Here is the core part of the code used (which calls a few pqR internal routines not in R Cor...
2017 Oct 03
0
Revert to R 3.2.x code of logicalSubscript in subscript.c?
...s some substantial performance improvements for subscripting over R Core versions. This is especially true for the current development version of pqR (probably leading to a new release in about a month). You can look at a somewhat-stable snapshot of recent pqR development at https://github.com/radfordneal/pqR/tree/05e32fa6 In particular, src/main/subscript.c might be of interest. Note that you should read mods-dir/README if you want to build this, and in particular, you need to run create-configure in the top-level source directory first. I modified your tests a bit, including producing versio...
2015 Jan 19
3
[PATCH] Makefile: add support for git svn clones
On 19/01/2015 4:13 PM, Nathan Kurz wrote: > On Mon, Jan 19, 2015 at 1:00 PM, Felipe Balbi <balbi at kernel.org> wrote: >> I just thought that such a small patch which causes no visible change to >> SVN users and allow for git users to build R would be acceptable, but if >> it isn't, that's fine too. > > Felipe --- > > It would appear that you are
2010 Aug 21
1
Speed improvement to evalList
I've been inspired to look at the R source code by some strange timing results that I wrote about on my blog at radfordneal.wordpress.com (see the posts on "Speeding up parentheses..." and "Two surprising things...". I discovered that the strange speed advantage of curly brackets over parentheses is partially explained by an inefficiency in the evalList and evalListKeepMissing procedures in eval....