[Bioc-devel] change names(assays(SummarizedExperiment)) w/o copy?
hi, Is there a way that I can change the names of the assays slot of a SummarizedExperiment, without making a new copy of the data contained within? Assume I get an SE which has already been constructed, but no names on the assays() SimpleList. thanks, Mike library(GenomicRanges) gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1291106 691710298 91.4 1590760 85.0 Vcells 117861991925843 14.7 1724123 13.2 m - matrix(1:2e7, ncol=10) gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 129 69.01967602 105.1 1590760 85.0 Vcells 11178604 85.3 22482701 171.6 21178631 161.6 # made a ~75 Mb matrix colnames(m) - letters[1:10] gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1291149 69.01967602 105.1 1590760 85.0 Vcells 11178679 85.3 22482701 171.6 21179851 161.6 se - SummarizedExperiment(m) gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1302603 69.61967602 105.1 1623929 86.8 Vcells 12189777 93.1 22482701 171.6 21179851 161.6 # so far no copying names(assays(se)) - counts gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1303174 69.61967602 105.1 1623929 86.8 Vcells 22190847 169.4 23686836 180.8 22203423 169.4 # last step made a copy sessionInfo() R Under development (unstable) (2014-05-07 r65539) Platform: x86_64-apple-darwin12.5.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicRanges_1.17.12 GenomeInfoDb_1.1.3IRanges_1.99.13 [4] S4Vectors_0.0.6 BiocGenerics_0.11.2 loaded via a namespace (and not attached): [1] RCurl_1.95-4.1 stats4_3.2.0 XVector_0.5.6 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] names, mcols and metadata are not changed in [- operator of class Vector
Hi Sebastian,
This is the expected behavior and it's motivated by how [- behaves on
ordinary vectors:
x - setNames(1:3, LETTERS[1:3])
Then:
x
A B C
1 2 3
Replacing the first two elements:
x[2:1] - x[1:2]
Then:
x
A B C
2 1 3
The names are preserved.
So we need to think of [- as an operator that touches the values of
a vector-like object without touching its structure or its attributes.
People sometimes rely on this behavior to stuff the entire object with
a given value:
x[] - some_value
They wouldn't expect this to destroy the names or metadata cols that
are on 'x'.
Hope that makes sense,
Cheers,
H.
On 05/07/2014 11:59 AM, Sebastian Gibb wrote:
Dear all,
today I observed an unexpected behaviour (at least for me) using the [-
operator on classes that inherited Vector.
I want to change the order of some elements inside the Vector (in my use case it
is an AAStringSet object). If I use an index in [- the names, the
elementMetadata and the metadata are not replaced by their counterparts, e.g.:
###
library(IRanges)
i - IRanges(1:3, 4:6)
names(i) - LETTERS[1:3]
i
# IRanges of length 3
# start end width names
# [1] 1 4 4 A
# [2] 2 5 4 B
# [3] 3 6 4 C
i[2:1] - i[1:2]
i
# IRanges of length 3
# start end width names
# [1] 2 5 4 A
# [2] 1 4 4 B
# [3] 3 6 4 C
## names should be B, A, C; the elementMetadata and metadata are in the wrong
## order, too.
## expected output:
# IRanges of length 3
# start end width names
# [1] 2 5 4 B
# [2] 1 4 4 A
# [3] 3 6 4 C
###
I tried to figure out the reason for this and ended up with the replaceROWS
method (in {IRanges,S4Vectors}/R/Vector-class.R).
In this method the mcols, metadata and names are just restored. To be honest I
do not really understand this function.
Why is the new value first append to the original vector (`ans - c(x, value)`)
and subsequently extracted? Would a simple replace, e.g. `x[i] - value` not be
enough?
In my opinion the last three lines should restore the original metadata
*and* replace the corresponding metadata by their new counterparts.
### replaceROWS from IRanges/R/Vector-class.R
setMethod(replaceROWS, Vector,
function(x, i, value)
{
idx - seq_along(x)
i - extractROWS(setNames(idx, names(x)), i)
## Assuming that objects of class 'class(x)' can be combined with c().
ans - c(x, value)
idx[i] - length(x) + seq_len(length(value))
## Assuming that [ works on objects of class 'class(x)'.
ans - ans[idx]
## Restore the original decoration.
metadata(ans) - metadata(x)
names(ans) - names(x)
mcols(ans) - mcols(x)
ans
}
)
###
Kind regards,
Sebastian
___
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
___
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Re: [Bioc-devel] change names(assays(SummarizedExperiment)) w/o copy?
On 05/07/2014 12:06 PM, Michael Love wrote: hi, Is there a way that I can change the names of the assays slot of a SummarizedExperiment, without making a new copy of the data contained within? Assume I get an SE which has already been constructed, but no names on the assays() SimpleList. Hi Mike -- names(assays(se)) = counts extracts the assays from se, then applies the names to the SimpleList, then re-assigns the SimpleList to the SummarizedExperiment. The memory copy (of big data) is actually in the extraction assays(se) m = matrix(0, 0, 0); tracemem(m) [1] 0x3449b4e8 se = SummarizedExperiment(m) a = assays(se) tracemem[0x3449b4e8 - 0x34ef64f0]: lapply lapply lapply lapply endoapply endoapply assays assays which can actually be avoided by asking for the assays without their dimnames a = assays(se, withDimnames=FALSE) and from there names(a) = counts assays(se) = a verifying that we haven't actually copied the matrix .Internal(inspect(assays(se, withDimnames=FALSE)[[1]])) @3449b4e8 14 REALSXP g0c0 [NAM(2),TR,ATT] (len=0, tl=0) ATTRIB: @3449b4b0 02 LISTSXP g0c0 [] TAG: @b9c778 01 SYMSXP g0c0 [LCK,gp=0x4000] dim (has value) @3449a118 13 INTSXP g0c1 [NAM(2)] (len=2, tl=0) 0,0 .Internal(inspect(m)) @3449b4e8 14 REALSXP g0c0 [NAM(2),TR,ATT] (len=0, tl=0) ATTRIB: @3449b4b0 02 LISTSXP g0c0 [] TAG: @b9c778 01 SYMSXP g0c0 [LCK,gp=0x4000] dim (has value) @3449a118 13 INTSXP g0c1 [NAM(2)] (len=2, tl=0) 0,0 One would hope (a) that I'd followed through on a previous promise to just apply the dimnames up-front, so that there is no need to use withDimnames=FALSE to avoid the copying (there might have been a price on the way in) and (b) that the following would work names(assays(se, withDimnames=FALSE)) = counts it didn't names(assays(se, withDimnames=FALSE)) = counts Error in slot(x, nm) : no slot of name withDimnames for this object of class SummarizedExperiment but does in 1.17.13 Martin thanks, Mike library(GenomicRanges) gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1291106 691710298 91.4 1590760 85.0 Vcells 117861991925843 14.7 1724123 13.2 m - matrix(1:2e7, ncol=10) gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 129 69.01967602 105.1 1590760 85.0 Vcells 11178604 85.3 22482701 171.6 21178631 161.6 # made a ~75 Mb matrix colnames(m) - letters[1:10] gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1291149 69.01967602 105.1 1590760 85.0 Vcells 11178679 85.3 22482701 171.6 21179851 161.6 se - SummarizedExperiment(m) gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1302603 69.61967602 105.1 1623929 86.8 Vcells 12189777 93.1 22482701 171.6 21179851 161.6 # so far no copying names(assays(se)) - counts gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1303174 69.61967602 105.1 1623929 86.8 Vcells 22190847 169.4 23686836 180.8 22203423 169.4 # last step made a copy sessionInfo() R Under development (unstable) (2014-05-07 r65539) Platform: x86_64-apple-darwin12.5.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicRanges_1.17.12 GenomeInfoDb_1.1.3IRanges_1.99.13 [4] S4Vectors_0.0.6 BiocGenerics_0.11.2 loaded via a namespace (and not attached): [1] RCurl_1.95-4.1 stats4_3.2.0 XVector_0.5.6 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] names, mcols and metadata are not changed in [- operator of class Vector
Hi Hervé,
thanks for the explanation. I never recognized that this happens with ordinary
vectors, too.
Of course, I see that it would be a bad style to overload [- for my own
class to behave like I want to.
So I need to update the metadata manually.
Kind regards,
Sebastian
On 2014-05-07 20:18:58, hpa...@fhcrc.org wrote:
Hi Sebastian,
This is the expected behavior and it's motivated by how [- behaves on
ordinary vectors:
x - setNames(1:3, LETTERS[1:3])
Then:
x
A B C
1 2 3
Replacing the first two elements:
x[2:1] - x[1:2]
Then:
x
A B C
2 1 3
The names are preserved.
So we need to think of [- as an operator that touches the values of
a vector-like object without touching its structure or its attributes.
People sometimes rely on this behavior to stuff the entire object with
a given value:
x[] - some_value
They wouldn't expect this to destroy the names or metadata cols that
are on 'x'.
Hope that makes sense,
Cheers,
H.
On 05/07/2014 11:59 AM, Sebastian Gibb wrote:
Dear all,
today I observed an unexpected behaviour (at least for me) using the [-
operator on classes that inherited Vector.
I want to change the order of some elements inside the Vector (in my use
case it
is an AAStringSet object). If I use an index in [- the names, the
elementMetadata and the metadata are not replaced by their counterparts,
e.g.:
###
library(IRanges)
i - IRanges(1:3, 4:6)
names(i) - LETTERS[1:3]
i
# IRanges of length 3
# start end width names
# [1] 1 4 4 A
# [2] 2 5 4 B
# [3] 3 6 4 C
i[2:1] - i[1:2]
i
# IRanges of length 3
# start end width names
# [1] 2 5 4 A
# [2] 1 4 4 B
# [3] 3 6 4 C
## names should be B, A, C; the elementMetadata and metadata are in the
wrong
## order, too.
## expected output:
# IRanges of length 3
# start end width names
# [1] 2 5 4 B
# [2] 1 4 4 A
# [3] 3 6 4 C
###
I tried to figure out the reason for this and ended up with the
replaceROWS
method (in {IRanges,S4Vectors}/R/Vector-class.R).
In this method the mcols, metadata and names are just restored. To be
honest I
do not really understand this function.
Why is the new value first append to the original vector (`ans - c(x,
value)`)
and subsequently extracted? Would a simple replace, e.g. `x[i] - value`
not be
enough?
In my opinion the last three lines should restore the original metadata
*and* replace the corresponding metadata by their new counterparts.
### replaceROWS from IRanges/R/Vector-class.R
setMethod(replaceROWS, Vector,
function(x, i, value)
{
idx - seq_along(x)
i - extractROWS(setNames(idx, names(x)), i)
## Assuming that objects of class 'class(x)' can be combined with
c().
ans - c(x, value)
idx[i] - length(x) + seq_len(length(value))
## Assuming that [ works on objects of class 'class(x)'.
ans - ans[idx]
## Restore the original decoration.
metadata(ans) - metadata(x)
names(ans) - names(x)
mcols(ans) - mcols(x)
ans
}
)
###
Kind regards,
Sebastian
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax:(206) 667-1319
___
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[Bioc-devel] Tracking Current release (http://www.bioconductor.org/packages/current redirect to http://www.bioconductor.org/packages/2.14)
I maintain a collection of Debian packages of CRAN and BioC[1] for public use; currently, whenever BioC makes a new release, it requires manual intervention for me to point at the new release location. It would be helpful if there was a http://www.bioconductor.org/packages/current redirect to the current release, or if there was another easily parsable method to obtain the current bioC release version. FWICT, neither http://bioconductor.org/getBioC.R nor http://bioconductor.org/biocLite.R encode that information either,[2] unless that's what CURRENT_R_DEVEL_VERSION - 2.14.0 is supposed to be. 1: http://debian-r.debian.net/ 2: I should also point out that the current methodology of installing BioC using code from a remote host is problematic as it exposes users to MITM attacks because it is never checked for authenticity via PGP or at the very least, SSL. As such, sourcing that script and using variables populated by it isn't really acceptable. -- Don Armstrong http://www.donarmstrong.com I never until now realized that the primary job of any emoticon is to say excuse me, that didn't make any sense. ;-P -- Cory Doctorow ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Tracking Current release (http://www.bioconductor.org/packages/current redirect to http://www.bioconductor.org/packages/2.14)
Hi Don -- On 05/07/2014 06:21 PM, Don Armstrong wrote: I maintain a collection of Debian packages of CRAN and BioC[1] for public use; currently, whenever BioC makes a new release, it requires manual intervention for me to point at the new release location. It would be helpful if there was a http://www.bioconductor.org/packages/current redirect to the current release, or if there was another easily parsable method to obtain the current bioC release version. Bioconductor releases are tied to R versions and the 'current' Bioc for a particular R, in a brand new installation, is source(http://bioconductor.org/biocLite.R;) biocVersion() (this is BiocInstaller::biocVersion(), where the biocLite.R script has arranged, modulo MITM concerns below, to install the version of the BiocInstaller package relevant to your version of R). I personally think of this as the canonical location, but... http://bioconductor.org/packages/release goes to the current release 'biocViews', with packages under release/ being the current release versions. http://bioconductor.org/bioc-version is probably what you'll end up using (though I believe it's hand curated), and tools:::.BioC_version_associated_with_R_version (this is a function in R-3.1) gives the version that R thinks is the current BioC version (this can become stale, e.g., R-3.0.1 was released when BioC-2.12 was the current version, but part way through the R point release BioC 2.13 became available [or at least, that's how I remember it]). FWICT, neither http://bioconductor.org/getBioC.R nor http://bioconductor.org/biocLite.R encode that information either,[2] unless that's what CURRENT_R_DEVEL_VERSION - 2.14.0 is supposed to be. 1: http://debian-r.debian.net/ 2: I should also point out that the current methodology of installing BioC using code from a remote host is problematic as it exposes users to MITM attacks because it is never checked for authenticity via PGP or at the very least, SSL. As such, sourcing that script and using variables populated by it isn't really acceptable. Of course this is a valid concern and we can work toward a more secure approach. Perhaps I could take the opportunity to ask a naive question about debian binary distributions of R. What is the directory into which packages are installed by sudo? In particular, are they unversioned, /usr/lib/R/library etc, as opposed to say /usr/lib/R-3.1/library ? I'm asking because a number of users seem to show up with say R-3.1 reporting a mix of R-3.1 and R-3.0.2 packages, usually to ill effect; this is not necessarily likely for user-installed packages, because the system directories won't be writeable and R will prompt with a versioned directory ~/R/x86_64-unknown-linux-gnu-library/3.1 as the location to install libraries. I'm wondering if mixed package versions would happen if their package manager failed to remove previously installed packages from the /usr/lib/R/library directory, or if the user installed multiple versions of R. Of course this could merely reflect users installing R without the help of package managers, and either way it might point to changes in the way R installs itself. Martin -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Tracking Current release (http://www.bioconductor.org/packages/current redirect to http://www.bioconductor.org/packages/2.14)
- Original Message - From: Martin Morgan mtmor...@fhcrc.org To: bioc-devel@r-project.org Sent: Wednesday, May 7, 2014 10:07:10 PM Subject: Re: [Bioc-devel] Tracking Current release (http://www.bioconductor.org/packages/current redirect to http://www.bioconductor.org/packages/2.14) Hi Don -- On 05/07/2014 06:21 PM, Don Armstrong wrote: I maintain a collection of Debian packages of CRAN and BioC[1] for public use; currently, whenever BioC makes a new release, it requires manual intervention for me to point at the new release location. It would be helpful if there was a http://www.bioconductor.org/packages/current redirect to the current release, or if there was another easily parsable method to obtain the current bioC release version. Bioconductor releases are tied to R versions and the 'current' Bioc for a particular R, in a brand new installation, is source(http://bioconductor.org/biocLite.R;) biocVersion() (this is BiocInstaller::biocVersion(), where the biocLite.R script has arranged, modulo MITM concerns below, to install the version of the BiocInstaller package relevant to your version of R). I personally think of this as the canonical location, but... http://bioconductor.org/packages/release goes to the current release 'biocViews', with packages under release/ being the current release versions. http://bioconductor.org/bioc-version is probably what you'll end up using (though I believe it's hand curated), and This is automatically generated, as is http://bioconductor.org/js/versions.js which also includes the devel version number. Dan tools:::.BioC_version_associated_with_R_version (this is a function in R-3.1) gives the version that R thinks is the current BioC version (this can become stale, e.g., R-3.0.1 was released when BioC-2.12 was the current version, but part way through the R point release BioC 2.13 became available [or at least, that's how I remember it]). FWICT, neither http://bioconductor.org/getBioC.R nor http://bioconductor.org/biocLite.R encode that information either,[2] unless that's what CURRENT_R_DEVEL_VERSION - 2.14.0 is supposed to be. 1: http://debian-r.debian.net/ 2: I should also point out that the current methodology of installing BioC using code from a remote host is problematic as it exposes users to MITM attacks because it is never checked for authenticity via PGP or at the very least, SSL. As such, sourcing that script and using variables populated by it isn't really acceptable. Of course this is a valid concern and we can work toward a more secure approach. Perhaps I could take the opportunity to ask a naive question about debian binary distributions of R. What is the directory into which packages are installed by sudo? In particular, are they unversioned, /usr/lib/R/library etc, as opposed to say /usr/lib/R-3.1/library ? I'm asking because a number of users seem to show up with say R-3.1 reporting a mix of R-3.1 and R-3.0.2 packages, usually to ill effect; this is not necessarily likely for user-installed packages, because the system directories won't be writeable and R will prompt with a versioned directory ~/R/x86_64-unknown-linux-gnu-library/3.1 as the location to install libraries. I'm wondering if mixed package versions would happen if their package manager failed to remove previously installed packages from the /usr/lib/R/library directory, or if the user installed multiple versions of R. Of course this could merely reflect users installing R without the help of package managers, and either way it might point to changes in the way R installs itself. Martin -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Rd] Problem running checks after building R-patched
I am compiling the latest R-patched (Revision: 65533) Ubuntu Lucid (10.04). Building succeeds but make check stops with an error. The output in the terminal from make check: Testing examples for package ‘base’ Testing examples for package ‘tools’ Error: testing 'tools' failed Execution halted make[3]: *** [test-Examples-Base] Error 1 make[2]: *** [test-Examples] Error 2 make[1]: *** [test-all-basics] Error 1 make: *** [check] Error 2 The last lines in the output of tests/Examples/tools-Ex.Rout.fail are ### ** Examples gVigns - pkgVignettes(grid) ## Don't show: `%=f=%` - function(a, b) normalizePath(a) == normalizePath(b) with(gVigns, + stopifnot(engines == utils::Sweave, + pkgdir %=f=% system.file(package=grid), + dir%=f=% system.file(package=grid, doc), + (n. - length(docs)) = 12, # have 13 + n. == length(names), n. == length(engines), + length(msg) == 0) ) # as it is a 'base' package Error: (n. - length(docs)) = 12 is not TRUE Execution halted How do I fix this, if possible? Berend __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Problem running checks after building R-patched
Berend Hasselman b...@xs4all.nl on Wed, 7 May 2014 09:24:46 +0200 writes: I am compiling the latest R-patched (Revision: 65533) Ubuntu Lucid (10.04). Building succeeds but make check stops with an error. The output in the terminal from make check: Testing examples for package ‘base’ Testing examples for package ‘tools’ Error: testing 'tools' failed Execution halted make[3]: *** [test-Examples-Base] Error 1 make[2]: *** [test-Examples] Error 2 make[1]: *** [test-all-basics] Error 1 make: *** [check] Error 2 The last lines in the output of tests/Examples/tools-Ex.Rout.fail are ### ** Examples gVigns - pkgVignettes(grid) ## Don't show: `%=f=%` - function(a, b) normalizePath(a) == normalizePath(b) with(gVigns, + stopifnot(engines == utils::Sweave, + pkgdir %=f=% system.file(package=grid), + dir%=f=% system.file(package=grid, doc), + (n. - length(docs)) = 12, # have 13 + n. == length(names), n. == length(engines), + length(msg) == 0) ) # as it is a 'base' package Error: (n. - length(docs)) = 12 is not TRUE Execution halted How do I fix this, if possible? Berend Well, as it works correctly for others, why don't you execute the above code in your (self installed ?) version of R, and find out why -- I think -- the vignettes of grid were not built / installed correctly ? Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Problem running checks after building R-patched
On 07-05-2014, at 11:23, Martin Maechler maech...@stat.math.ethz.ch wrote: Berend Hasselman b...@xs4all.nl on Wed, 7 May 2014 09:24:46 +0200 writes: I am compiling the latest R-patched (Revision: 65533) Ubuntu Lucid (10.04). Building succeeds but make check stops with an error. The output in the terminal from make check: Testing examples for package ‘base’ Testing examples for package ‘tools’ Error: testing 'tools' failed Execution halted make[3]: *** [test-Examples-Base] Error 1 make[2]: *** [test-Examples] Error 2 make[1]: *** [test-all-basics] Error 1 make: *** [check] Error 2 The last lines in the output of tests/Examples/tools-Ex.Rout.fail are ### ** Examples gVigns - pkgVignettes(grid) ## Don't show: `%=f=%` - function(a, b) normalizePath(a) == normalizePath(b) with(gVigns, + stopifnot(engines == utils::Sweave, + pkgdir %=f=% system.file(package=grid), + dir%=f=% system.file(package=grid, doc), + (n. - length(docs)) = 12, # have 13 + n. == length(names), n. == length(engines), + length(msg) == 0) ) # as it is a 'base' package Error: (n. - length(docs)) = 12 is not TRUE Execution halted How do I fix this, if possible? Berend Well, as it works correctly for others, why don't you execute the above code in your (self installed ?) version of R, and find out why -- I think -- the vignettes of grid were not built / installed correctly ? Martin I have the release version R-3.1.0 installed (built and checked with NO error messages). I don't have pdflatex installed; that is detected by configure. I have found a difference between ……/tests/Examples/tools-Ex.R in R-3.1.0 and R-patched. After running this command diff R-3.1.0-build/tests/Examples/tools-Ex.R R-patched-build/tests/Examples/tools-Ex.R diff-3.1.0-3.1.0patched-tools-Ex.R.txt the file with the differences contains this: 155a156,184 nameEx(buildVignettes) ### * buildVignettes flush(stderr()); flush(stdout()) ### Name: buildVignettes ### Title: List and Build Package Vignettes ### Aliases: buildVignettes pkgVignettes ### Keywords: utilities documentation ### ** Examples gVigns - pkgVignettes(grid) ## Don't show: `%=f=%` - function(a, b) normalizePath(a) == normalizePath(b) with(gVigns, stopifnot(engines == utils::Sweave, pkgdir %=f=% system.file(package=grid), dir%=f=% system.file(package=grid, doc), (n. - length(docs)) = 12, # have 13 n. == length(names), n. == length(engines), length(msg) == 0) ) # as it is a 'base' package ## End Don't show stopifnot(grid %in% gVigns$names, inherits(gVigns, pkgVignettes)) cleanEx() which would indicate that tool-Ex.R contains an additional test. Berend __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] precedence (was 'historical NA question')
Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. The manual page for precedence is $ component select %x special operator - unary minus : sequence operator ^ **exponentiation * / mult/div + - add/sub = = == != logical ! not | and/or - - assignment Terry Therneau __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] historical significance of Pr(Chisq) 2.2e-16
Where does the value 2.2e-16 come from in p-values for chisq tests such as those reported below? Anova(cm.mod2) Analysis of Deviance Table (Type II tests) Response: Freq LR Chisq Df Pr(Chisq) B 11026.2 1 2.2e-16 *** W 7037.5 1 2.2e-16 *** Age 886.6 8 2.2e-16 *** B:W 3025.2 1 2.2e-16 *** B:Age 1130.4 8 2.2e-16 *** W:Age 332.9 8 2.2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] historical significance of Pr(Chisq) 2.2e-16
Presumably from .Machine$double.eps [1] 2.220446e-16 Whether this means the tail probability is actually that small, or that the routine that computes it can't get any more accuracy than that, you'll have to dig deeper. John .. John P. Nolan Math/Stat Department 227 Gray Hall, American University 4400 Massachusetts Avenue, NW Washington, DC 20016-8050 jpno...@american.edu voice: 202.885.3140 web: academic2.american.edu/~jpnolan .. -r-devel-boun...@r-project.org wrote: - To: r-devel r-devel@r-project.org From: Michael Friendly Sent by: r-devel-boun...@r-project.org Date: 05/07/2014 10:02AM Subject: [Rd] historical significance of Pr(Chisq) 2.2e-16 Where does the value 2.2e-16 come from in p-values for chisq tests such as those reported below? Anova(cm.mod2) Analysis of Deviance Table (Type II tests) Response: Freq LR Chisq Df Pr(Chisq) B 11026.2 1 2.2e-16 *** W 7037.5 1 2.2e-16 *** Age 886.6 8 2.2e-16 *** B:W 3025.2 1 2.2e-16 *** B:Age 1130.4 8 2.2e-16 *** W:Age 332.9 8 2.2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ 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] historical significance of Pr(Chisq) 2.2e-16
See ?format.pval cheers, jari oksanen From: r-devel-boun...@r-project.org [r-devel-boun...@r-project.org] on behalf of Michael Friendly [frien...@yorku.ca] Sent: 07 May 2014 17:02 To: r-devel Subject: [Rd] historical significance of Pr(Chisq) 2.2e-16 Where does the value 2.2e-16 come from in p-values for chisq tests such as those reported below? Anova(cm.mod2) Analysis of Deviance Table (Type II tests) Response: Freq LR Chisq Df Pr(Chisq) B 11026.2 1 2.2e-16 *** W 7037.5 1 2.2e-16 *** Age 886.6 8 2.2e-16 *** B:W 3025.2 1 2.2e-16 *** B:Age 1130.4 8 2.2e-16 *** W:Age 332.9 8 2.2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ 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] precedence (was 'historical NA question')
On Wed, 7 May 2014, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. The manual page for precedence is $ component select %x special operator - unary minus : sequence operator ^ **exponentiation * / mult/div + - add/sub = = == != logical ! not | and/or - - assignment which did lead to some head scratching after plotting exp(-x^2) :-) luke Terry Therneau __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: luke-tier...@uiowa.edu Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] precedence (was 'historical NA question')
On 5/7/14, 5:21 AM, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. Historically interesting, but there was never a guarantee that Version 3 of S (the blue book) was back-compatible with earlier versions. We gave users some help in getting on the road to converting, that was all (see Appendix 4 to the blue book). For that one brief moment, we felt free to innovate. John The manual page for precedence is $ component select %x special operator - unary minus : sequence operator ^ **exponentiation * / mult/div + - add/sub = = == != logical ! not | and/or - - assignment Terry Therneau __ 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
[Rd] yinch() is NOT nonsense with log='y'
May I request a modest change in the documentation and warning for xinch, yinch, and xyinch? Consider the following example: plot(1:2, log='y') yinch(1) [1] 0.1961134 Warning message: In yinch(1) : y log scale: yinch() is nonsense In fact, in this environment, yinch(y) translates a vertical displacement of y inches into the corresponding change in the log10 scale. For a realistic example of such a use, see the first example of the current R-Forge version of the new animate function in the Ecfun package: This places the Rlogo on a plot(..., log='y') without distortion. Thanks, Spencer Graves __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Historical NA question (Herv? Pag?s)
Equivalence certainly does not mean that literally replacing some text will
not change the result.
From R language definition, p. 11:
Except for the syntax, there is no difference between applying an operator
and calling a
function. In fact, x + y can equivalently be written ‘+‘(x, y). Notice that
since ‘+’ is a nonstandard
function name, it needs to be quoted.
A doubt that anybody would interpret the above as implying that the following
expressions should be equivalent:
2 * 2 + 2
2 * +(2,2)
I believe that S's %xxx% notation predates Mathematica's generic infix, ~XXX~,
notation, which also has high priority, independent of the meaning of the
symbol XXX.
--
Dr Georgi Boshnakov tel: (+44) (0)161 306 3684
School of Mathematics fax: (+44) (0)161 306 3669
Alan Turing Building 1.125
The University of Manchester email: georgi.boshna...@manchester.ac.uk
Oxford Road
Manchester M13 9PL
UK
Date: Tue, 06 May 2014 13:57:14 -0700
From: Herv? Pag?s hpa...@fhcrc.org
To: William Dunlap wdun...@tibco.com
Cc: Michael Friendly frien...@yorku.ca, r-devel@r-project.org
r-devel@r-project.org
Subject: Re: [Rd] Historical NA question
Message-ID: 53694caa.3080...@fhcrc.org
Content-Type: text/plain; charset=UTF-8; format=flowed
On 05/06/2014 01:44 PM, William Dunlap wrote:
Run the following function over the output of
parse(yourSourceCode.R) to edit the parse tree:
inToIsElement - function (expr)
{
# expr should be an expression or a call, not a function.
# The output of parse(keep.source=FALSE) or quote() is good.
if (is.call(expr) identical(expr[[1]], as.name(%in%))) {
expr[[1]] - as.name(is.element)
}
if (is.recursive(expr)) {
for(i in seq_along(expr)) {
expr[[i]] - Recall(expr[[i]])
}
}
expr
}
E.g.,
txt - function(els, negSet, posSet){
+ -els %in% negSet # commentary
+ els %in% posSet
+ }
inToIsElement(parse(text=txt, keep.source=FALSE))[[1]]
function(els, negSet, posSet) {
is.element(-els, negSet) is.element(els, posSet)
}
It assumes that you didn't make any precedence errors with %in%.
Thanks Bill. I appreciate that you are really trying to help me with my
precedence problem. Maybe I should clarify that I can live with it
though. Anyway, it's always good to know how to make substitutions in
the parse tree.
Cheers,
H.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Tue, May 6, 2014 at 1:28 PM, Herv? Pag?s hpa...@fhcrc.org wrote:
On 05/06/2014 01:15 PM, William Dunlap wrote:
In your example els%in%set gave the same result as
is.element(els,set), but because of precedence issues putting a unary
minus in front caused them to be given different inputs - one got -els
and the other got just els for the first argument.
So you confirm that to use your solution (i.e. replace my use of
'els%in%set' with 'is.element(els,set)') I need to think about
precedence?
To change one to
the other you have to edit the parsed expression, not the text. If
you used is.element in the first place you would avoid precedence
issues.
If you ... in the first place. A, but that's not what I did. So
that doesn't help me.
H.
(I avoid creating %xxx% functions because the precedence is
not often what I want.)
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Tue, May 6, 2014 at 1:06 PM, Herv? Pag?s hpa...@fhcrc.org wrote:
On 05/06/2014 12:36 PM, William Dunlap wrote:
When does els%in%set give a different result than is.element(els,set)?
I assumed they were copied form S+, where they are the same except
for argument names, but I may be wrong.
els - 2:1
set - 1:6
- els%in%set
[1] FALSE FALSE
- is.element(els,set)
[1] -1 -1
So following your advice doesn't really help me leave my precedence
problems behind.
H.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Tue, May 6, 2014 at 12:23 PM, Herv? Pag?s hpa...@fhcrc.org wrote:
On 05/06/2014 08:54 AM, William Dunlap wrote:
You can also use is.element(els,set) instead of the equivalent
els%in%set
No they are not *equivalent*. Equivalent means you could substitute
one by the other in your code without changing its behavior.
H.
and leave your precedence problems behind.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Mon, May 5, 2014 at 10:35 PM, peter dalgaard pda...@gmail.com
wrote:
On 06 May 2014, at 01:05 , Herv? Pag?s hpa...@fhcrc.org wrote:
BTW, that %in% has precedence over arithmetic operations is
surprising,
error-prone, and doesn't cover any reasonable use case (who needs to
multiply the logical vector returned by %in% by some value?) but
that's
another story:
The point here is that the %foo% operators all have the _same_
precedence. In principle, they can be user-coded, and there is no way
to
express what precedence is desirable. It may
Re: [Rd] precedence (was 'historical NA question')
No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html Sorry I couldn't resist ;-) H. On 05/07/2014 09:16 AM, John Chambers wrote: On 5/7/14, 5:21 AM, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. Historically interesting, but there was never a guarantee that Version 3 of S (the blue book) was back-compatible with earlier versions. We gave users some help in getting on the road to converting, that was all (see Appendix 4 to the blue book). For that one brief moment, we felt free to innovate. John The manual page for precedence is $ component select %x special operator - unary minus : sequence operator ^ **exponentiation * / mult/div + - add/sub = = == != logical ! not | and/or - - assignment Terry Therneau __ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] precedence (was 'historical NA question')
On May 7, 2014, at 3:37 PM, Hervé Pagès hpa...@fhcrc.org wrote: No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html Sorry I couldn't resist ;-) Yeah, but that's just yet another trip down the rabbit hole - why is -2 parsed as `-`(2) and not a single constant? Is there a way to express a negative constant in R? Hmm… On 05/07/2014 09:16 AM, John Chambers wrote: On 5/7/14, 5:21 AM, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. Historically interesting, but there was never a guarantee that Version 3 of S (the blue book) was back-compatible with earlier versions. We gave users some help in getting on the road to converting, that was all (see Appendix 4 to the blue book). For that one brief moment, we felt free to innovate. John The manual page for precedence is $ component select %x special operator - unary minus : sequence operator ^ **exponentiation * / mult/div + - add/sub = = == != logical ! not | and/or - - assignment Terry Therneau __ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ 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] historical significance of Pr(Chisq) 2.2e-16
It may come a time before the pchisq() function had the lower.tail argument. In those days you had the compute the upper tail as 1-pchisq(x2, df). For any eps2.2e-16 (.Machine$double.eps), 1-eps==1 so 1-(1-eps)==0 so you would get, e.g., 1-pchisq(100,2) [1] 0 and people would say 'but the p-value is not 0: it may be very small but not zero' so anova's printing functions would say 2.2e-16 to mollify them. Now we have the lower.tail=FALSE argument pchisq(100,2,lower.tail=FALSE) [1] 1.92875e-22 and don't need the 2.2e-16 but no one has seen fit to change things. Bill Dunlap TIBCO Software wdunlap tibco.com On Wed, May 7, 2014 at 7:02 AM, Michael Friendly frien...@yorku.ca wrote: Where does the value 2.2e-16 come from in p-values for chisq tests such as those reported below? Anova(cm.mod2) Analysis of Deviance Table (Type II tests) Response: Freq LR Chisq Df Pr(Chisq) B 11026.2 1 2.2e-16 *** W 7037.5 1 2.2e-16 *** Age 886.6 8 2.2e-16 *** B:W 3025.2 1 2.2e-16 *** B:Age 1130.4 8 2.2e-16 *** W:Age 332.9 8 2.2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ 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] precedence (was 'historical NA question')
On 07 May 2014, at 21:52 , Simon Urbanek simon.urba...@r-project.org wrote: On May 7, 2014, at 3:37 PM, Hervé Pagès hpa...@fhcrc.org wrote: No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html Sorry I couldn't resist ;-) Yeah, but that's just yet another trip down the rabbit hole - why is -2 parsed as `-`(2) and not a single constant? Is there a way to express a negative constant in R? Hmm… It's painful, but bquote(.(-2)^2) -2^2 eval(bquote(.(-2)^2)) [1] 4 bquote(.(-2)^2)[[2]] [1] -2 mode(bquote(.(-2)^2)[[2]]) [1] numeric The difficulty is that the tokenizer, which recognizes language elements before the parser goes to work on the grammatical structure, is unable to distinguish the -2 in -2 + 2 from the one in -2 ^ y. And since constants are generated by the tokenizer, negative ones are not generated. I don't think it is completely out of reach for the parser to recognize the pattern unary minus a numeric constant and fold it into a constant of the opposite sign, but I'm not volunteering... (and anyways, it is part of the bigger issue of general constant folding --- I suppose that Luke has a handle on that.) On 05/07/2014 09:16 AM, John Chambers wrote: On 5/7/14, 5:21 AM, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. Historically interesting, but there was never a guarantee that Version 3 of S (the blue book) was back-compatible with earlier versions. We gave users some help in getting on the road to converting, that was all (see Appendix 4 to the blue book). For that one brief moment, we felt free to innovate. John The manual page for precedence is $ component select %x special operator - unary minus : sequence operator ^ **exponentiation * / mult/div + - add/sub = = == != logical ! not | and/or - - assignment Terry Therneau __ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ 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 -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] precedence (was 'historical NA question')
On 05/07/2014 12:52 PM, Simon Urbanek wrote: On May 7, 2014, at 3:37 PM, Hervé Pagès hpa...@fhcrc.org wrote: No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html Sorry I couldn't resist ;-) Yeah, but that's just yet another trip down the rabbit hole - why is -2 parsed as `-`(2) and not a single constant? You wouldn't want -2 to be parsed as a single constant exactly for the reason that you wouldn't want -2^2 to return 4. Having -2^2 treated the same way as -x^2 is a sane feature. Is there a way to express a negative constant in R? Hmm… Maybe some people have some use cases for this (speed ?). Personally I don't. Of course it would require a special syntax, something that would probably be as ugly and confusing as the L suffix used for integer constants (L means long int in C). H. On 05/07/2014 09:16 AM, John Chambers wrote: On 5/7/14, 5:21 AM, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. Historically interesting, but there was never a guarantee that Version 3 of S (the blue book) was back-compatible with earlier versions. We gave users some help in getting on the road to converting, that was all (see Appendix 4 to the blue book). For that one brief moment, we felt free to innovate. John The manual page for precedence is $ component select %x special operator - unary minus : sequence operator ^ **exponentiation * / mult/div + - add/sub = = == != logical ! not | and/or - - assignment Terry Therneau __ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] precedence (was 'historical NA question')
On 05/07/2014 02:01 PM, peter dalgaard wrote: On 07 May 2014, at 21:52 , Simon Urbanek simon.urba...@r-project.org wrote: On May 7, 2014, at 3:37 PM, Hervé Pagès hpa...@fhcrc.org wrote: No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html Sorry I couldn't resist ;-) Yeah, but that's just yet another trip down the rabbit hole - why is -2 parsed as `-`(2) and not a single constant? Is there a way to express a negative constant in R? Hmm… It's painful, but bquote(.(-2)^2) -2^2 eval(bquote(.(-2)^2)) [1] 4 bquote(.(-2)^2)[[2]] [1] -2 mode(bquote(.(-2)^2)[[2]]) [1] numeric The difficulty is that the tokenizer, which recognizes language elements before the parser goes to work on the grammatical structure, is unable to distinguish the -2 in -2 + 2 from the one in -2 ^ y. Are you saying that the tokenizer could be made smarter and recognize -2 as a token in -2 ^ y, just because you didn't put a space between - and 2? So in -2 ^ y it would be token, but not in - 2^y. An therefore precedence would now depend on whether there is a space after the minus or not, or something like that? I'm confused. H. And since constants are generated by the tokenizer, negative ones are not generated. I don't think it is completely out of reach for the parser to recognize the pattern unary minus a numeric constant and fold it into a constant of the opposite sign, but I'm not volunteering... (and anyways, it is part of the bigger issue of general constant folding --- I suppose that Luke has a handle on that.) On 05/07/2014 09:16 AM, John Chambers wrote: On 5/7/14, 5:21 AM, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. Historically interesting, but there was never a guarantee that Version 3 of S (the blue book) was back-compatible with earlier versions. We gave users some help in getting on the road to converting, that was all (see Appendix 4 to the blue book). For that one brief moment, we felt free to innovate. John The manual page for precedence is $ component select %x special operator - unary minus : sequence operator ^ **exponentiation * / mult/div + - add/sub = = == != logical ! not | and/or - - assignment Terry Therneau __ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] precedence (was 'historical NA question')
On May 7, 2014, at 5:17 PM, Hervé Pagès hpa...@fhcrc.org wrote: On 05/07/2014 12:52 PM, Simon Urbanek wrote: On May 7, 2014, at 3:37 PM, Hervé Pagès hpa...@fhcrc.org wrote: No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html Sorry I couldn't resist ;-) Yeah, but that's just yet another trip down the rabbit hole - why is -2 parsed as `-`(2) and not a single constant? You wouldn't want -2 to be parsed as a single constant exactly for the reason that you wouldn't want -2^2 to return 4. Having -2^2 treated the same way as -x^2 is a sane feature. On what grounds? -2 is one value - negative two - and if you square it, you get four - so that's not even a question of precedence. It's just a matter of interpretation: do you see the constant -2 or do you see the constant 2 with unary minus? When you print -2 you get -2 - and that's not a positive constant with an unary minus - or is it? ;) - aaah, will we ever know … R is good at hiding that subtlety from us: a = quote(-2^2) b = bquote(.(-2)^2) a -2^2 b -2^2 eval(a) [1] -4 eval(b) [1] 4 Is there a way to express a negative constant in R? Hmm… Maybe some people have some use cases for this (speed ?). Wrong tree ;). You kick-started the trip but failed to follow the path it takes into the depths of the human mind … :P (or was that computer mind? ;)) Cheers, Simon Personally I don't. Of course it would require a special syntax, something that would probably be as ugly and confusing as the L suffix used for integer constants (L means long int in C). H. On 05/07/2014 09:16 AM, John Chambers wrote: On 5/7/14, 5:21 AM, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. Historically interesting, but there was never a guarantee that Version 3 of S (the blue book) was back-compatible with earlier versions. We gave users some help in getting on the road to converting, that was all (see Appendix 4 to the blue book). For that one brief moment, we felt free to innovate. John The manual page for precedence is $ component select %x special operator - unary minus : sequence operator ^ **exponentiation * / mult/div + - add/sub = = == != logical ! not | and/or - - assignment Terry Therneau __ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] precedence (was 'historical NA question')
On May 7, 2014, at 5:41 PM, Hervé Pagès hpa...@fhcrc.org wrote: On 05/07/2014 02:01 PM, peter dalgaard wrote: On 07 May 2014, at 21:52 , Simon Urbanek simon.urba...@r-project.org wrote: On May 7, 2014, at 3:37 PM, Hervé Pagès hpa...@fhcrc.org wrote: No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html Sorry I couldn't resist ;-) Yeah, but that's just yet another trip down the rabbit hole - why is -2 parsed as `-`(2) and not a single constant? Is there a way to express a negative constant in R? Hmm… It's painful, but bquote(.(-2)^2) -2^2 eval(bquote(.(-2)^2)) [1] 4 bquote(.(-2)^2)[[2]] [1] -2 mode(bquote(.(-2)^2)[[2]]) [1] numeric The difficulty is that the tokenizer, which recognizes language elements before the parser goes to work on the grammatical structure, is unable to distinguish the -2 in -2 + 2 from the one in -2 ^ y. Are you saying that the tokenizer could be made smarter and recognize -2 as a token in -2 ^ y, just because you didn't put a space between - and 2? So in -2 ^ y it would be token, but not in - 2^y. An therefore precedence would now depend on whether there is a space after the minus or not, or something like that? I'm confused. Nope, precedence would not change at all. -2 and - 2 are two different things - in case you didn't realize that spaces are important, try a-2 vs a -2. So, again, if -2 is a value then there is no precedence issue, since you have only operator in -2 ^ y namely ^. In - 2 ^ y you have two operators, so precedence matters. Cheers, Simon H. And since constants are generated by the tokenizer, negative ones are not generated. I don't think it is completely out of reach for the parser to recognize the pattern unary minus a numeric constant and fold it into a constant of the opposite sign, but I'm not volunteering... (and anyways, it is part of the bigger issue of general constant folding --- I suppose that Luke has a handle on that.) On 05/07/2014 09:16 AM, John Chambers wrote: On 5/7/14, 5:21 AM, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. Historically interesting, but there was never a guarantee that Version 3 of S (the blue book) was back-compatible with earlier versions. We gave users some help in getting on the road to converting, that was all (see Appendix 4 to the blue book). For that one brief moment, we felt free to innovate. John The manual page for precedence is $ component select %x special operator - unary minus : sequence operator ^ **exponentiation * / mult/div + - add/sub = = == != logical ! not | and/or - - assignment Terry Therneau __ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] precedence (was 'historical NA question')
On 07/05/2014, 5:55 PM, Simon Urbanek wrote: On May 7, 2014, at 5:41 PM, Hervé Pagès hpa...@fhcrc.org wrote: On 05/07/2014 02:01 PM, peter dalgaard wrote: On 07 May 2014, at 21:52 , Simon Urbanek simon.urba...@r-project.org wrote: On May 7, 2014, at 3:37 PM, Hervé Pagès hpa...@fhcrc.org wrote: No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html Sorry I couldn't resist ;-) Yeah, but that's just yet another trip down the rabbit hole - why is -2 parsed as `-`(2) and not a single constant? Is there a way to express a negative constant in R? Hmm… It's painful, but bquote(.(-2)^2) -2^2 eval(bquote(.(-2)^2)) [1] 4 bquote(.(-2)^2)[[2]] [1] -2 mode(bquote(.(-2)^2)[[2]]) [1] numeric The difficulty is that the tokenizer, which recognizes language elements before the parser goes to work on the grammatical structure, is unable to distinguish the -2 in -2 + 2 from the one in -2 ^ y. Are you saying that the tokenizer could be made smarter and recognize -2 as a token in -2 ^ y, just because you didn't put a space between - and 2? So in -2 ^ y it would be token, but not in - 2^y. An therefore precedence would now depend on whether there is a space after the minus or not, or something like that? I'm confused. Nope, precedence would not change at all. -2 and - 2 are two different things - in case you didn't realize that spaces are important, try a-2 vs a -2. So, again, if -2 is a value then there is no precedence issue, since you have only operator in -2 ^ y namely ^. In - 2 ^ y you have two operators, so precedence matters. Is there a language where - 2^2 gives a different answer than -2^2? (Substitute ** or any other exponentiation operator for ^ if you like.) This is important, because I'd like to avoid ever attempting any important calculation in that language. Duncan Murdoch Cheers, Simon H. And since constants are generated by the tokenizer, negative ones are not generated. I don't think it is completely out of reach for the parser to recognize the pattern unary minus a numeric constant and fold it into a constant of the opposite sign, but I'm not volunteering... (and anyways, it is part of the bigger issue of general constant folding --- I suppose that Luke has a handle on that.) On 05/07/2014 09:16 AM, John Chambers wrote: On 5/7/14, 5:21 AM, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. Historically interesting, but there was never a guarantee that Version 3 of S (the blue book) was back-compatible with earlier versions. We gave users some help in getting on the road to converting, that was all (see Appendix 4 to the blue book). For that one brief moment, we felt free to innovate. John The manual page for precedence is $ component select %x special operator - unary minus : sequence operator ^ **exponentiation * / mult/div + - add/sub = = == != logical ! not | and/or - - assignment Terry Therneau __ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ 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] precedence (was 'historical NA question')
On 05/07/2014 02:55 PM, Simon Urbanek wrote: On May 7, 2014, at 5:41 PM, Hervé Pagès hpa...@fhcrc.org wrote: On 05/07/2014 02:01 PM, peter dalgaard wrote: On 07 May 2014, at 21:52 , Simon Urbanek simon.urba...@r-project.org wrote: On May 7, 2014, at 3:37 PM, Hervé Pagès hpa...@fhcrc.org wrote: No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html Sorry I couldn't resist ;-) Yeah, but that's just yet another trip down the rabbit hole - why is -2 parsed as `-`(2) and not a single constant? Is there a way to express a negative constant in R? Hmm… It's painful, but bquote(.(-2)^2) -2^2 eval(bquote(.(-2)^2)) [1] 4 bquote(.(-2)^2)[[2]] [1] -2 mode(bquote(.(-2)^2)[[2]]) [1] numeric The difficulty is that the tokenizer, which recognizes language elements before the parser goes to work on the grammatical structure, is unable to distinguish the -2 in -2 + 2 from the one in -2 ^ y. Are you saying that the tokenizer could be made smarter and recognize -2 as a token in -2 ^ y, just because you didn't put a space between - and 2? So in -2 ^ y it would be token, but not in - 2^y. An therefore precedence would now depend on whether there is a space after the minus or not, or something like that? I'm confused. Nope, precedence would not change at all. -2 and - 2 are two different things - in case you didn't realize that spaces are important, try a-2 vs a -2. Yes, there is an precedent where space matters. I just hope you're not saying you'd like to see that repeated for -2 vs - 2. So, again, if -2 is a value then there is no precedence issue, since you have only operator in -2 ^ y namely ^. If you make -2 a value, then yes you *effectively* change precedence from a user point of view. You can be picky about terminology and argue that it's not an operator precedence issue because there is no operator involved but that doesn't change the fact that now it's a very bad idea. I can't believe serious programmers are discussing ways to make -2^2 return 4. H. In - 2 ^ y you have two operators, so precedence matters. Cheers, Simon H. And since constants are generated by the tokenizer, negative ones are not generated. I don't think it is completely out of reach for the parser to recognize the pattern unary minus a numeric constant and fold it into a constant of the opposite sign, but I'm not volunteering... (and anyways, it is part of the bigger issue of general constant folding --- I suppose that Luke has a handle on that.) On 05/07/2014 09:16 AM, John Chambers wrote: On 5/7/14, 5:21 AM, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. Historically interesting, but there was never a guarantee that Version 3 of S (the blue book) was back-compatible with earlier versions. We gave users some help in getting on the road to converting, that was all (see Appendix 4 to the blue book). For that one brief moment, we felt free to innovate. John The manual page for precedence is $ component select %x special operator - unary minus : sequence operator ^ **exponentiation * / mult/div + - add/sub = = == != logical ! not | and/or - - assignment Terry Therneau __ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] precedence (was 'historical NA question')
On 05/07/2014 02:45 PM, Simon Urbanek wrote: On May 7, 2014, at 5:17 PM, Hervé Pagès hpa...@fhcrc.org wrote: On 05/07/2014 12:52 PM, Simon Urbanek wrote: On May 7, 2014, at 3:37 PM, Hervé Pagès hpa...@fhcrc.org wrote: No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html Sorry I couldn't resist ;-) Yeah, but that's just yet another trip down the rabbit hole - why is -2 parsed as `-`(2) and not a single constant? You wouldn't want -2 to be parsed as a single constant exactly for the reason that you wouldn't want -2^2 to return 4. Having -2^2 treated the same way as -x^2 is a sane feature. On what grounds? The last few centuries of mathematics. Some clever people have been thinking about defining the rules for writing concise algebraic expressions that do not leave room for interpretation/ambiguities. -2 is one value - negative two - and if you square it, you get four - so that's not even a question of precedence. It's just a matter of interpretation: do you see the constant -2 or do you see the constant 2 with unary minus? In -2^2, there is no question I see the latter. I'm a little biased though, because, you know, I have some respect and admiration for the tradition. H. When you print -2 you get -2 - and that's not a positive constant with an unary minus - or is it? ;) - aaah, will we ever know … R is good at hiding that subtlety from us: a = quote(-2^2) b = bquote(.(-2)^2) a -2^2 b -2^2 eval(a) [1] -4 eval(b) [1] 4 Is there a way to express a negative constant in R? Hmm… Maybe some people have some use cases for this (speed ?). Wrong tree ;). You kick-started the trip but failed to follow the path it takes into the depths of the human mind … :P (or was that computer mind? ;)) Cheers, Simon Personally I don't. Of course it would require a special syntax, something that would probably be as ugly and confusing as the L suffix used for integer constants (L means long int in C). H. On 05/07/2014 09:16 AM, John Chambers wrote: On 5/7/14, 5:21 AM, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. Historically interesting, but there was never a guarantee that Version 3 of S (the blue book) was back-compatible with earlier versions. We gave users some help in getting on the road to converting, that was all (see Appendix 4 to the blue book). For that one brief moment, we felt free to innovate. John The manual page for precedence is $ component select %x special operator - unary minus : sequence operator ^ **exponentiation * / mult/div + - add/sub = = == != logical ! not | and/or - - assignment Terry Therneau __ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] precedence (was 'historical NA question')
On 05/07/2014 02:45 PM, Simon Urbanek wrote: On May 7, 2014, at 5:17 PM, Hervé Pagès hpa...@fhcrc.org wrote: On 05/07/2014 12:52 PM, Simon Urbanek wrote: On May 7, 2014, at 3:37 PM, Hervé Pagès hpa...@fhcrc.org wrote: No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html Sorry I couldn't resist ;-) Yeah, but that's just yet another trip down the rabbit hole - why is -2 parsed as `-`(2) and not a single constant? You wouldn't want -2 to be parsed as a single constant exactly for the reason that you wouldn't want -2^2 to return 4. Having -2^2 treated the same way as -x^2 is a sane feature. On what grounds? -2 is one value - negative two - and if you square it, you get four - so that's not even a question of precedence. It's just a matter of interpretation: do you see the constant -2 or do you see the constant 2 with unary minus? When you print -2 you get -2 - and that's not a positive constant with an unary minus - or is it? ;) - aaah, will we ever know … R is good at hiding that subtlety from us: a = quote(-2^2) b = bquote(.(-2)^2) a -2^2 b -2^2 eval(a) [1] -4 eval(b) [1] 4 Is there a way to express a negative constant in R? Hmm… Maybe some people have some use cases for this (speed ?). Wrong tree ;). You kick-started the trip but failed to follow the path it takes into the depths of the human mind … :P (or was that computer mind? ;)) BTW I don't see anything deep here, except maybe for the rabbit hole you've put yourself in. Just sayin'... H. Cheers, Simon Personally I don't. Of course it would require a special syntax, something that would probably be as ugly and confusing as the L suffix used for integer constants (L means long int in C). H. On 05/07/2014 09:16 AM, John Chambers wrote: On 5/7/14, 5:21 AM, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. Historically interesting, but there was never a guarantee that Version 3 of S (the blue book) was back-compatible with earlier versions. We gave users some help in getting on the road to converting, that was all (see Appendix 4 to the blue book). For that one brief moment, we felt free to innovate. John The manual page for precedence is $ component select %x special operator - unary minus : sequence operator ^ **exponentiation * / mult/div + - add/sub = = == != logical ! not | and/or - - assignment Terry Therneau __ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
