Re: [Rd] package building problem under Windows Vista
There does seem to be some general problem associated with Sweave
and graphics when I try it on my Vista system with
[1] R version 2.7.0 RC (2008-04-17 r45367)
Using tradeCosts-article.Rnw from the tradeCosts package:
setwd(path.to.tradeCosts-article.Rnw)
Sweave(tradeCosts-article.Rnw)
appears to work properly; however, if we try it from the
command line:
R CMD Sweave tradeCosts-article.Rnw
to simulate what happens when trying to build the package it
indicates that in chunk 2 that pdf is masked from grDevices.
Then in chunk 17, when plotting is attempted the first time,
it chokes.
Maybe someone familiar with the relevant internals can explain.
I have shown chunks 1, 2 and 17 as output from Stangle,
the Rnw file up to the end of chunk 2 and the error log
from Sweave in the sections below.
-
###
### chunk number 1:
###
options(digits = 3, width = 60, scipen = 99)
set.seed(1)
cat.df.without.rownames - function (d, file = ){
stopifnot(is.data.frame(d))
row.names(d) - 1:nrow(d)
x - NULL
conn - textConnection(x, w, local = TRUE)
capture.output(print(d), file = conn)
close(conn)
cat(substring(x, first = max(nchar(row.names(d))) + 2), sep = \n,
file = file)
}
###
### chunk number 2:
###
library(tradeCosts)
data(trade.mar.2007)
head(trade.mar.2007)
###
### chunk number 17:
###
plot(result.batched, time.series.bps)
-
\documentclass[a4paper]{report}
\usepackage[round]{natbib}
\usepackage{Rnews}
\usepackage{fancyvrb}
\usepackage{Sweave}
\hyphenation{tradeCosts}
\hyphenation{tradeCostsResults}
\hyphenation{decision}
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontsize=\small,fontshape=sl}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{fontsize=\small}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontsize=\small,fontshape=sl}
%% \SweaveOpts{prefix.string=graphics/portfolio}
\bibliographystyle{abbrvnat}
\begin{document}
\begin{article}
\title{Trade Costs}
\author{Jeff Enos, David Kane, Arjun Ravi Narayan, Aaron Schwartz,
Daniel Suo and Luyi Zhao}
%%\VignetteIndexEntry{Trade Costs}
%%\VignetteDepends{tradeCosts}
echo = FALSE=
options(digits = 3, width = 60, scipen = 99)
set.seed(1)
cat.df.without.rownames - function (d, file = ){
stopifnot(is.data.frame(d))
row.names(d) - 1:nrow(d)
x - NULL
conn - textConnection(x, w, local = TRUE)
capture.output(print(d), file = conn)
close(conn)
cat(substring(x, first = max(nchar(row.names(d))) + 2), sep = \n,
file = file)
}
@
\maketitle
\setkeys{Gin}{width=0.95\textwidth}
\section*{Introduction}
Trade costs are the costs a trader must pay to implement a decision to
buy or sell a security. Consider a single trade of a single equity
security. Suppose on the evening of August 1, a trader decides to
purchase 10,000 shares of IBM at \$10, the \emph{decision price} of
the trade. The next day, the trader's broker buys 10,000 shares in a
rising market and pays \$11 per share, the trade's \emph{execution price}.
How much did it cost to implement this trade? In the most basic
ex-post analysis, trade costs are calculated by comparing the
execution price of a trade to a benchmark price.\footnote{For an
in-depth discussion of both ex-ante modeling and ex-post measurement
of trade costs, see \citet{kissell:glantz}.} Suppose we
wished to compare the execution price to the price of the security at
the time of the decision in the above example. Since the trader's
decision occurred at \$10 and the broker paid \$11, the cost of the
trade relative to the decision price was $\$11 - \$10 = \$1$ per
share, or \$10,000 (9.1\% of the total value of the execution).
Measuring costs relative to a trade's decision price captures costs
associated with the delay in the release of a trade into the market
and movements in price after the decision was made but before the
order is completed. It does not, however, provide a means to
determine whether the broker's execution reflects a fair price. For
example, the price of \$11 would be a poor price if most transactions
in IBM on August 2 occurred at \$10.50. For this purpose a better
benchmark would be the day's volume-weighted average price, or VWAP.
If VWAP on August 2 was \$10.50 and the trader used this as her
benchmark, then the trade cost would be \$0.50 per share, or \$500.
The first version of the \pkg{tradeCosts} package provides a simple
framework for calculating the cost of trades relative to a benchmark
price, such as VWAP or decision price, over multiple periods and basic
reporting and plotting facilities to analyse these costs.
Re: [Rd] package building problem under Windows Vista
Note that CRAN is also having a problem with the package so its not just you: http://cran.r-project.org/bin/windows/contrib/2.7/check/tm-check.log I also have a problem with the vignettes (note there are two) but as with you this works: Rcmd build --no-vignettes tradeCosts I don't have any special environment variables set for temporary directories and I use C:\Program Files\R\... for R. I use Rcmd.bat and sweave.bat from batchfiles found at: http://batchfiles.googlecode.com which finds R in the registry so no paths need be set. I am on Vista but you seem to have SP1 which I don't have yet. I can build other packages so there is probably something that needs fixing in their vignettes. On Sat, Apr 19, 2008 at 7:52 AM, John Fox [EMAIL PROTECTED] wrote: Dear list members, I've encountered the following problem trying to build a package under Windows Vista (SP1). The problem occurs with both R 2.6.2 and R 2.7.0 RC (from which this output was produced). The package builds just fine on my XP (SP2) machine. Please see some further comments below. -- snip - Microsoft Windows [Version 6.0.6001] Copyright (c) 2006 Microsoft Corporation. All rights reserved. d:\R-packagesR CMD build tradeCosts * checking for file 'tradeCosts/DESCRIPTION' ... OK * preparing 'tradeCosts': * checking DESCRIPTION meta-information ... OK * installing the package to re-build vignettes installing R.css in C:/Users/JOHNFO~1/AppData/Local/Temp/Rinst602447586 -- Making package tradeCosts adding build stamp to DESCRIPTION installing NAMESPACE file and metadata Error in file(file, r) : unable to open connection Calls: Anonymous - parseNamespaceFile - parse - file In addition: Warning message: In file(file, r) : cannot open file 'C:/Users/JOHNFO~1/AppData/Local/Temp/Rinst602447586/tradeCos ts/NAMESPACE', reason 'Permission denied' Execution halted make[2]: *** [nmspace] Error 1 make[1]: *** [all] Error 2 make: *** [pkg-tradeCosts] Error 2 *** Installation of tradeCosts failed *** Removing 'C:/Users/JOHNFO~1/AppData/Local/Temp/Rinst602447586/tradeCosts' * creating vignettes ... OK * removing junk files * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'tradeCosts_0.3-0.tar.gz' d:\R-packages -- snip - I believe that the error is related to the vignette in the package, since I can build packages without a vignette. Clearly there is a file-permission problem but: (1) I'm using an account with administrator privileges; (2) R is installed into c:\R (and the problem persists even when I install R into d:\R); (3) the problem persists when I run the command window and R itself as administrator, and when I turn off account controls; (4) the problems persists when I reset the environment variables temp and tmp to d:\temp and set the permissions to d:\temp so that all groups and users have full control over that directory. I'm tempted to dump Vista but I've been trying to persist with it since most people (e.g., my students) buying new Windows machines will be getting it. Although I've read section 2.24 of the R for Windows FAQ, it's quite possible that I've missed something of relevance there. Any help would be appreciated. Thanks in advance, John John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario, Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox __ 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] Progress window on updating
I am updating some packages using the packages menu and noticed that the progress window says 100% in the title done all the time. It works, its just that the progress percentage is wrong. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Overriding axis formatting with custom Axis method, Axis.numeric etc
Try this:
Axis.AsIs = AxisFUN = function(x=NULL, at=NULL, ..., side,
labels=TRUE) {
if (is.null(at)) at = pretty(x)
axis(at=at, ..., side=side, labels=labels, col=red, lwd=5)
}
plot(I(1:10))
On Mon, Apr 7, 2008 at 7:22 AM, Sklyar, Oleg (MI London)
[EMAIL PROTECTED] wrote:
Dear list:
I would like to override the default way R formats plot axes with a
custom method(s). Obviously I would prefer to define it as general as
possible avoiding writing a custom method for each individual class
where possible.
The plot.default method (and I assume other methods as well) calls
Axis(...) to produce the axis layout depending on data. In this sense it
seems reasonable to (re)define Axis methods rather than change plot
methods (which are impossible to control as there can be too many custom
ones).
Now my question is how can I redefine Axis that it is automatically
called by plot.default and other plot methods? Or which Axis-method
signatures are already defined that I should redefine?
What I have succeeded so far was defining Axis.numeric and Axis.myClass,
which are called by default if I supply data of class numeric or
myClass. For example, a simple code like
Axis.numeric = AxisFUN = function(x=NULL, at=NULL, ..., side,
labels=TRUE) {
if (is.null(at)) at = pretty(x)
axis(at=at, ..., side=side, labels=labels, col=red, lwd=5)
}
run with plot(1:5,1:5) will format both axes red.
However, if I execute it with plot(1:5) only x axis plotting is
intercepted leaving y at default formatting although it is also numeric.
Why and what should I define to intercept for plotting the y axis or for
plotting axes in boxplot etc. Simply importing and overriding Axis as
function does not bring anything, it wouldn't get called.
Also I was not able to use S4 methods to redefine Axis. Overriding it
with the code from above using any of the following signatures also
didn't work for me - they are simply ignored:
setGeneric(Axis)
setMethod(Axis, signature(x=missing,at=numeric), AxisFUN)
setMethod(Axis, signature(x=numeric,at=missing), AxisFUN)
setMethod(Axis, signature(x=missing,at=ANY), AxisFUN)
setMethod(Axis, signature(x=ANY,at=missing), AxisFUN)
setMethod(Axis, signature(x=ANY,at=ANY), AxisFUN)
Any ideas?
Thanks,
Oleg
Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
[EMAIL PROTECTED]
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Re: [Rd] [R] How to improve the OPTIM results
On Sun, Apr 6, 2008 at 12:59 PM, Kurt Hornik [EMAIL PROTECTED] wrote: Dirk Eddelbuettel writes: On 6 April 2008 at 08:37, Spencer Graves wrote: | moved to R-devel [...] | However, the comment from Hans Borchers (below) raises a related | question: What might be the best way to build a collaboration with | existing optimization initiatives, possibly making R a platform of | choice for making it easy for users to access and compare alternative | optimization methods? Are you (used in the plural) aware of Kurt's more recent advances into OR? There are new-ish packages RSymphony, Rglpk and other things at CRAN. Not only by me: there's also Rcplex and TSP and there are at least three more COIN-OR package interfaces in the pipeline. It would be nice if there were a CRAN Task View to pull all this together. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] __FILE__ for R
Although its kludgy this previously (and still works) too:
parent.frame(2)$ofile
if called from top level within a sourced file.
On Fri, Apr 4, 2008 at 11:50 AM, hadley wickham [EMAIL PROTECTED] wrote:
Sorry, that should be:
FILE - (function() {
attr(body(sys.function()), srcfile)
})()$filename
Hadley
On Fri, Apr 4, 2008 at 10:34 AM, hadley wickham [EMAIL PROTECTED] wrote:
I've often missed the ability to get the directory of the currently
running script. It's actually been possible for a while:
FILE - (function() {
attr(body(sys.function()), srcfile)
})()
thanks to Duncan's recent changes to file parsing. This is pretty
useful for sourcing in files relative to the current script, rather
than the working directory.
Hadley
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Re: [Rd] R CMD check should check date in description
I think its somewhat inspiring to be able to get R CMD check to the point that there are no warnings so having a situation where a warning is ok would interfere with that. On Fri, Apr 4, 2008 at 3:54 PM, hadley wickham [EMAIL PROTECTED] wrote: I recently thought about this. I see several issues. * How can we determine if it is old? Relative to the time when the package was uploaded to a repository? * Some developers might actually want a different date for a variety of reasons ... * What we currently say in R-exts is The optional `Date' field gives the release date of the current version of the package. It is strongly recommended to use the -mm-dd format conforming to the ISO standard. Many packages do not comply with the latter (but I have some code to sanitize most of these), and release date may be a moving target. The best that I could think of is to teach R CMD build to *add* a Date field if there was none. That sounds like a good solution to me. Otherwise, maybe just a message from R CMD check? i.e. just like failing the codetools checks, it might be perfectly ok, but you should be doing it consciously, not by mistake. Hadley -- http://had.co.nz/ __ 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] callCC in 2.7.0
Can I suggest some clarification of the help page for callCC plainly stating that it is intended to exit from a deeply nested set of calls. On a casual reading I thought the exact same thing as f.jamitsky. On Tue, Apr 1, 2008 at 6:32 AM, Luke Tierney [EMAIL PROTECTED] wrote: No. First class continuations of the kind provided in scheme can be used as a means to implement generators, but downward-only continuations as currently provided in R are not sufficient for that. This version is intended only as a non-local exit mechanism. Best, luke On Mon, 31 Mar 2008, f.jamitzky wrote: callcc is similar to the yield keyword in python and c# it lets you define e.g. a generator of lists of numbers. Gabor Grothendieck wrote: Would anyone like to explain if callCC in R 2.7.0 gives anything that on.exit does not already provide? It seems that the exit condition once defined cannot be added to overridden whereas with on.exit multiple on.exit's add additional on.exits rather than being ignored. Is this important? __ 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: [EMAIL PROTECTED] 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] data(lh) time serie parameters
On Sun, Mar 30, 2008 at 5:52 AM, Jean lobry [EMAIL PROTECTED] wrote: Dear all, I'm confused by the time serie parameters in data(lh) : sueoka:~ lobry$ R --vanilla --quiet tsp(lh) [1] 1 48 1 because documentation says: QUOTE A regular time series giving the luteinizing hormone in blood samples at 10 mins intervals from a human female, 48 samples. UNQUOTE So that I would expect the time serie to end at 480 minutes or 8 hours. Shouldn't we have something like: tsp(lh) - c(10, 480, 0.1) # in Minutes or tsp(lh) - c(1/6, 8, 6)# in Hours It seems they are using 10 minutes as the unit of measurement. If you wish to change it to hours you might want to use this instead: lh.hr - ts(lh, start = 0, frequency = 6) so that cycle(lh.hr) starts out at 1. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] callCC in 2.7.0
Would anyone like to explain if callCC in R 2.7.0 gives anything that on.exit does not already provide? It seems that the exit condition once defined cannot be added to overridden whereas with on.exit multiple on.exit's add additional on.exits rather than being ignored. Is this important? __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] callCC in 2.7.0
I think the only relationship to that is the name since it does not appear to allow one to leave a function in the middle of its processing and re-enter it back at that point -- which is what would be needed. On Sun, Mar 30, 2008 at 12:04 PM, [EMAIL PROTECTED] wrote: Would anyone like to explain if callCC in R 2.7.0 gives anything that on.exit does not already provide? It seems that the exit condition once defined cannot be added to overridden whereas with on.exit multiple on.exit's add additional on.exits rather than being ignored. Is this important? It facilitates a completely different style of programming - see http://en.wikipedia.org/wiki/Continuation-passing_style -- http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] callCC in 2.7.0
Also in trying it out again it seems that its not like
on.exit but more like return:
F - function(f) { f(10); print(2); f(20); 3}
callCC(F)
acts the same as:
F - function() { return(10); print(2); f(20); 3}
F()
and there is no documented way to restart F
at the point it left off so I assume it can't.
On Sun, Mar 30, 2008 at 12:34 PM, Gabor Grothendieck
[EMAIL PROTECTED] wrote:
I think the only relationship to that is the name since
it does not appear to allow one to leave a function
in the middle of its processing and re-enter it back
at that point -- which is what would be needed.
On Sun, Mar 30, 2008 at 12:04 PM, [EMAIL PROTECTED] wrote:
Would anyone like to explain if callCC in R 2.7.0 gives
anything that on.exit does not already provide?
It seems that the exit condition once defined cannot
be added to overridden whereas with on.exit multiple
on.exit's add additional on.exits rather than being ignored.
Is this important?
It facilitates a completely different style of programming - see
http://en.wikipedia.org/wiki/Continuation-passing_style
--
http://had.co.nz/
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Re: [Rd] callCC in 2.7.0
Sorry it should be as follows:
fib - function(i, a = 0, b = 1) {
if (i == 0) b else fib(i-1, b, a+b)
}
Now, how do we transform that to use callCC?
On Sun, Mar 30, 2008 at 1:42 PM, Gabor Grothendieck
[EMAIL PROTECTED] wrote:
OK. Can you show code to implement the tail recursive version of
fib using callCC in R, say.
Here it is transformed to tail recursive style:
fib - function(i, a = 0, b = 1) {
if (i == 0) a else fib(i-1, b, a+b)
Now, how do I add callCC to all this so that the fib call
presumably does not create a new stack instance?
On Sun, Mar 30, 2008 at 1:31 PM, Luke Tierney [EMAIL PROTECTED] wrote:
On Sun, 30 Mar 2008, Gabor Grothendieck wrote:
I think the only relationship to that is the name since
it does not appear to allow one to leave a function
in the middle of its processing and re-enter it back
at that point -- which is what would be needed.
The article conflates basic CPS with having first class continuations
as in Scheme. The discussion about compilers and tail calls only
requires downward-only continuations of the kind provided by R's
current callCC. The user interface and coroutine discussion requires
continuations that can be run outside of their creating context. The
most sophisticated variant, as provided in Scheme, also allows
continuations to be run more than once. I don't think any of the
examples in the Wikipedia article need that, but there is some
interesting work on using that to model web browsing behavior.
At any rate, there is plenty of precedent for using callCC as the name
for the construct here even when the continuation is no longer valid
outside of the creating callCC call. So the relationship is more than
just the name.
luke
On Sun, Mar 30, 2008 at 12:04 PM, [EMAIL PROTECTED] wrote:
Would anyone like to explain if callCC in R 2.7.0 gives
anything that on.exit does not already provide?
It seems that the exit condition once defined cannot
be added to overridden whereas with on.exit multiple
on.exit's add additional on.exits rather than being ignored.
Is this important?
It facilitates a completely different style of programming - see
http://en.wikipedia.org/wiki/Continuation-passing_style
--
http://had.co.nz/
__
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--
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: [EMAIL PROTECTED]
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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Re: [Rd] callCC in 2.7.0
I came across this in googling for continuations and was surprised when
I found it in R 2.7.0 and since I had not come across it before I assumed
it was added just now.
Can you explain how its intended to be used with an example
that is more realistic than in the example section.
On Sun, Mar 30, 2008 at 1:14 PM, Luke Tierney [EMAIL PROTECTED] wrote:
On Sun, 30 Mar 2008, Gabor Grothendieck wrote:
Also in trying it out again it seems that its not like
on.exit but more like return:
Yes -- if you can point out what in the documentation ever gave the
idea it might be like on.exit then we can fix the documentation.
F - function(f) { f(10); print(2); f(20); 3}
callCC(F)
acts the same as:
F - function() { return(10); print(2); f(20); 3}
F()
and there is no documented way to restart F
at the point it left off so I assume it can't.
The documentation descriped this as a downward-only version -- that is
standard terminology for a callCC that produces continuations that are
no longer valid after the callCC call exits.
Not sure why your original question was about callCC in 2.7.0 -- I
believe callCC was added in 2.5.0, the same time as codetools became
recommended, and hasn't changed since. It is not a function every R
user needs to have in their repertoire, but it can be very useful in
some situations.
luke
On Sun, Mar 30, 2008 at 12:34 PM, Gabor Grothendieck
[EMAIL PROTECTED] wrote:
I think the only relationship to that is the name since
it does not appear to allow one to leave a function
in the middle of its processing and re-enter it back
at that point -- which is what would be needed.
On Sun, Mar 30, 2008 at 12:04 PM, [EMAIL PROTECTED] wrote:
Would anyone like to explain if callCC in R 2.7.0 gives
anything that on.exit does not already provide?
It seems that the exit condition once defined cannot
be added to overridden whereas with on.exit multiple
on.exit's add additional on.exits rather than being ignored.
Is this important?
It facilitates a completely different style of programming - see
http://en.wikipedia.org/wiki/Continuation-passing_style
--
http://had.co.nz/
__
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--
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: [EMAIL PROTECTED]
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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Re: [Rd] callCC in 2.7.0
OK. Can you show code to implement the tail recursive version of
fib using callCC in R, say.
Here it is transformed to tail recursive style:
fib - function(i, a = 0, b = 1) {
if (i == 0) a else fib(i-1, b, a+b)
Now, how do I add callCC to all this so that the fib call
presumably does not create a new stack instance?
On Sun, Mar 30, 2008 at 1:31 PM, Luke Tierney [EMAIL PROTECTED] wrote:
On Sun, 30 Mar 2008, Gabor Grothendieck wrote:
I think the only relationship to that is the name since
it does not appear to allow one to leave a function
in the middle of its processing and re-enter it back
at that point -- which is what would be needed.
The article conflates basic CPS with having first class continuations
as in Scheme. The discussion about compilers and tail calls only
requires downward-only continuations of the kind provided by R's
current callCC. The user interface and coroutine discussion requires
continuations that can be run outside of their creating context. The
most sophisticated variant, as provided in Scheme, also allows
continuations to be run more than once. I don't think any of the
examples in the Wikipedia article need that, but there is some
interesting work on using that to model web browsing behavior.
At any rate, there is plenty of precedent for using callCC as the name
for the construct here even when the continuation is no longer valid
outside of the creating callCC call. So the relationship is more than
just the name.
luke
On Sun, Mar 30, 2008 at 12:04 PM, [EMAIL PROTECTED] wrote:
Would anyone like to explain if callCC in R 2.7.0 gives
anything that on.exit does not already provide?
It seems that the exit condition once defined cannot
be added to overridden whereas with on.exit multiple
on.exit's add additional on.exits rather than being ignored.
Is this important?
It facilitates a completely different style of programming - see
http://en.wikipedia.org/wiki/Continuation-passing_style
--
http://had.co.nz/
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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: [EMAIL PROTECTED]
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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Re: [Rd] callCC in 2.7.0
Thanks. So its intended to jump straight out of deeply nested
calls without having to manage the unwinding.
On Sun, Mar 30, 2008 at 4:22 PM, Luke Tierney [EMAIL PROTECTED] wrote:
On Sun, 30 Mar 2008, Gabor Grothendieck wrote:
Sorry it should be as follows:
fib - function(i, a = 0, b = 1) {
if (i == 0) b else fib(i-1, b, a+b)
}
Now, how do we transform that to use callCC?
On Sun, Mar 30, 2008 at 1:42 PM, Gabor Grothendieck
[EMAIL PROTECTED] wrote:
OK. Can you show code to implement the tail recursive version of
fib using callCC in R, say.
Here it is transformed to tail recursive style:
fib - function(i, a = 0, b = 1) {
if (i == 0) a else fib(i-1, b, a+b)
Now, how do I add callCC to all this so that the fib call
presumably does not create a new stack instance?
What makes you think callCC has anything to contribute here?
The Wikipedia article Hadley cited says that using CPS effectively is
difficult without tail call optimization, which R does not have and
can't, at least not without some restrictions, because the stack is
avialable via sys.xyz functions. It does _not_ say that having
explicit continuations implies having tail call optimization.
If you want to, you can rewrite your fib in CPS, something like
fibCPS - function(k, i, a = 0, b = 1) {
if (i == 0) k(b) else fibCPS(k, i-1, b, a+b)
}
and you can then use callCC to bridge between the nonCPS and CPS
world, e.g. with
fib - function(i) callCC(function(k) fibCPS(k, i, 0, 1))
This will grow the stack just like any other recursion in R. A
(minor) difference compared to your original fib is that the final
exit happens in a single jump rather than a sequence of returns.
The point of adding the current downward-only callCC to R is to
provide a clean, lexically scoped non-local exit mechanism for exiting
from complex, possibly recursive function calls. Dylan provides this
as part of its 'block' construct (also as an exit or continuation
function); Common Lisp has 'block'/'return-from' constructs that use
lexically scoped block name symbols.
For a slightly more realistic example than the ones currently in the
help page: Here is some code that implements a simple binary tree data
structure, and a function that visits the nodes of the tree and calls
a specified function on the value in each node:
mkTree - function(value, left, right)
list(isLeaf = FALSE, value = value, left = left, right = right)
mkLeaf - function(value) list(isLeaf = TRUE, value = value)
visit - function(node, fun) {
if (node$isLeaf) fun(node$value)
else {
visit(node$left, fun)
visit(node$right, fun)
fun(node$value)
}
}
A simple example tree:
x - mkTree(1, mkTree(2, mkLeaf(3), mkLeaf(4)),
mkTree(5, mkLeaf(6), mkLeaf(7)))
You can use visit() to print out the node values with
visit(x, print)
[1] 3
[1] 4
[1] 2
[1] 6
[1] 7
[1] 5
[1] 1
If you want to use a function like visit() to traverse the tree but
want the traversal to stop when some condition is met then you can
either rewrite visit to allow for this, making it more complicated, or
you can use a non-local exit. That is where callCC comes in. To
print all values until you find one equal to 7 you can use
callCC(function(exit) {
+ fun - function(value) {
+ if (value == 7) exit(NULL)
+ else print(value)
+ }
+ visit(x, fun)
+ })
[1] 3
[1] 4
[1] 2
[1] 6
NULL
One can also imagine situations where this might be useful in a
function passed to an optimizer like optim. Given that our 'break'
only breaks out of one loop level, callCC can also be useful for
breaking out of a set of nested loops.
I first wrote this particular version of callCC when prototyping the
tryCatch mechanism in pure R code where one needs a means to jump from
a point where a condition is signaled to the point where the handler
is established. The current tryCatch implementation does things
differently because it needs to integrate with the error handling at
the C level. Currently I use callCC in the constantFold function in
codetools (which is why callCC was added when codetools became
recommended). This use is similar to the tree example.
luke
On Sun, Mar 30, 2008 at 1:31 PM, Luke Tierney [EMAIL PROTECTED] wrote:
On Sun, 30 Mar 2008, Gabor Grothendieck wrote:
I think the only relationship to that is the name since
it does not appear to allow one to leave a function
in the middle of its processing and re-enter it back
at that point -- which is what would be needed.
The article conflates basic CPS with having first class continuations
as in Scheme. The discussion about compilers and tail calls only
requires downward-only continuations of the kind provided by R's
Re: [Rd] cpu usage high with windows change dir / winDialogString (PR#11045)
On Sat, Mar 29, 2008 at 12:06 PM, Duncan Murdoch [EMAIL PROTECTED] wrote: On 28/03/2008 12:05 PM, [EMAIL PROTECTED] wrote: Good afternoon, This is possibly a windows only bug, definitely of comparatively low importance - but for the sake of completeness here we go. I've searched http://bugs.R-project.org/ etc., but can find no mention. For RGui.exe, the CPU usage goes to 100% for certain dialog boxes for the duration that the dialog box is visible, e.g. * check CPU usage is low * On the RGui.exe menu chose File / Change dir... * the CPU usage goes to 100% * hit OK * the CPU usage goes back down again What is the bug here? I'd guess it's not R using the cpu, rather some other process hooked to the dialog, but even if it really is R, why is this a bug? Maybe R is sitting in a loop consuming all the resources of the system? __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] cpu usage high with windows change dir / winDialogString (PR#11045)
On Sat, Mar 29, 2008 at 12:32 PM, Duncan Murdoch [EMAIL PROTECTED] wrote: On 29/03/2008 12:23 PM, Gabor Grothendieck wrote: On Sat, Mar 29, 2008 at 12:06 PM, Duncan Murdoch [EMAIL PROTECTED] wrote: On 28/03/2008 12:05 PM, [EMAIL PROTECTED] wrote: Good afternoon, This is possibly a windows only bug, definitely of comparatively low importance - but for the sake of completeness here we go. I've searched http://bugs.R-project.org/ etc., but can find no mention. For RGui.exe, the CPU usage goes to 100% for certain dialog boxes for the duration that the dialog box is visible, e.g. * check CPU usage is low * On the RGui.exe menu chose File / Change dir... * the CPU usage goes to 100% * hit OK * the CPU usage goes back down again What is the bug here? I'd guess it's not R using the cpu, rather some other process hooked to the dialog, but even if it really is R, why is this a bug? Maybe R is sitting in a loop consuming all the resources of the system? It's a SHBrowseForFolder call, with a callback. If there's a bug, it looks to me as though it's in Windows. Duncan Murdoch I wonder if any of the numerous settings in the _browseinfo structure might be impacting this such as looking for networking folders and if the user's networking setup impacts this since it could start performing some network functions to find files over a network. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] cut.Date and cut.POSIXt problem
cut.Date and cut.POSIXt indicate that the breaks argument can be an integer followed by a space followed by year, etc. but it seems the integer is ignored. For example, I assume that breaks = 3 months is supposed to cut it into quarters but, in fact, it cuts it into months as if 3 had not been there. d - seq(Sys.Date(), length = 12, by = month) cut(d, 3 months) [1] 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 Levels: 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 cut(as.POSIXct(d), 3 months) [1] 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 Levels: 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 cut(as.POSIXlt(d), 3 months) [1] 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 Levels: 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] cut.Date and cut.POSIXt problem
I am using [1] R version 2.6.2 alpha (2008-01-26 r44181) and also get the same under: R version 2.7.0 Under development (unstable) (2008-03-13 r44752) On Tue, Mar 18, 2008 at 2:09 PM, Roger D. Peng [EMAIL PROTECTED] wrote: Seems it did work as advertised in R 2.6.0 but is still broken in R-devel. Will take a look. -roger Gabor Grothendieck wrote: cut.Date and cut.POSIXt indicate that the breaks argument can be an integer followed by a space followed by year, etc. but it seems the integer is ignored. For example, I assume that breaks = 3 months is supposed to cut it into quarters but, in fact, it cuts it into months as if 3 had not been there. d - seq(Sys.Date(), length = 12, by = month) cut(d, 3 months) [1] 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 Levels: 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 cut(as.POSIXct(d), 3 months) [1] 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 Levels: 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 cut(as.POSIXlt(d), 3 months) [1] 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 Levels: 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] cut.Date and cut.POSIXt problem
By the way, it would be nice if the breaks argument accepted the word quarter directly since its quite a common break to need when using dates. On Tue, Mar 18, 2008 at 2:29 PM, Gabor Grothendieck [EMAIL PROTECTED] wrote: I am using [1] R version 2.6.2 alpha (2008-01-26 r44181) and also get the same under: R version 2.7.0 Under development (unstable) (2008-03-13 r44752) On Tue, Mar 18, 2008 at 2:09 PM, Roger D. Peng [EMAIL PROTECTED] wrote: Seems it did work as advertised in R 2.6.0 but is still broken in R-devel. Will take a look. -roger Gabor Grothendieck wrote: cut.Date and cut.POSIXt indicate that the breaks argument can be an integer followed by a space followed by year, etc. but it seems the integer is ignored. For example, I assume that breaks = 3 months is supposed to cut it into quarters but, in fact, it cuts it into months as if 3 had not been there. d - seq(Sys.Date(), length = 12, by = month) cut(d, 3 months) [1] 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 Levels: 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 cut(as.POSIXct(d), 3 months) [1] 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 Levels: 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 cut(as.POSIXlt(d), 3 months) [1] 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 Levels: 2008-03-01 2008-04-01 2008-05-01 2008-06-01 2008-07-01 2008-08-01 2008-09-01 2008-10-01 2008-11-01 2008-12-01 2009-01-01 2009-02-01 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] extract function [ and empty index
Use TRUE. On Sun, Mar 9, 2008 at 5:05 AM, Laurent Gautier [EMAIL PROTECTED] wrote: Dear list, I am having a question regarding the extract function [. The man page says that one usage with k-dimensional arrays is to specify k indices to [, with an empty index indicating that all entries in that dimension are selected. The question is the following: is there an R object qualifying as an empty index ? I understand that the lazy evaluation of parameters allows one to have genuinely missing parameters, but I would like to have an object instead. I understand that one can always have an if/else workaround, but I thought should ask, just in case. I tried with NULL but with little success, as it appears to give the same results as an empty vector. m = matrix(1, 2, 2) m[1, NULL] numeric(0) m[1, integer(0)] numeric(0) Since I was at it, I noted that the result obtained with numeric(0) definitely makes sense but could as well be seen as challenging the concept of an empty index presented in the man page (One could somehow expect the presence of an object meaning everything rather than missingness meaning it). Thanks, Laurent __ 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] add=TRUE in plot.default()
On Sun, Mar 9, 2008 at 6:27 PM, hadley wickham [EMAIL PROTECTED] wrote: Yes. The ability to plot things on top of each other is important. The simplicity created by having a single interface for adding to plots outweighs the complexity of yet another parameter. The add parameter only interacts with other parameters superficially -- some parameters of plot (like log) are related to the shape of the axes, and should be inherited from what is on the plot already. But what about when the new data is outside the range of the current plot? plot/lines/points already works that way so this is just an interface issue. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [patch] add=TRUE in plot.default()
Its not a matter of desirable or not -- its a matter that its a different point. The par(new= ) to get an old graph is completely confusing and its annoying that one has to suddenly switch to lines and points and cannot consistently use plot. That remains true whether or not there is auto expansion. On Sun, Mar 9, 2008 at 7:51 PM, hadley wickham [EMAIL PROTECTED] wrote: But what about when the new data is outside the range of the current plot? plot/lines/points already works that way so this is just an interface issue. That may be the way it is, but I don't see how you could argue that it's desirable behaviour. Hadley -- http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] merging environments
On Fri, Mar 7, 2008 at 3:15 PM, hadley wickham [EMAIL PROTECTED] wrote:
2008/3/7 Ben Bolker [EMAIL PROTECTED]:
Despite the spirited arguments of various R-core folks
who feel that mle() doesn't need a data argument, and
that users would be better off learning to deal with function
closures, I am *still* trying to make such things work
in a reasonably smooth fashion ...
Is there a standard idiom for merging environments?
i.e., suppose a function has an environment that I want
to preserve, but _add_ the contents of a data list --
would something like this do it? Is there a less ugly
way?
x - 0
y - 1
z - 2
f - function() {
x+y+z
}
f2 - function(fun,data) {
L - ls(pos=environment(fun))
mapply(assign,names(data),data,
MoreArgs=list(envir=environment(fun)))
print(ls(pos=environment(fun)))
}
f2(f,list(a=1))
I think you're doomed to be ugly if you don't use closures - I think
any explicit manipulation of environments is worse than the implicit
manipulation by closures.
f - function(data) with(data, x + y + z)
f2 - function(fun, data) function() fun(data)
f2(f, list(x = 10))()
Although it would be even nicer if you could do:
f - function() x + y + z
f2 - function(fun, data) function() with(data, fun())
This last one is close to what you can do with proto and is referred
to as the method of proxies here:
http://r-proto.googlecode.com/files/prototype_approaches.pdf
f - function() x + y + z
f2 - function(fun, ...) with(proto(environment(fun), ..., g = fun), g())
f2(f, x = 1, y = 2, z = 3)
The proto call creates an anonymous proto object whose parent is
the parent of fun. The anonymous proto object contains the ...
arguments to f2 and g.g is just fun with its environment reset to
the anonymous proto object. We then call g.
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Re: [Rd] Warnings generated by log2()/log10() are really large/takes a long time to display
On Wed, Feb 27, 2008 at 5:50 AM, Henrik Bengtsson [EMAIL PROTECTED] wrote:
On Wed, Feb 27, 2008 at 12:56 AM, Prof Brian Ripley
[EMAIL PROTECTED] wrote:
On Wed, 27 Feb 2008, Martin Maechler wrote:
Thank you Henrik,
HenrikB == Henrik Bengtsson [EMAIL PROTECTED]
on Tue, 26 Feb 2008 22:03:24 -0800 writes:
{with many superfluous empty statements ( i.e., trailing ; ):
Indeed!
I like to add a personal touch to the code I'm writing ;)
Seriously, I added them here as a bait in order to get a chance to say
that I finally found a good reason for adding the semicolons. If you
cut'n'paste code from certain web pages it may happen that
newlines/carriage returns are not transferred and all code is pasted
into the same line at the R prompt. With semicolons you still get a
valid syntax. I cannot remember under what conditions this happened -
I have seen that too and many others have as well since in some forums
(not related to R) its common to indent all source lines by two spaces. Any
line appearing without indentation must have been wrapped.
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Re: [Rd] Unix-like touch to update modification timestamp of file?
If you only need Windows then this will do it even without RTools: shell(copy /b /v myfile +,,nul) On Wed, Feb 27, 2008 at 11:12 AM, Earl F. Glynn [EMAIL PROTECTED] wrote: Henrik Bengtsson [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED]... is it possible to update the modification time stamp of a file using R (on file systems supporting it)? For a Windows PC, if you have RTools in your path (from http://www.murdoch-sutherland.com/Rtools/installer.html), then you should be able to use the touch that's in the RTools\bin directory: system(touch sample.dat) efg Earl F. Glynn Bioinformatics Stowers Institute for Medical Research __ 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] how to write dput-able objects
You might want to look at the proto package. proto objects won't
immediately dput either but it would not be hard to convert them to
restorable character strings because the proto methods normally
have their object as their parent environment so its implicit in the
definition. First define a proto object p with one variable 'a' and one
method 'f' and a child object, q, whose 'a' component overrides the
'a' in its parent.
library(proto)
p - proto(a=1, f = function(.) .$a - .$a + 1)
q - p$proto(a = 2)
p$as.list()
$a
[1] 1
$f
function(.) .$a - .$a + 1
environment: 0x01d6e284
name.proto(p)
[1] p
name.proto(p$parent.env())
[1] R_GlobalEnv
q$as.list()
$a
[1] 2
name.proto(q)
[1] q
name.proto(q$parent.env())
[1] p
Note that the strings above have everything
you would need to restore them. We don't
need the environment since we already know that
f's environment must be p as it belongs to p.
On Mon, Feb 25, 2008 at 12:47 PM, Vadim Organovich
[EMAIL PROTECTED] wrote:
Hi,
One way of doing object-oriented programming in R is to use function
environment to hold object's data, see for example
@Article{Rnews:Chambers+Lang:2001a,
author = {John M. Chambers and Duncan Temple Lang},
title= {Object-Oriented Programming in {R}},
journal = {R News},
year= 2001,
volume = 1,
number = 3,
pages= {17--19},
month= {September},
url= http,
pdf= Rnews2001-3
}
One deficiency of this approach is that dput() does not export all data
pertained to the object. For example
objfactory - function(nm) {
+ list(name = function() nm)
+ }
obj - objfactory('foo')
obj$name()
[1] foo
dput(obj)
structure(list(name = function ()
nm), .Names = name)
As one can see the data piece of the obj, nm='foo', is not exported. Is there
a way to modify the original approach so that dput() will produce a
self-sufficient dump of the object?
Thanks,
Vadim
[[alternative HTML version deleted]]
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Re: [Rd] how to write dput-able objects
Try something like this. If ..Name exists in the proto object
it uses that as the name; otherwise, it uses the name.proto()
heuristic to find the name.
library(proto)
dput.proto - function(x, ...) {
y - as.list(x, all = TRUE)
if (!exists(..Name, x)) y$..Name - name.proto(x, parent.frame())
y$.parent.Name - name.proto(parent.env(x), parent.frame())
dput(y, ...)
}
p - proto(a = 1, f = function(.) { .$a - .$a + 1})
q - p$proto(a = 2)
dput.proto(p)
dput.proto(q)
Output:
library(proto)
p - proto(a = 1, f = function(.) { .$a - .$a + 1})
q - p$proto(a = 2)
dput.proto(p)
structure(list(.super = environment, .that = environment,
a = 1, f = function (.)
{
.$a - .$a + 1
}, ..Name = p, .parent.Name = R_GlobalEnv), .Names = c(.super,
.that, a, f, ..Name, .parent.Name))
dput.proto(q)
structure(list(.super = environment, .that = environment,
a = 2, ..Name = q, .parent.Name = p), .Names = c(.super,
.that, a, ..Name, .parent.Name))
On Mon, Feb 25, 2008 at 2:17 PM, Vadim Organovich
[EMAIL PROTECTED] wrote:
Thank you Gabor! This is very close indeed to what I need. If dput() were
generic one could code dput.proto() and that would be it.
Anyway, it is so close to what I need that I should be able to hack someting
to make it work for my purposes. Thanks again!
Vadim
From: Gabor Grothendieck [EMAIL PROTECTED]
Sent: Monday, February 25, 2008 12:16 PM
To: Vadim Organovich
Cc: r-devel@r-project.org
Subject: Re: [Rd] how to write dput-able objects
You might want to look at the proto package. proto objects won't
immediately dput either but it would not be hard to convert them to
restorable character strings because the proto methods normally
have their object as their parent environment so its implicit in the
definition. First define a proto object p with one variable 'a' and one
method 'f' and a child object, q, whose 'a' component overrides the
'a' in its parent.
library(proto)
p - proto(a=1, f = function(.) .$a - .$a + 1)
q - p$proto(a = 2)
p$as.list()
$a
[1] 1
$f
function(.) .$a - .$a + 1
environment: 0x01d6e284
name.proto(p)
[1] p
name.proto(p$parent.env())
[1] R_GlobalEnv
q$as.list()
$a
[1] 2
name.proto(q)
[1] q
name.proto(q$parent.env())
[1] p
Note that the strings above have everything
you would need to restore them. We don't
need the environment since we already know that
f's environment must be p as it belongs to p.
On Mon, Feb 25, 2008 at 12:47 PM, Vadim Organovich
[EMAIL PROTECTED] wrote:
Hi,
One way of doing object-oriented programming in R is to use function
environment to hold object's data, see for example
@Article{Rnews:Chambers+Lang:2001a,
author = {John M. Chambers and Duncan Temple Lang},
title= {Object-Oriented Programming in {R}},
journal = {R News},
year= 2001,
volume = 1,
number = 3,
pages= {17--19},
month= {September},
url= http,
pdf= Rnews2001-3
}
One deficiency of this approach is that dput() does not export all data
pertained to the object. For example
objfactory - function(nm) {
+ list(name = function() nm)
+ }
obj - objfactory('foo')
obj$name()
[1] foo
dput(obj)
structure(list(name = function ()
nm), .Names = name)
As one can see the data piece of the obj, nm='foo', is not exported. Is
there a way to modify the original approach so that dput() will produce a
self-sufficient dump of the object?
Thanks,
Vadim
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Re: [Rd] Aliasing a function
formals can be used like this: f - g formals(f) - pairlist(a=1,b=2,c=3) On Sat, Feb 23, 2008 at 5:40 PM, hadley wickham [EMAIL PROTECTED] wrote: A simple way to alias a function is to do : g - function(a = 1, b = 2, c = 3) a + b * c f - function(...) g(...) but formals (etc) is no longer very helpful. Is there an easy way to programmatically create: f - function(a=1, b=2, c=3) g(a=a, b=b, c=c) This comes up in ggplot2 where I alias many functions to hide the fact that I'm using proto in the background, and I'd like the aliased functions to be a little more user friendly in terms of revealing what are valid arguments (and also to match up with the rdoc files which I am building). Any ideas? Thanks, Hadley -- http://had.co.nz/ __ 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] Aliasing a function
I assume he wants to be able to change the formals although its confusing since the example uses the same formals in both cases. On Sat, Feb 23, 2008 at 6:32 PM, John Fox [EMAIL PROTECTED] wrote: Dear Hadley, Why not just f - g ? Regards, John John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario, Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] project.org] On Behalf Of hadley wickham Sent: February-23-08 5:40 PM To: R-devel Subject: [Rd] Aliasing a function A simple way to alias a function is to do : g - function(a = 1, b = 2, c = 3) a + b * c f - function(...) g(...) but formals (etc) is no longer very helpful. Is there an easy way to programmatically create: f - function(a=1, b=2, c=3) g(a=a, b=b, c=c) This comes up in ggplot2 where I alias many functions to hide the fact that I'm using proto in the background, and I'd like the aliased functions to be a little more user friendly in terms of revealing what are valid arguments (and also to match up with the rdoc files which I am building). Any ideas? Thanks, Hadley -- http://had.co.nz/ __ 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
[Rd] NEWS and ChangeLog in available.packages()
With the newly available NEWS and ChangeLog links on the CRAN pages for packages it would be nice if available.packages() gave information on those. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] NEWS and ChangeLog in available.packages()
On Feb 18, 2008 11:59 AM, Martin Maechler [EMAIL PROTECTED] wrote: GaGr == Gabor Grothendieck [EMAIL PROTECTED] on Mon, 18 Feb 2008 10:19:05 -0500 writes: GaGr With the newly available NEWS and ChangeLog links on GaGr the CRAN pages for packages it would be nice if GaGr available.packages() gave information on those. how would you propose? It returns a character matrix, and that probably should not be changed. Currently the Depends (and Imports, Contains and Suggests) are character strings containing components to form one large string so maybe there could be a Docs whose substrings could include NEWS, ChangeLog and the vignette and demo names or maybe separate ones for NEWS/ChangeLog, vignettes and demos. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Arithmetic bug? (found when use POSIXct) (PR#10776)
OK. Good point. Note that that article was written 4 years ago when R was at version 1.9 and POSIXt did not fully support subseconds. At that time, POSIXct could represent subseconds internally but it was not used as POSIXlt did not yet support it and that and the associated digits.sec option did not come until R version 2.3, released two years after the article was written. Try setting the digits.secs option before you run the command like this: options(digits.secs = 3) dp - Sys.time() dp-as.POSIXct(format(dp,tz=GMT)) Time difference of -5 hours On Feb 17, 2008 3:50 PM, [EMAIL PROTECTED] wrote: Hi Gabo, FAQ 7.31 does not apply to this. numeric in R is 64bit which is large eno= ugh to handle this. I figured out the cause is that Sys.time() gives millisecond value while b-as.POSIXct(format(a,tz=3DGMT)) cuts off that part.=20 Then of course a-b is not 5 hours! Do it again with options(digits=3D22) and you will see what actually happ= ened there. The recommended code from R News is not aware the truth that POSIXlt can re= present sub-second time. Cheers, B _ Helping your favorite cause is as easy as instant messaging.=A0You IM, we g= ive. [[alternative HTML version deleted]] __ 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] Arithmetic bug? (found when use POSIXct) (PR#10776)
See FAQ 7.31 or explain what you believe to be the problem. On Feb 16, 2008 1:05 PM, [EMAIL PROTECTED] wrote: Full_Name: Bo Zhou Version: 2.6.1 (2007-11-26) OS: Windows XP Submission from: (NULL) (207.237.54.242) Hi, I found an arithmetic problem when I'm doing something with POSIXct The code to reproduce it is as follows (This is the recommended way of finding out time zone difference on R News 2004-1 Page 32 URL http://cran.r-project.org/doc/Rnews/Rnews_2004-1.pdf) a=Sys.time() b-as.POSIXct(format(a,tz=GMT)) a-b unclass(a) unclass(b) unclass(a)-unclass(b) as.numeric(a) as.numeric(b) as.numeric(a)-as.numeric(b) The result on my machine a=Sys.time() b-as.POSIXct(format(a,tz=GMT)) a-b Time difference of -4.69 hours unclass(a) [1] 1203184447 unclass(b) [1] 1203202447 attr(,tzone) [1] unclass(a)-unclass(b) [1] -17999.89 attr(,tzone) [1] as.numeric(a) [1] 1203184447 as.numeric(b) [1] 1203202447 as.numeric(a)-as.numeric(b) [1] -17999.89 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] assigning NULLs to elements of a list
But what about by name? a - list(a = 1, b = 2, c = 3) a$b - NULL On Feb 13, 2008 9:39 AM, Oleg Sklyar [EMAIL PROTECTED] wrote: Hmm, I think the pretty traditional R style does the job... a = list(1,2,3) a[-2] So I really do not see a good reason for doing a[2] = NULL instead of a = a[-2] Jeffrey J. Hallman wrote: From your tone, I gather you don't much like this behavior, and I can see your point, as it not very intuitive that setting a list element to NULL deletes any existing element at that index. But is there a better way to delete an element from a list? Maybe there should be. Jeff Prof Brian Ripley [EMAIL PROTECTED] writes: I have just came across an (unexpected to me) behaviour of lists when assigning NULLs to list elements. I understand that a NULL is a valid R object, thus assigning a NULL to a list element should yield exactly the same result as assigning any other object. So I was surprised when assigning a NULL in fact removed the element from the list. Is this an intended behaviour? If so, does anybody know where is it documented and what is a good way around? Yes, it was apparently intended: R has long done this. x - list(a=c(1L,2L), b=matrix(runif(4),2,2), c=LETTERS[1:3]) x[2] - list(NULL) is what I think you are intending. See e.g. the comment in subassign.c /* If val is NULL, this is an element deletion */ /* if there is a match to nlist otherwise x */ /* is unchanged. The attributes need adjustment. */ -- Dr Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-494466 __ 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] lm with factors for which only one level occurs
Consider the following: lm(conc ~ Type, CO2, subset = Plant == Quebec) Error in `contrasts-`(`*tmp*`, value = contr.treatment) : contrasts can be applied only to factors with 2 or more levels Here Type is a factor for which only one level occurs within the Quebec subset. This is something that one would think would be possible to handle in lm. (Note that singular.ok = TRUE is the default.) I came across this when automatically performing lm's on the levels of a conditioning variable, such as Plant in the above example, and found I had to unexpectedly special case situations like the above. lmList() in lme4 is likely adversely affected by this as well. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Choosing CRAN Mirror in Windows GUI
When you choose the CRAN Mirror in the Windows GUI Packages menu in R version 2.6.2 alpha (2008-01-26 r44181) the first mirror is highlighted when you open it even if the mirror had been set. If the mirror had previously been set then that previously set mirror should be highlighted rather than the first mirror. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] a != a*1 != a+0 != +a
I don't think global options are desirable.
I would make your operators work in a single way and if the user
wants a different way he can call whatever functions you provide
directly instead of using the operators.
If you really need two ways with operators I would define a subclass
with operators working in the alternative way and have as.whatever
methods that converts back and forth.
Another possibility is to have the way it works be a special
attribute of the object itself (other than class).
On Feb 4, 2008 9:25 AM, Robin Hankin [EMAIL PROTECTED] wrote:
hits=1.0 tests=MANY_EXCLAMATIONS
X-USF-Spam-Flag: NO
Hi
I am writing a package for multivariate polynomials ('multipols')
using S3 methods.
The package includes a Ops.multipol() function for the
arithmetic methods; I would like
to define some sort of user-specified Boolean option which, if
set, would force results to be simplified as they are produced.
Call this option trim. Trimming a multipol results in
a smaller array that is more manageable.
Mostly one wants to trim, sometimes not.
Would options() be a good way to manage this?
One issue is the behaviour of unary operators + and -.
If trim is TRUE, then a is one thing, but +a returns
trim(a), which might be different.
Also 1*a would be different from a and a+0
Does the List consider this to be Good Practice?
Has anyone got comments?
--
Robin Hankin
Uncertainty Analyst and Neutral Theorist,
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
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Re: [Rd] Pb with lapply()
The problem of promises not being evaluated in
lists has been discussed before.
I think its fixed in the development version of R. See
r44139 on Jan 24, 2008 in http://developer.r-project.org/R.svnlog.2007
On Jan 31, 2008 1:26 PM, [EMAIL PROTECTED] wrote:
Hi,
If needed, lapply() tries to convert its first argument into a list
before it starts doing something with it:
lapply
function (X, FUN, ...)
{
FUN - match.fun(FUN)
if (!is.vector(X) || is.object(X))
X - as.list(X)
.Internal(lapply(X, FUN))
}
But in practice, things don't always seem to work as suggested by
this code (at least to the eyes of a naive user).
I have defined an as.list method for my S4 class A:
setClass(A, representation(data=list))
[1] A
setMethod(as.list, A, function(x, ...) [EMAIL PROTECTED])
Creating a new generic function for as.list in .GlobalEnv
[1] as.list
Testing it:
a - new(A, data=list(8, 2:0))
as.list(a)
[[1]]
[1] 8
[[2]]
[1] 2 1 0
OK.
But lapply() doesn't work on 'a':
lapply(a, typeof)
Error in as.vector(x, list) : cannot type 'S4' coerce to vector
I still have to do the 'as.list(a)' part myself for things to work:
lapply(as.list(a), typeof)
[[1]]
[1] double
[[2]]
[1] integer
Seems like using force() inside lapply() would solve the problem:
lapply2 - function(X, FUN, ...)
{
FUN - match.fun(FUN)
if (!is.vector(X) || is.object(X))
X - force(as.list(X))
.Internal(lapply(X, FUN))
}
It works now:
lapply2(a, typeof)
[[1]]
[1] double
[[2]]
[1] integer
Cheers,
H.
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Re: [Rd] Pb with lapply()
I just checked and the code that previously triggered the promises in lists bug seems to work now so I guess it is a different problem. # code below previously triggered errors but now works # R 2.6.2 (2008-01-26 r44181) on Vista f - function(x) environment() z - as.list(f(7)) dput(z) structure(list(x = 7), .Names = x) z[[1]] == 7 force(z[[1]]) == 7 On Jan 31, 2008 2:33 PM, [EMAIL PROTECTED] wrote: Hi Gabor, Quoting Gabor Grothendieck [EMAIL PROTECTED]: The problem of promises not being evaluated in lists has been discussed before. I think its fixed in the development version of R. See r44139 on Jan 24, 2008 in http://developer.r-project.org/R.svnlog.2007 I'm using R-devel r44238 and the problem is still here. Cheers, H. sessionInfo() R version 2.7.0 Under development (unstable) (2008-01-29 r44238) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Feature request: about lag(), which.min() and cat().
On Jan 31, 2008 8:24 AM, Matthieu Stigler [EMAIL PROTECTED] wrote: lag() If one wants to construct a time series model, it is often useful to have the lags matrix. This is available with embed(ts,k) but the time series class disappears. So it would be nice that the argument k of lag() also admit values of length 1, which would give the same result as embed() but keep the class. In his wish list of 1 January 2008 (point 8), Gabor Grothendieck spoke about a function Lag. Maybe also a function lags otherwise if the idea of length(k)1 is not good? It would be nice. Note that lag.zoo in the zoo package does supports this for zoo objects. library(zoo) z - zoo((11:20)^2) lag(z, 1:2) lag1 lag2 1 144 169 2 169 196 3 196 225 4 225 256 5 256 289 6 289 324 7 324 361 8 361 400 9 400 NA # regress z on lag(z, 1:2) using dyn package library(dyn) dyn$lm(z ~ lag(z, 1:2)) Call: lm(formula = dyn(z ~ lag(z, 1:2))) Coefficients: (Intercept) lag(z, 1:2)1 lag(z, 1:2)2 2 2-1 # as a workaround one could convert to zoo and back x - ts((11:20)^2) as.ts(lag(as.zoo(x), 1:2)) Time Series: Start = 1 End = 9 Frequency = 1 lag1 lag2 1 144 169 2 169 196 3 196 225 4 225 256 5 256 289 6 289 324 7 324 361 8 361 400 9 400 NA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [wishlist, patch] Removing .bzr/ directory when calling R CMD build (PR#10625)
If you place an .Rbuildignore file in the top level of your package with this line single line as its contents: [.]bzr$ then the .bzr file will not be included. On Jan 23, 2008 1:45 PM, [EMAIL PROTECTED] wrote: Full_Name: Ben Goodrich Version: 2.6.1 OS: Debian Submission from: (NULL) (128.103.222.166) bzr is another version control system and adds a .bzr folder to the top-level directory of a package, similar to .svn and .git for subversion and git respectively. However, while R CMD build removes directories called .svn, .git, and some others, it does not remove .bzr . As a result, the .bzr folder is unnecessarily included in the cleanly built package and there are accurate but unnecessary warnings that say certain subdirectories of the .bzr directory are empty. I believe the following patch, which is lightly tested with R-devel, is sufficient to remove the .bzr folder and prevent these warnings. It does not, however, remove the .bzrignore file (if it exists) but perhaps it should be augmented to do so. --- src/scripts/build.in2008-01-23 11:42:47.0 -0500 +++ build.in2008-01-23 11:45:02.0 -0500 @@ -215,6 +215,7 @@ print EXCLUDE $File::Find::name\n if(-d $_ /^\.svn$/); print EXCLUDE $File::Find::name\n if(-d $_ /^\.arch-ids$/); print EXCLUDE $File::Find::name\n if(-d $_ /^\.git$/); + print EXCLUDE $File::Find::name\n if(-d $_ /^\.bzr$/); ## Windows DLL resource file push(@exclude_patterns, ^src/ . $pkgname . _res\\.rc); my $filename = $File::Find::name; __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [wishlist, patch] Removing .bzr/ directory when calling R CMD build (PR#10625)
On Jan 23, 2008 2:23 PM, Ben Goodrich [EMAIL PROTECTED] wrote: Gabor Grothendieck wrote: If you place an .Rbuildignore file in the top level of your package with this line single line as its contents: [.]bzr$ then the .bzr file will not be included. Thank you for the suggestion. In order to remove both the .bzr/ directory and the .bzrignore file, it seems to be necessary to specify [.]bzr$ [.]bzrignore or perhaps [.]bzr.* __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] seekViewport error
On Jan 23, 2008 9:38 PM, Paul Murrell [EMAIL PROTECTED] wrote: Hi Gabor Grothendieck wrote: Why does the seekViewport at the bottom give an error? Because the viewport is popped after GRID.cellGrob.84 is drawn. grid.ls() shows the viewport because it recurses down into the legend frame grob. Compare your output with (grid-generated numbering differs) ... grid.ls(recurs=FALSE, view=TRUE) ROOT GRID.rect.28 plot1.toplevel.vp plot1.xlab.vp plot1.xlab 1 plot1.ylab.vp plot1.ylab 1 plot1.strip.1.1.off.vp GRID.segments.29 1 plot1.strip.left.1.1.off.vp GRID.segments.30 GRID.text.31 1 plot1.panel.1.1.off.vp GRID.segments.32 GRID.text.33 GRID.segments.34 1 plot1.panel.1.1.vp GRID.points.35 GRID.points.36 GRID.points.37 1 plot1.panel.1.1.off.vp GRID.rect.38 1 plot1.legend.top.vp GRID.frame.9 1 plot1. 1 1 If you look at what viewports are actually available, via current.vpTree(), you'll see that GRID.VP.24 is not there. The problem (see also https://stat.ethz.ch/pipermail/r-help/2008-January/151655.html) is that cellGrobs (children of frame grobs) use their 'vp' component to store the viewport that positions them within the parent frame. This means that the viewport is pushed and then popped (as per normal behaviour for 'vp' components). A possible solution that I am currently trialling uses a special 'cellvp' slot instead so that the cellGrob viewports are pushed and then upped. That way they remain available after the cellGrob has drawn, so you can downViewport() to them. The disadvantage of this approach is that the viewports no longer appear in the grid.ls() listing (because grid.ls() has no way of knowing about special components of grobs that contain viewports). This effect can already be seen by the fact that the viewport for the frame grob (GRID.frame.70) is not shown in the grid.ls() output. On the other hand, the viewports will be visible via current.vpTree() ... Perhaps some convention could be adopted which, if followed, would let grid.ls know? If that worked at least for graphics generated from lattice and ggplot2 that would likely satisfy a significant percentage of uses. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] experiments with slot functions and possible problems NOTE
If the intention is to place fList's contents in the global environment
then you need to specify that in addtoenv or else it assumes
the parent environment.
flistA - list(foo = function () 1:10, bar = function() log(foo()))
makefun - function(fList) addtoenv(fList, .GlobalEnv)
makefun(flistA)
$foo
function() {
1:10
}
$bar
function() {
log(foo())
}
foo()
[1] 1 2 3 4 5 6 7 8 9 10
bar()
[1] 0.000 0.6931472 1.0986123 1.3862944 1.6094379 1.7917595 1.9459101
[8] 2.0794415 2.1972246 2.3025851
Note that this takes advantage of the fact that in your example flistA was
defined in the global environment in the first place. Had that not been the
case we would have had to reset the environment of bar so that it could
find foo.
By the way. What about just attach(flistA) ?
On Jan 21, 2008 8:30 AM, Thomas Petzoldt [EMAIL PROTECTED] wrote:
Hello,
first of all, thanks to LT for \pkg{codeutils}. I agree that it is
indeed very useful to identify errors and also to encourage re-thinking
past solutions. My problem:
I want to compare different sets of related sub-functions which should
be used alternatively by the same top-level function. Sets of related
functions should be bound together (as lists) and the workspace should
be as clean as possible.
Finally, these functions are to be called by top-level functions that
work with such sets.
What's the best way to do this?
- clutter the workspace with lots of functions?
OR:
- ignore notes about possible problems
OR:
- a third way?
Thanks in advance
Thomas P.
An example:
##=
## 1) One possible set of functions
flistA - list(
foo = function() {
1:10
},
bar = function() {
log(foo())
}
)
## .. we may also have alternative sets,
##e.g. flistB, flistC, ... etc
## 2) Now we try to construct closures
## 2a) non-nested
makefun1 - function(flist) {
with(flist,
function() foo()
)
}
## 2b) nested call
makefun2 - function(flist) {
with(flist,
function() bar()
)
}
## 2c) or use an alternative way with a special function
## addtoenv, suggested by Gabor Grothendieck some times ago:
addtoenv - function(L, p = parent.frame()) {
for(nm in names(L)) {
assign(nm, L[[nm]], p)
environment(p[[nm]]) - p
}
L
}
makefun3 - function(flist) {
addtoenv(flist)
function() bar()
}
## 3) now we create the top-level functions
##with one particular set of functions
m1 - makefun1(flistA)
m2 - makefun2(flistA)
m3 - makefun3(flistA)
m1()
## this was no problem, trivial
m2()
# Error in bar() : could not find function foo
m3()
# works, but even in that case we get problems
# if we do this in a package:
# * checking R code for possible problems ... NOTE
# bar: no visible global function definition for 'foo'
## tested with R version 2.6.1 and
## R 2.7.0 Under development, svn rev. 44061
--
Thomas Petzoldt
Technische Universitaet Dresden
Institut fuer Hydrobiologie
01062 Dresden
GERMANY
http://tu-dresden.de/Members/thomas.petzoldt
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Re: [Rd] Great tool
Tracking down the free variables in a function when reworking old code. On Jan 21, 2008 12:41 PM, Charles C. Berry [EMAIL PROTECTED] wrote: On Sun, 20 Jan 2008, Gabor Grothendieck wrote: I agree. Its incredibly useful. OK gentlemen, you have piqued my curiosity. Can you give an example or two of situations you encountered in which a codetools function was so helpful? Chuck On Jan 20, 2008 11:02 PM, Henrik Bengtsson [EMAIL PROTECTED] wrote: Hi, I just have drop a note to say that the 'codetools' (and the part of R CMD check that use it) is a pleasure to use and saves me from hours of troubleshooting. Each time it finds something I am amazed how accurate it is. Thanks to Luke T. and everyone else involved in creating it. Cheers, Henrik __ 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 Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Updating library
Thanks. That did it. On Jan 19, 2008 2:19 AM, Prof Brian Ripley [EMAIL PROTECTED] wrote: You need to use 'Run as admininistrator' for just the session updating those packages (assuming you installed R with administrator privileges and are running it without: you did not say). This is covered in rw-FAQ Q2.24. On Fri, 18 Jan 2008, Gabor Grothendieck wrote: On Vista my R installation is in C:\Program Files\R\R-2.6.0 and there is a library here: %userprofile%\Documents\R\win-library\2.6 If I use the GUI Packages menu to update my library it works ok _except_ for any packages such as lattice and the VR bundle that come with R. For those I get this (this is what I got when I tried to update lattice but I get a similar message for the VR bundle as well): update.packages(ask='graphics') --- Please select a CRAN mirror for use in this session --- Warning in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : 'lib = C:/PROGRA~1/R/R-26~1.0/library' is not writable Error in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : unable to install packages I am using R-2.6.1 (even though the directory says 2.6.0) since I tend to write over the prior directory if its just an upgrade involving the last digit of the R version. R.version.string [1] R version 2.6.1 Patched (2007-12-06 r43610) How should I go about updating lattice and the VR bundle? __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, [EMAIL PROTECTED] 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] Updating library
Ideally one could just choose the packages | update menu and it would just work. Possibilities include updating packages into the private library if they otherwise fail to install or providing an error message on what to do. On Jan 19, 2008 9:13 AM, Uwe Ligges [EMAIL PROTECTED] wrote: hits=-2.6 tests=BAYES_00 X-USF-Spam-Flag: NO Peter Dalgaard wrote: Prof Brian Ripley wrote: You need to use 'Run as admininistrator' for just the session updating those packages (assuming you installed R with administrator privileges and are running it without: you did not say). This is covered in rw-FAQ Q2.24. I only have WINE to hand here and package installation doesn't quite work there, but shouldn't it also work in the absense of administrative privileges to just install lattice and VR into your private win-library and update them there? Sure, but that works. What Gabor reported is that updating lattice/VR and co did not succeed. And it did not, because it was installed in R's default library (which can only be updated with administrator privileges in his case, we guess). Gabor could install lattice/VR into his private library and after that updating will succeed. Best, uwe -p On Fri, 18 Jan 2008, Gabor Grothendieck wrote: On Vista my R installation is in C:\Program Files\R\R-2.6.0 and there is a library here: %userprofile%\Documents\R\win-library\2.6 If I use the GUI Packages menu to update my library it works ok _except_ for any packages such as lattice and the VR bundle that come with R. For those I get this (this is what I got when I tried to update lattice but I get a similar message for the VR bundle as well): update.packages(ask='graphics') --- Please select a CRAN mirror for use in this session --- Warning in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : 'lib = C:/PROGRA~1/R/R-26~1.0/library' is not writable Error in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : unable to install packages I am using R-2.6.1 (even though the directory says 2.6.0) since I tend to write over the prior directory if its just an upgrade involving the last digit of the R version. R.version.string [1] R version 2.6.1 Patched (2007-12-06 r43610) How should I go about updating lattice and the VR bundle? __ 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
[Rd] Updating library
On Vista my R installation is in C:\Program Files\R\R-2.6.0 and there is a library here: %userprofile%\Documents\R\win-library\2.6 If I use the GUI Packages menu to update my library it works ok _except_ for any packages such as lattice and the VR bundle that come with R. For those I get this (this is what I got when I tried to update lattice but I get a similar message for the VR bundle as well): update.packages(ask='graphics') --- Please select a CRAN mirror for use in this session --- Warning in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : 'lib = C:/PROGRA~1/R/R-26~1.0/library' is not writable Error in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : unable to install packages I am using R-2.6.1 (even though the directory says 2.6.0) since I tend to write over the prior directory if its just an upgrade involving the last digit of the R version. R.version.string [1] R version 2.6.1 Patched (2007-12-06 r43610) How should I go about updating lattice and the VR bundle? __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] as.function()
On Jan 14, 2008 6:50 AM, Duncan Murdoch [EMAIL PROTECTED] wrote:
Robin Hankin wrote:
Hi
[this after some considerable thought as to R-help vs R-devel]
I want to write a (S3) method for as.function();
toy example follows.
Given a matrix a, I need to evaluate trace(ax) as a function of
(matrix) x.
Here's a trace function:
tr - function (a) {
i - seq_len(nrow(a))
return(sum(a[cbind(i, i)]))
}
How do I accomplish the following:
a - crossprod(matrix(rnorm(12),ncol=3))
class(a) - foo
f - as.function(a) # need help to write as.function.foo()
x - diag(3)
f(x) #should give tr(ax)
a - 4
f(x) # should still give tr(ax) even though a has been
reassigned.
Brian's answer was what you want. A less general version is this:
as.function.foo - function(x, ...) {
+function(b) tr(x %*% b)
+ }
This can also be done using the proto package. p has two
components b and f. q inherits f from p but has its own b.
library(proto)
p - proto(b = 1:4, f = function(., x) sum(diag(x %*% .$b)))
q - p$proto(b = 5:8)
p$f(1:4)
q$f(1:4)
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Re: [Rd] as.function()
The gsubfn package can do something like that too. If you
preface a function with fn$ then it will interpret certain formula
arguments as functions. If all we want is the function itself we
can use force, the identity function, to recover it:
library(gsubfn)
fn$force(~ 2*x + 3*y^2)
function (x, y)
2 * x + 3 * y^2
If there are free variables in the formula that you don't want to
include in the argument list the left hand side can be used to
specify the argument list:
fn$force(x + y ~ 2*x + a*y^2)
function (x, y)
2 * x + a * y^2
On Jan 14, 2008 1:05 PM, Tony Plate [EMAIL PROTECTED] wrote:
How about this as a version that automatically constructs the argument
list (and make into a method for as.function as appropriate)?
makefun - function(expr)
{
f - function() {}
body(f) - expr
vars - all.vars(expr)
if (length(vars)) {
args - alist(x=)[rep(1,length(vars))]
names(args) - vars
formals(f) - args
}
environment(f) - globalenv()
return(f)
}
makefun(expression(2*x + 3*y^2))
function (x, y)
2 * x + 3 * y^2
makefun(expression(2*x + 3*y^2 - z))
function (x, y, z)
2 * x + 3 * y^2 - z
makefun(expression(p1 + p2))
function (p1, p2)
p1 + p2
-- Tony Plate
Henrique Dallazuanna wrote:
Try this:
as.function.foo - function(obj, ...)
{
newobj - function(x, ...){}
body(newobj) - obj
return(newobj)
}
x - expression(2*x + 3*x^2)
foo - as.function.foo(x)
foo(2)
Hope this help
On 14/01/2008, Robin Hankin [EMAIL PROTECTED] wrote:
Antonio
thanks for your help here, but it doesn't answer my question.
Perhaps if I outline my motivation it would help.
I want to recreate the ability of
the polynom package to do the following:
library(polynom)
p - polynomial(1:4)
p
1 + 2*x + 3*x^2 + 4*x^3
MySpecialFunction - as.function(p)
MySpecialFunction(1:10)
[1] 10 49 142 313 586 985 1534 2257 3178 4321
p - 4
MySpecialFunction(1:10)
[1] 10 49 142 313 586 985 1534 2257 3178 4321
See how the user can define object MySpecialFunction,
which outlives short-lived polynomial p.
Unfortunately, I don't see a way to modify as.function.polynomial()
to do what I want.
best wishes
rksh
On 14 Jan 2008, at 08:45, Antonio, Fabio Di Narzo wrote:
2008/1/14, Robin Hankin [EMAIL PROTECTED]:
Hi
[this after some considerable thought as to R-help vs R-devel]
I want to write a (S3) method for as.function();
toy example follows.
Given a matrix a, I need to evaluate trace(ax) as a function of
(matrix) x.
Here's a trace function:
tr - function (a) {
i - seq_len(nrow(a))
return(sum(a[cbind(i, i)]))
}
How do I accomplish the following:
a - crossprod(matrix(rnorm(12),ncol=3))
class(a) - foo
f - as.function(a) # need help to write as.function.foo()
x - diag(3)
f(x) #should give tr(ax)
What about the following?
as.function.foo - function(a, ...)
function(x)
sum(diag(a*x))
However, I don't see the need for an S3 method. Why don't simply use
(?):
mulTraceFun - function(a)
function(x)
sum(diag(a*x))
So you also have a more meaningful name than an anonymous
'as.function'.
HTH,
Antonio.
a - 4
f(x) # should still give tr(ax) even though a has been
reassigned.
This would'nt work with my proposal, because of lexical scoping.
[my real example is very much more complicated than this but
I need this toy one too and I can't see how to modify
as.function.polynomial()
to do what I want]
--
Robin Hankin
Uncertainty Analyst and Neutral Theorist,
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
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--
Antonio, Fabio Di Narzo
Ph.D. student at
Department of Statistical Sciences
University of Bologna, Italy
--
Robin Hankin
Uncertainty Analyst and Neutral Theorist,
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
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Re: [Rd] R Bugs link broken
With the dash it goes to section 9.1 entitled R Bugs but with the %20 it goes to the top. It should go to 9.1; however, it looks likes someone fixed it since I posted. On Jan 9, 2008 11:54 AM, Gabor Grothendieck [EMAIL PROTECTED] wrote: The link to R Bugs in the posting guide http://www.r-project.org/posting-guide.html is broken. The - that should be in the link: http://cran.r-project.org/doc/FAQ/R-FAQ.html#R-Bugs is currently %20: http://cran.r-project.org/doc/FAQ/R-FAQ.html#R%20Bugs __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R Bugs link broken
The link to R Bugs in the posting guide http://www.r-project.org/posting-guide.html is broken. The - that should be in the link: http://cran.r-project.org/doc/FAQ/R-FAQ.html#R-Bugs is currently %20: http://cran.r-project.org/doc/FAQ/R-FAQ.html#R%20Bugs __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] read.table: aborting based on a time constraint
That was supposed to be file.info()$size
On Jan 9, 2008 3:27 PM, Gabor Grothendieck [EMAIL PROTECTED] wrote:
Use file.file()$size to find out how large the file is
and skip files larger than some cutoff.
On Jan 9, 2008 2:01 PM, Derek Stephen Elmerick [EMAIL PROTECTED] wrote:
Hello –
I am trying to write code that will read in multiple datasets;
however, I would like to skip any dataset where the read-in process
takes longer than some fixed cutoff. A generic version of the function
is the following:
for(k in 1:number.of.datasets)
{
X[k]=read.table(…)
}
The issue is that I cannot find a way to embed logic that will abort
the read-in process of a specific dataset without manual intervention.
I scanned the help manual and other postings, but no luck based on my
search. Any thoughts?
Thanks,
Derek
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Re: [Rd] nls (with SSlogis model and upper limit) never returns (PR#10544)
On my Windows Vista system it returns an answer: values - list(x=10:30, y=c(23.85, 28.805, 28.195, 26.23, 25.005, 20.475, + 17.33, 14.97, 11.765, 8.857, 5.3725, 5.16, 4.2105, 2.929, 2.174, 1.25, 1.0255, + 0.612, 0.556, 0.4025, 0.173)) y.max - max(values$y) model - nls(y ~ SSlogis(x, asym, xmid, scal), data=values, algorithm=port, + start=c(asym=y.max, xmid=15, scal=-0.5), upper=c(y.max, Inf, Inf)) model Nonlinear regression model model: y ~ SSlogis(x, asym, xmid, scal) data: values asym xmid scal 28.805 17.268 -2.223 residual sum-of-squares: 32.02 Algorithm port, convergence message: relative convergence (4) R.version.string # Vista [1] R version 2.6.1 Patched (2007-12-06 r43610) On Jan 4, 2008 9:45 AM, [EMAIL PROTECTED] wrote: Full_Name: Hendrik Weisser Version: 2.6.1 OS: Linux Submission from: (NULL) (139.19.102.218) The following computation never finishes and locks R up: values - list(x=10:30, y=c(23.85, 28.805, 28.195, 26.23, 25.005, 20.475, 17.33, 14.97, 11.765, 8.857, 5.3725, 5.16, 4.2105, 2.929, 2.174, 1.25, 1.0255, 0.612, 0.556, 0.4025, 0.173)) y.max - max(values$y) model - nls(y ~ SSlogis(x, asym, xmid, scal), data=values, algorithm=port, start=c(asym=y.max, xmid=15, scal=-0.5), upper=c(y.max, Inf, Inf)) This used to work with R version 2.5.1 patched. The problem does _not_ occur if the parameter scal=-0.5 in the nls call is changed, e. g. to scal=-0.6 or scal=-0.4. Simply calling model - nls(y ~ SSlogis(x, asym, xmid, scal), data=values) also works, but this does not use the upper bound for the asym parameter, which was the point. __ 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] Typo in DateTimeClasses.Rd
In:
trunk/src/library/base/man/DateTimeClasses.Rd
this:
\section{Sub-section Accuracy}{
should be
\section{Sub-second Accuracy}{
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[Rd] Wish List
Most of the items on this list have been mentioned before but it may be useful to see them altogether and at any rate every year I have posted my R wishlist at the beginning of the year. High priority items pertain to the foundations of R (promises, environments) since those form the basis of everything else and the foundation needs to be looked after first. The medium items are focused on scripting since with a few additional features R could work more smoothly with other software. For the Low priority items we listed the rest. They are not necessarily low in terms of desirability but I wanted to focus the high and medium items on foundations and scripting. There is also a section at the end focusing on addon packages. These may be strictly speaking part of R but are widely used. High 1. Some way of inspecting promises. It is possible to get the expression associated with a promise using substitute but not its environment. Also need a way to copy a promise without forcing it. See: https://stat.ethz.ch/pipermail/r-devel/2007-September/046966.html 2. Fix bug when promises are stored in lists: f - function(x) environment() as.list(f(0))$x == 0 # gives error. Should be TRUE. 3. If a package uses LazyLoad: true then R changes the class of certain top level objects. This does not occur if Lazyload: false is used. For an example see: https://stat.ethz.ch/pipermail/r-devel/2007-October/047118.html 4. If two environment variables point to the same environment they cannot have different attributes. This effectively thwarts subclassing of environments (contrary to OO principles). Medium 5. Sweave. A common scanario is spawning a Sweave job from another program (such as from a program controlling a web site). The caller needs to pass some information to the Sweave program such as the file name of a report to produce. Its possible to spawn R and have R spawn sweave but given the existence of R CMD Sweave it would be nice to be able to just spawn R CMD Sweave directly. Features that would help here would be: - support --args or some other method of passing arguments from R CMD Sweave line to the Sweave script - have a facility whereby R CMD Sweave can directly generate the .pdf file and an argument which allows the caller to define the name of the resulting pdf file, e.g. -o. (With automated reports one may need to have many different outputs from the same Rnw file so its important to name them differently.) - an -x argument similar to Perl/Python/Ruby such that if one calls R CMD Sweave -x abc myfile.Rnw then all lines up to the first one matching the indicated regexp, abc here, are skipped. This facilitates combining the script with a shell or batch file if the previous is not enough. Thus one could spawn this from their program: R CMD Sweave --pdf myfile.Rnw -o myfile-123.pdf --args 23 and it would generate a pdf file from myfile.Rnw of the indicated name passing 23 as arg1 to the R code embedded in the Sweave file. See: https://stat.ethz.ch/pipermail/r-devel/2007-October/047195.html https://stat.ethz.ch/pipermail/r-help/2007-December/148091.html 6. -x flag on Rscript as in perl/python/ruby. Useful for combining batch and R file into a single file on non-UNIX systems. It would cause all lines until a line starting with #!Rscript to be skipped by the R processor. See: https://www.stat.math.ethz.ch/pipermail/r-devel/2007-January/044433.html Also see http://www.datafocus.com/docs/perl/pod/perlwin32.asp#running_perl_scripts since the same considerations as for Perl scripts applies. There is also some discussion here: https://stat.ethz.ch/pipermail/r-help/2007-November/145279.html https://stat.ethz.ch/pipermail/r-help/2007-November/145301.html Low 7. Define Lag - function(x, k = 1, ...) lag(x, -k, ,..) so the user has his choice of which orientation he prefers. Many packages could make use of it if it were in the core of R including zoo, dyn, dynlm, fame and others. This would also address comments such as in ISSUE 4 on this page which is associated with a popular book on time series: http://www.stat.pitt.edu/stoffer/tsa2/Rissues.htm 8. On Windows, package build tools should check that Cygwin is in correct position on PATH and issue meaningful error if not. If you get this wrong currently its quite hard to diagnose unless you know about it. 9. Implement the R shell() and shell.exec() commands on non-Windows systems. 10. print.function should be improved to make it obvious how to find what the user is undoubtedly looking for in both the S3 and S4 cases. That would address one of the criticisms here: http://www.stat.columbia.edu/~cook/movabletype/archives/2007/08/they_started_me.html (The other criticisms at this link are worth addressing too -- ggplot2 and several existing or upcoming books on grid, lattice and ggplot R graphics are presumably addressing the criticism that creating
[Rd] Predictable grid names
One thing that makes modifying lattice grid objects difficult is that if
you create the same plot twice you get different grid names for
some grid objects:
1. I wonder if there is some possibility in grid to reset the
names after a grid.newpage(), say, so that one can get predictable
names or some other strategy for getting predictable names.
Sort of like a set.seed() for grid except this has nothing to do with
random numbers.
2. grid.ls() is a great improvement over what previously existed but another
thing that would be nice would be to be able to list out more info with
the grid object so one can more easily identify it. Sort of like ls -l.
And/or maybe a where clause restricting which objects are listed, e.g. just
list grid objects that are dark green. I have been using the
following to show the
color values (which displays them if they are in the gp list but not
otherwise) but it would be nice to have something more general and
built in. Or perhaps something already exists that I am not aware of.
library(lattice)
library(grid)
# show tree with names and col values
recurse - function(x, indent = ) {
if (!is.null(x$name)) {
cat(indent, x$name)
if (!is.null(x$gp)) cat( col:, x$gp$col)
cat(\n)
}
for (ch in x$children) Recall(ch, indent = paste(indent, .))
}
xyplot(Sepal.Length ~ Sepal.Width, iris, group = Species, col = 11:13,
auto.key = TRUE)
gg - grid.grab()
recurse(gg)
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[Rd] seekViewport error
Why does the seekViewport at the bottom give an error? xyplot(Sepal.Length ~ Sepal.Width, iris, group = Species, col = 11:13, + auto.key = TRUE) grid.ls(view = TRUE) ROOT GRID.rect.89 plot1.toplevel.vp plot1.xlab.vp plot1.xlab 1 plot1.ylab.vp plot1.ylab 1 plot1.strip.1.1.off.vp GRID.segments.90 1 plot1.strip.left.1.1.off.vp GRID.segments.91 GRID.text.92 1 plot1.panel.1.1.off.vp GRID.segments.93 GRID.text.94 GRID.segments.95 1 plot1.panel.1.1.vp GRID.points.96 GRID.points.97 GRID.points.98 1 plot1.panel.1.1.off.vp GRID.rect.99 1 plot1.legend.top.vp GRID.frame.70 GRID.VP.18 GRID.cellGrob.72 GRID.rect.71 1 GRID.VP.19 GRID.cellGrob.74 GRID.text.73 1 GRID.VP.20 GRID.cellGrob.76 GRID.text.75 1 GRID.VP.21 GRID.cellGrob.78 GRID.text.77 1 GRID.VP.22 GRID.cellGrob.80 GRID.points.79 1 GRID.VP.23 GRID.cellGrob.82 GRID.points.81 1 GRID.VP.24 GRID.cellGrob.84 GRID.points.83 1 1 plot1. 1 1 seekViewport(GRID.VP.24) Error in downViewport.vpPath(vpPathDirect(name), strict, recording = recording) : Viewport 'GRID.VP.24' was not found R.version.string # Vista [1] R version 2.6.1 Patched (2007-12-06 r43610) packageDescription(grid)$Version [1] 2.6.1 packageDescription(lattice)$Version [1] 0.17-2 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Wrong length of POSIXt vectors (PR#10507)
If it were simply deprecated and then changed then everyone using it would get a warning during the period of deprecation so it would not be so bad. Given that its current behavior is not very useful I suspect its not widely used anyways. | haven't followed the whole discussion so sorry if these points have already been made. On Dec 15, 2007 5:17 PM, Martin Maechler [EMAIL PROTECTED] wrote: TP == Tony Plate [EMAIL PROTECTED] on Fri, 14 Dec 2007 13:58:30 -0700 writes: TP Duncan Murdoch wrote: On 12/13/2007 1:59 PM, Tony Plate wrote: Duncan Murdoch wrote: On 12/11/2007 6:20 AM, [EMAIL PROTECTED] wrote: Full_Name: Petr Simecek Version: 2.5.1, 2.6.1 OS: Windows XP Submission from: (NULL) (195.113.231.2) Several times I have experienced that a length of a POSIXt vector has not been computed right. Example: tv-structure(list(sec = c(50, 0, 55, 12, 2, 0, 37, NA, 17, 3, 31 ), min = c(1L, 10L, 11L, 15L, 16L, 18L, 18L, NA, 20L, 22L, 22L ), hour = c(12L, 12L, 12L, 12L, 12L, 12L, 12L, NA, 12L, 12L, 12L), mday = c(13L, 13L, 13L, 13L, 13L, 13L, 13L, NA, 13L, 13L, 13L), mon = c(5L, 5L, 5L, 5L, 5L, 5L, 5L, NA, 5L, 5L, 5L), year = c(105L, 105L, 105L, 105L, 105L, 105L, 105L, NA, 105L, 105L, 105L), wday = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, NA, 1L, 1L, 1L), yday = c(163L, 163L, 163L, 163L, 163L, 163L, 163L, NA, 163L, 163L, 163L), isdst = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, -1L, 1L, 1L, 1L)), .Names = c(sec, min, hour, mday, mon, year, wday, yday, isdst ), class = c(POSIXt, POSIXlt)) print(tv) # print 11 time points (right) length(tv) # returns 9 (wrong) tv is a list of length 9. The answer is right, your expectation is wrong. I have tried that on several computers with/without switching to English locales, i.e. Sys.setlocale(LC_TIME, en). I have searched a help pages but I cannot imagine how that could be OK. See this in ?POSIXt: Class 'POSIXlt' is a named list of vectors... You could define your own length measurement as length.POSIXlt - function(x) length(x$sec) and you'll get the answer you expect, but be aware that length.XXX methods are quite rare, and you may surprise some of your users. On the other hand, isn't the fact that length() currently always returns 9 for POSIXlt objects likely to be a surprise to many users of POSIXlt? The back of The New S Language says Easy-to-use facilities allow you to organize, store and retrieve all sorts of data. ... S functions and data organization make applications easy to write. Now, POSIXlt has methods for c() and vector subsetting [ (and many other vector-manipulation methods - see methods(class=POSIXlt)). Hence, from the point of view of intending to supply easy-to-use facilities ... [for] all sorts of data, isn't it a little incongruous that length() is not also provided -- as 3 functions (any others?) comprise a core set of vector-manipulation functions? Would it make sense to have an informal prescription (e.g., in R-exts) that a class that implements a vector-like object and provides at least of one of functions 'c', '[' and 'length' should provide all three? It would also be easy to describe a test-suite that should be included in the 'test' directory of a package implementing such a class, that had some tests of the basic vector-manipulation functionality, such as: # at this point, x0, x1, x3, x10 should exist, as vectors of the # class being tested, of length 0, 1, 3, and 10, and they should # contain no duplicate elements length(x0) [1] 1 length(c(x0, x1)) [1] 2 length(c(x1,x10)) [1] 11 all(x3 == x3[seq(len=length(x3))]) [1] TRUE all(x3 == c(x3[1], x3[2], x3[3])) [1] TRUE length(c(x3[2], x10[5:7])) [1] 4 It would also be possible to describe a larger set of vector manipulation functions that should be implemented together, including e.g., 'rep', 'unique', 'duplicated', '==', 'sort', '[-', 'is.na', head, tail ... (many of which are provided for POSIXlt). Or is there some good reason that length() cannot be provided (while 'c' and '[' can) for some vector-like classes such as POSIXlt? What you say sounds good in general, but the devil is in the details. Changing the meaning of length(x) for some objects has fairly widespread effects. Are they all positive? I don't know. Adding a prescription like the one you suggest would be good if it's easy to implement, but bad if it's already widely violated. How many base or CRAN or Bioconductor packages violate it currently? Do the ones that provide all 3 methods do so in a
Re: [Rd] creating lagged variables
The problem is the representation.
If we transform it into a zoo time series, z, with one
series per column and one time point per row then we
can just merge the series with its lag.
DF - data.frame(id = c(1, 1, 1, 2, 2, 2), time = c(1, 2,
+ 3, 1, 2, 3), value = c(-0.56047565, -0.23017749, 1.55870831,
+ 0.07050839, 0.12928774, 1.71506499))
library(zoo)
z - do.call(merge, by(DF, DF$id, function(x) zoo(x$value, x$time)))
merge(z, lag(z, -1))
1.z2.z 1.lag(z, -1) 2.lag(z, -1)
1 -0.5604756 0.07050839 NA NA
2 -0.2301775 0.12928774 -0.5604756 0.07050839
3 1.5587083 1.71506499 -0.2301775 0.12928774
On Dec 13, 2007 1:21 PM, Antonio, Fabio Di Narzo
[EMAIL PROTECTED] wrote:
Hi all.
I'm looking for robust ways of building lagged variables in a dataset
with multiple individuals.
Consider a dataset with variables like the following:
##
set.seed(123)
d - data.frame(id = rep(1:2, each=3), time=rep(1:3, 2), value=rnorm(6))
##
d
id time value
1 11 -0.56047565
2 12 -0.23017749
3 13 1.55870831
4 21 0.07050839
5 22 0.12928774
6 23 1.71506499
I want to compute the lagged variable 'value(t-1)', taking subject id
into account.
My current effort produced the following:
##
my_lag - function(dt, varname, timevarname='time', lag=1) {
vname - paste(varname, if(lag0) '.' else '', lag, sep='')
timevar - dt[[timevarname]]
dt[[vname]] - dt[[varname]][match(timevar, timevar + lag)]
dt
}
lag_by - function(dt, idvarname='id', ...)
do.call(rbind, by(dt, dt[[idvarname]], my_lag, ...))
##
With the previous data I get:
lag_by(d, varname='value')
id time value value.1
1.1 11 -0.56047565 NA
1.2 12 -0.23017749 -0.56047565
1.3 13 1.55870831 -0.23017749
2.4 21 0.07050839 NA
2.5 22 0.12928774 0.07050839
2.6 23 1.71506499 0.12928774
So that seems working. However, I was thinking if there is a
smarter/cleaner/more robust way to do the job. For instance, with the
above function I get dataframe rows re-ordering as a side-effect
(anyway this is of no concern in my current analysis)...
Any suggestion?
All the bests,
Fabio.
--
Antonio, Fabio Di Narzo
Ph.D. student at
Department of Statistical Sciences
University of Bologna, Italy
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Re: [Rd] List comprehensions for R
That seems quite nice.
Note that there has been some related code posted. See:
http://tolstoy.newcastle.edu.au/R/help/03b/6406.html
which discusses some R idioms for list comprehensions.
Also the gsubfn package has some functionality in this direction. We
preface any function with fn$ to allow functions in its arguments
to be specified as formulas. Its more R-ish than your code and
applies to more than just list comprehensions while your code is
more faithful to list comprehensions.
library(gsubfn)
fn$sapply(0:11/11, ~ sin(x))
[1] 0. 0.09078392 0.18081808 0.26935891 0.35567516 0.43905397
[7] 0.51880673 0.59427479 0.66483486 0.72990422 0.78894546 0.84147098
fn$sapply(0:4, y ~ fn$sapply(0:3, x ~ x*y))
[,1] [,2] [,3] [,4] [,5]
[1,]00000
[2,]01234
[3,]02468
[4,]0369 12
fn$sapply(0:4, y ~ fn$sapply(0:y, x ~ x*y))
[[1]]
[1] 0
[[2]]
[1] 0 1
[[3]]
[1] 0 2 4
[[4]]
[1] 0 3 6 9
[[5]]
[1] 0 4 8 12 16
unlist(fn$sapply(1:4, y ~ fn$sapply(1:y, x ~ x*y)))
[1] 1 2 4 3 6 9 4 8 12 16
On Dec 9, 2007 4:41 PM, David C. Norris
[EMAIL PROTECTED] wrote:
Below is code that introduces a list comprehension syntax into R,
allowing expressions like:
.[ sin(x) ~ x - (0:11)/11 ]
[1] 0. 0.09078392 0.18081808 0.26935891 0.35567516 0.43905397
[7] 0.51880673 0.59427479 0.66483486 0.72990422 0.78894546 0.84147098
.[ .[x*y ~ x - 0:3] ~ y - 0:4]
[,1] [,2] [,3] [,4] [,5]
[1,]00000
[2,]01234
[3,]02468
[4,]0369 12
.[ .[x+y ~ x - 0:y] ~ y - 0:4]
[[1]]
[1] 0
[[2]]
[1] 1 2
[[3]]
[1] 2 3 4
[[4]]
[1] 3 4 5 6
[[5]]
[1] 4 5 6 7 8
.[ x*y ~ {x - 1:4; y-1:x} ]
[1] 1 2 4 3 6 9 4 8 12 16
These constructions are supported by the following code.
Regards,
David
##
## Define syntax for list/vector/array comprehensions
##
. - structure(NA, class=comprehension)
comprehend - function(expr, vars, seqs, comprehension=list()){
if(length(vars)==0) # base case
comprehension[[length(comprehension)+1]] - eval(expr)
else
for(elt in eval(seqs[[1]])){
assign(vars[1], elt, inherits=TRUE)
comprehension - comprehend(expr, vars[-1], seqs[-1], comprehension)
}
comprehension
}
## Support general syntax like .[{exprs} ~ {generators}]
[.comprehension - function(x, f){
f - substitute(f)
## To allow omission of braces around a lone comprehension generator,
## as in 'expr ~ var - seq' we make allowances for two shapes of f:
##
## (1)(`-` (`~` expr
## var)
## seq)
## and
##
## (2)(`~` expr
## (`{` (`-` var1 seq1)
## (`-` var2 seq2)
## ...
## (`-` varN - seqN)))
##
## In the former case, we set gens - list(var - seq), unifying the
## treatment of both shapes under the latter, more general one.
syntax.error - Comprehension expects 'expr ~ {x1 - seq1; ... ; xN
- seqN}'.
if(!is.call(f) || (f[[1]]!='-' f[[1]]!='~'))
stop(syntax.error)
if(is(f,'-')){ # (1)
lhs - f[[2]]
if(!is.call(lhs) || lhs[[1]] != '~')
stop(syntax.error)
expr - lhs[[2]]
var - as.character(lhs[[3]])
seq - f[[3]]
gens - list(call('-', var, seq))
} else { # (2)
expr - f[[2]]
gens - as.list(f[[3]])[-1]
if(any(lapply(gens, class) != '-'))
stop(syntax.error)
}
## Fill list comprehension .LC
vars - as.character(lapply(gens, function(g) g[[2]]))
seqs - lapply(gens, function(g) g[[3]])
.LC - comprehend(expr, vars, seqs)
## Provided the result is rectangular, convert it to a vector or array
## TODO: Extend to handle .LC structures more than 2-deep.
if(!length(.LC))
return(.LC)
dim1 - dim(.LC[[1]])
if(is.null(dim1)){
lengths - sapply(.LC, length)
if(all(lengths == lengths[1])){ # rectangular
.LC - unlist(.LC)
if(lengths[1] 1) # matrix
dim(.LC) - c(lengths[1], length(lengths))
} else { # ragged
# leave .LC as a list
}
} else { # elements of .LC have dimension
dim - c(dim1, length(.LC))
.LC - unlist(.LC)
dim(.LC) - dim
}
.LC
}
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Re: [Rd] Building packages
An svn checkout directory can contain a mix of files that are mirrored in the svn and not mirrored. In particular, if you add a new file into your checkout directory it will not automatically go into the repository on your next commit unless you specifically place that file under svn control so junk files remain local. You can exclude files from R CMD build using the .Rbuildignore file. See the Writing Extensions manual. On Dec 7, 2007 11:07 AM, Barry Rowlingson [EMAIL PROTECTED] wrote: I've started a new package and I'm trying to work out the best way to do it. I'm managing my package source directory with SVN, but R CMD build likes to dump things in the inst/doc directory when making vignette PDF files. I don't want to keep these in SVN (they aren't strictly 'source'), so it set me thinking. One of the other projects I work with has an out-of-source build system. You make a 'build' directory, run a config system (cmake-based) and then 'make' does everything in the build directory without touching the source tree. Very nice and neat. How much work would it take to have something similar for building R packages? At present I've just got some svn:ignore settings to stop SVN bothering me. I also hit the problem of vignettes needing the package to be installed before being able to build them, but not being able to install the package because the vignettes wouldn't build without the package already being installed. The fix is to build with --no-vignettes, then install the package, then build with the vignettes enabled. Seems kludgy, plus it means that vignettes are always built with the currently installed package and not the currently-being-installed package. So I install and do a second pass to get it all right again. Or am I doing it wrong? Once I get smooth running of R package development and SVN I might write it up for R-newsletter - there's a couple of other tricks I've had to employ... Barry __ 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] suggested modification to the 'mle' documentation?
On Dec 7, 2007 8:43 AM, Duncan Murdoch [EMAIL PROTECTED] wrote: On 12/7/2007 8:10 AM, Peter Dalgaard wrote: Ben Bolker wrote: At this point I'd just like to advertise the bbmle package (on CRAN) for those who respectfully disagree, as I do, with Peter over this issue. I have added a data= argument to my version of the function that allows other variables to be passed to the objective function. It seems to me that this is perfectly in line with the way that other modeling functions in R behave. This is at least cleaner than abusing the fixed argument. As you know, I have reservations, one of which is that it is not a given that I want it to behave just like other modeling functions, e.g. a likelihood function might refer to more than one data set, and/or data that are not structured in the traditional data frame format. The design needs more thought than just adding arguments. We should allow more general things to be passed as data arguments in cases where it makes sense. For example a list with names or an environment would be a reasonable way to pass data that doesn't fit into a data frame. I still prefer a design based a plain likelihood function. Then we can discuss how to construct such a function so that the data are incorporated in a flexible way. There are many ways to do this, I've shown one, here's another: f - function(lambda) -sum(dpois(x, lambda, log=T)) d - data.frame(x=rpois(1, 12.34)) environment(f)-evalq(environment(),d) We really need to expand as.environment, so that it can convert data frames into environments. You should be able to say: environment(f) - as.environment(d) and get the same result as environment(f)-evalq(environment(),d) But I'd prefer to avoid the necessity for users to manipulate the environment of a function. I think the pattern model( f, data=d ) being implemented internally as environment(f) - as.environment(d, parent = environment(f)) is very nice and general. It makes things like cross-validation, bootstrapping, etc. conceptually cleaner: keep the same formula/function f, but manipulate the data and see what happens. It does have problems when d is an environment that already has a parent, but I think a reasonable meaning in that case would be to copy its contents into a new environment with the new parent set. Duncan Murdoch Something close to that is already possible in proto and its cleaner in proto since the explicit environment manipulation is unnecessary as it occurs implicitly: 1. In terms of data frame d from Peter Dalgaard's post the code below is similar to my last post but it replaces the explicit manipulation of f's environemnt with the creation of proto object p on line ###. That line converts d to an anonymous proto object containing the components of d, in this case just x, and then creates a child object p which can access x via delegation/inheritance. library(proto) set.seed(1) f - function(lambda) -sum(dpois(x, lambda, log=T)) d - data.frame(x=rpois(100, 12.34)) p - proto(as.proto(as.list(d)), f = f) ### mle(p[[f]], start=list(lambda=10)) 2. Or the ### line could be replaced with the following line which places f and the components of d, in this case just x, directly into p: p - proto(f = f, envir = as.proto(as.list(d))) again avoiding the explicit reset of environment(f) and the evalq. mle(f, start=list(lambda=10)) Call: mle(minuslogl = f, start = list(lambda = 10)) Coefficients: lambda 12.3402 It is not at all an unlikely design to have mle() as a generic function which works on many kinds of objects, the default method being function(object,...) mle(minuslogl(obj)) and minuslogl is an extractor function returning (tada!) the negative log likelihood function. (My version also has a cool formula interface and other bells and whistles, and I would love to get feedback from other useRs about it.) cheers Ben Bolker __ 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] suggested modification to the 'mle' documentation?
On Dec 7, 2007 8:10 AM, Peter Dalgaard [EMAIL PROTECTED] wrote: Ben Bolker wrote: At this point I'd just like to advertise the bbmle package (on CRAN) for those who respectfully disagree, as I do, with Peter over this issue. I have added a data= argument to my version of the function that allows other variables to be passed to the objective function. It seems to me that this is perfectly in line with the way that other modeling functions in R behave. This is at least cleaner than abusing the fixed argument. As you know, I have reservations, one of which is that it is not a given that I want it to behave just like other modeling functions, e.g. a likelihood function might refer to more than one data set, and/or data that are not structured in the traditional data frame format. The design needs more thought than just adding arguments. I still prefer a design based a plain likelihood function. Then we can discuss how to construct such a function so that the data are incorporated in a flexible way. There are many ways to do this, I've shown one, here's another: f - function(lambda) -sum(dpois(x, lambda, log=T)) d - data.frame(x=rpois(1, 12.34)) environment(f)-evalq(environment(),d) mle(f, start=list(lambda=10)) Call: mle(minuslogl = f, start = list(lambda = 10)) Coefficients: lambda 12.3402 The explicit environment manipulation is what I was referring to but we can simplify it using proto. Create a proto object to hold f and x then pass the f in the proto object (rather than the original f) to mle. That works because proto automatically resets the environment of f when its added to avoiding the evalq. set.seed(1) library(proto) f - function(lambda) -sum(dpois(x, lambda, log=TRUE)) p - proto(f = f, x = rpois(100, 12.34)) mle(p[[f]], start = list(lambda = 10)) Call: mle(minuslogl = p[[f]], start = list(lambda = 10)) Coefficients: lambda 12.46000 It is not at all an unlikely design to have mle() as a generic function which works on many kinds of objects, the default method being function(object,...) mle(minuslogl(obj)) and minuslogl is an extractor function returning (tada!) the negative log likelihood function. (My version also has a cool formula interface and other bells and whistles, and I would love to get feedback from other useRs about it.) cheers Ben Bolker -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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] suggested modification to the 'mle' documentation?
The closure only works if you are defining the inner function yourself.
If you are not then its yet more work to redefine the environment of
the inner function or other workaround.
On Dec 6, 2007 6:01 PM, Peter Dalgaard [EMAIL PROTECTED] wrote:
Spencer Graves wrote:
Hello:
I wish to again express my appreciation to all who have
contributed to making R what it is today.
At this moment, I'm particularly grateful for whoever modified the
'mle' code so data no longer need be passed via global variables. I
remember struggling with this a couple of years ago, and I only today
discovered that it is no longer the case.
I'd like to suggest that the 'mle' help file be modified to
advertise this fact, e.g., by adding one of the two examples appearing
below.
In a word: No!!! That is not the design. A likelihood function is a
function of its parameters, and the fixed argument is for holding some
parameters fixed (e.g. during profiling).
To include data, just make a closure, e.g.
poissonLike - function(x., y.){
function(ymax=15, xhalf=6)
-sum(stats::dpois(y., lambda=ymax/(1+x./xhalf), log=TRUE))}
mll - poissonLike(x, y)
mle(ll,
Best Wishes,
Spencer Graves
x - 0:10
y - c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8)
# Pass data via function arguments rather than global variables
ll.5 - function(ymax=15, xhalf=6, x., y.)
-sum(stats::dpois(y., lambda=ymax/(1+x./xhalf), log=TRUE))
(fit.5 - mle(ll.5, start=list(ymax=15, xhalf=6),
fixed=list(x.=x, y.=y)))
ll3 - function(lymax=log(15), lxhalf=log(6), x., y.)
-sum(stats::dpois(y.,
lambda=exp(lymax)/(1+x./exp(lxhalf)), log=TRUE))
(fit3 - mle(ll3, start=list(lymax=0, lxhalf=0),
fixed=list(x.=x, y.=y)))
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--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Re: [Rd] faqs
And one other thing. In the GNU docs it says that if your NEWS file gets too big you can create an ONEWS file for the really old stuff. Is ONEWS supported too? On Nov 16, 2007 11:12 PM, Gabor Grothendieck [EMAIL PROTECTED] wrote: On Nov 15, 2007 10:51 AM, Gabor Grothendieck [EMAIL PROTECTED] wrote: On Nov 15, 2007 9:57 AM, Simon Urbanek [EMAIL PROTECTED] wrote: On Nov 14, 2007, at 11:55 PM, Gabor Grothendieck wrote: inst/NEWS would have the advantage of consistency with R itself which also has a NEWS file. I vote for NEWS for reasons above plus because that's what I use in my packages already ;). IMHO it should be installed automatically if present, i.e. it shouldn't be necessary to have it in inst/NEWS, just plain NEWS should suffice. I agree that that would be desirable. Also it would be nice if the HTML files here: http://cran.r-project.org/src/contrib/Descriptions/ each had a link to the NEWS file so one could get the news on a package prior to installing it. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] faqs
On Nov 15, 2007 10:51 AM, Gabor Grothendieck [EMAIL PROTECTED] wrote: On Nov 15, 2007 9:57 AM, Simon Urbanek [EMAIL PROTECTED] wrote: On Nov 14, 2007, at 11:55 PM, Gabor Grothendieck wrote: inst/NEWS would have the advantage of consistency with R itself which also has a NEWS file. I vote for NEWS for reasons above plus because that's what I use in my packages already ;). IMHO it should be installed automatically if present, i.e. it shouldn't be necessary to have it in inst/NEWS, just plain NEWS should suffice. I agree that that would be desirable. Also it would be nice if the HTML files here: http://cran.r-project.org/src/contrib/Descriptions/ each had a link to the NEWS file so one could get the news on a package prior to installing it. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] library path in Rd link
I think that's right -- it only works on NTFS systems. This page refers to it as an NTFS symbolic link: http://en.wikipedia.org/wiki/NTFS_symbolic_link On Nov 14, 2007 10:00 PM, Duncan Murdoch [EMAIL PROTECTED] wrote: On 14/11/2007 7:44 PM, Gabor Grothendieck wrote: On Nov 14, 2007 4:36 PM, Duncan Murdoch [EMAIL PROTECTED] wrote: On Unix-alikes, the workaround is to build soft links to all the packages in a standard location; but soft links don't work on Windows (and we don't want to get into the almost-undocumented hard links that exist on some Windows file systems). Symbolic links are available on Windows Vista: Does this work on FAT file systems, e.g. on a USB drive? It used to be that they only worked on NTFS. Duncan Murdoch C:\ mklink /? Creates a symbolic link. MKLINK [[/D] | [/H] | [/J]] Link Target /D Creates a directory symbolic link. Default is a file symbolic link. /H Creates a hard link instead of a symbolic link. /J Creates a Directory Junction. Linkspecifies the new symbolic link name. Target specifies the path (relative or absolute) that the new link refers to. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] faqs
On Nov 15, 2007 9:57 AM, Simon Urbanek [EMAIL PROTECTED] wrote: On Nov 14, 2007, at 11:55 PM, Gabor Grothendieck wrote: inst/NEWS would have the advantage of consistency with R itself which also has a NEWS file. I vote for NEWS for reasons above plus because that's what I use in my packages already ;). IMHO it should be installed automatically if present, i.e. it shouldn't be necessary to have it in inst/NEWS, just plain NEWS should suffice. I agree that that would be desirable. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] When to use LazyLoad, LazyData and ZipData?
On Nov 14, 2007 7:01 AM, Bjørn-Helge Mevik [EMAIL PROTECTED] wrote: Dear developeRs, I've searched the documentation, FAQ, and mailing lists, but haven't found the answer(*) to the following: When should one specify LazyLoad, LazyData, and ZipData? And what is the default if they are left unspecified? (*)Except that 1) If the package you are writing uses the methods package, specify LazyLoad: yes, and 2) The optional ZipData field controls whether the automatic Windows build will zip up the data directory or no: set this to no if your package will not work with a zipped data directory. There is some information and links regarding LazyLoad on the proto package home page, http://r-proto.googlecode.com, in the last section entitled Avoiding R Bugs in point #1. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] library path in Rd link
On Nov 14, 2007 4:36 PM, Duncan Murdoch [EMAIL PROTECTED] wrote: On Unix-alikes, the workaround is to build soft links to all the packages in a standard location; but soft links don't work on Windows (and we don't want to get into the almost-undocumented hard links that exist on some Windows file systems). Symbolic links are available on Windows Vista: C:\ mklink /? Creates a symbolic link. MKLINK [[/D] | [/H] | [/J]] Link Target /D Creates a directory symbolic link. Default is a file symbolic link. /H Creates a hard link instead of a symbolic link. /J Creates a Directory Junction. Linkspecifies the new symbolic link name. Target specifies the path (relative or absolute) that the new link refers to. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] faqs
Another possibility is to just place it at the end of the vignette. That is where it is in the proto package: http://cran.r-project.org/doc/vignettes/proto/proto.pdf Package documentation is already quite scattered and adding a faq() command would add just one more thing one has to do. Here are some places one might look already for documentation: package?mypackage vignette(...) library(help = mypackage) ?mycommand home page WISHLIST file NEWS file THANKS file svn log I personally would give a much higher priority to a standardized place to find change information. Some packages provide it. Some don't which is very frustrating since you see a new version and have no idea what has changed. If they do document it you often have to download the source just to get at the change information. On Nov 14, 2007 8:22 PM, roger koenker [EMAIL PROTECTED] wrote: An extremely modest proposal: It would be nice if packages could have a FAQ and if faq(package.name) would produce this faq. And if, by default faq() FAQ() would produce the admirable R faq... Apologies in advance if there is already a mechanism like this, but help.search() didn't reveal anything. url:www.econ.uiuc.edu/~rogerRoger Koenker email [EMAIL PROTECTED] Department of Economics vox:217-333-4558University of Illinois fax:217-244-6678Champaign, IL 61820 __ 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] How to overload the assignment operator?
Check out the g.data package in case that's what you are looking for. It uses promises until the data is actually used. On Nov 13, 2007 9:19 AM, Jens Oehlschlägel [EMAIL PROTECTED] wrote: Thanks Matthias, are you looking for setReplaceMethod? So far the package I m writing has avoided using anything from S4 and the implications of touching S4 are not clear to me. The package aims on providing an alternative to 'atomic' data stored in ram, i.e. large atomic data stored on disk. I need some advice how to do this maximally performant, which probably means pure S3!? Best regards Jens Oehlschlägel -- __ 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] years() in chron package not working in R 2.6.0 (PR#10415)
In chron, ?year says x must be a dates object and its not in the code below. On Nov 9, 2007 3:55 PM, [EMAIL PROTECTED] wrote: I loaded package chron in a newly installed version of R 2.6.0 and the years() function would not work. (This worked in 2.5). =20 x-as.Date(2006-01-01) years(x) NULL =20 sessionInfo() R version 2.6.0 (2007-10-03)=20 i386-pc-mingw32=20 =20 locale: LC_COLLATE=3DEnglish_United States.1252;LC_CTYPE=3DEnglish_United States.1252;LC_MONETARY=3DEnglish_United States.1252;LC_NUMERIC=3DC;LC_TIME=3DEnglish_United States.1252 =20 attached base packages: [1] tcltk stats graphics grDevices utils datasets methods base=20=20=20=20=20 =20 other attached packages: [1] fCalendar_260.72 fEcofin_260.72fUtilities_260.72 zoo_1.4-0 spatial_7.2-36=20=20=20 [6] RUnit_0.4.17 MASS_7.2-36 chron_2.3-15=20=20=20=20=20 =20 loaded via a namespace (and not attached): [1] grid_2.6.0 lattice_0.16-5 tools_2.6.0=20=20=20 =20 Thanks. =20 John Putz Sr. Energy Analyst The Energy Authority 425-460-1137 (o) 206-910-5229 (c) =20 [[alternative HTML version deleted]] __ 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] pairs, par
This hack will disable the on.exit temporarily:
pairs.data.frame - function(x, ...) {
on.exit - function(...) {}
environment(pairs.default) - environment()
pairs.default(x, ...)
}
pairs(iris)
par(usr)
# add points to lower right square
points(1:10/10, 1:10/10, col = red)
On 10/29/07, Oliver Soong [EMAIL PROTECTED] wrote:
I dug around in pairs, and I think it has something to do with the
on.exit(par(opar)) bit:
f - function() {
opar - par(mfrow = c(2, 2), mar = rep(0.5, 4), oma = rep(4, 4))
on.exit(par(opar))
for(i in 1:4) plot(0:1, 0:1)
par(c(mfg, omd, fig, plt, usr))
print(opar)
}
f()
par(xpd = NA)
par(c(omd, fig, plt, usr))
points(0 - 0.01 * 1:100, 0 - 0.01 * 1:100)
points(0 - 0.01 * 1:100, 1 + 0.01 * 1:100)
points(1 + 0.01 * 1:100, 0 - 0.01 * 1:100)
points(1 + 0.01 * 1:100, 1 + 0.01 * 1:100)
My guess is that there are 2 sets of graphical parameters, the ones
stored in par and the ones used by the plotting functions. Before
par(opar) gets called, the two are synchronized. When par(opar) gets
called, we somehow set new values for par without changing the ones
used by the plotting functions, and the data used by points becomes
out of sync with the par information.
This is reflected in this much simpler example:
x11()
par(c(omd, fig, plt, usr))
points(0, 0)
Again, par is defined, but this time the data used by the plotting
functions has not been set, and an error occurs.
Thanks for the workaround suggestion. I guess I can always define a
new plotting region to force par and the plotting data to
re-synchronize. It might be nice if those two didn't go out of sync,
as I had assumed par would always be reliable.
Oliver
On 10/29/07, Tony Plate [EMAIL PROTECTED] wrote:
I would look into the code for pairs(). Among other things, it sets and
restores par(mfrow=...). I suspect this is the relevant issue, not the
use of pairs(). I would try to figure out what state a graphics device
is in after resetting par(mfrow). When I try the following (R 2.6.0
patched, under Windows), I see a line on the plot, but not in a place
that corresponds to the axis that were drawn by the 'plot()' command:
par(mfrow=c(2,2))
plot(1:2)
par(mfrow=c(1,1))
lines(1:2,1:2)
(and if you want to be able to set up a new coordinate system on the
plotting device to draw on top of the plot left by pairs(), look at
par(new) something like plot(0:1, type='n', axes=F, xlab=))
hope this helps,
Tony Plate
Oliver Soong wrote:
Hi,
I posted over at R-help, and didn't get a response, but perhaps that
was the wrong forum for this question. I'm having some confusion over
the coordinate system after using pairs. I'm not interested in the
content of the actual pairs plot, although the number of pairs seems
to matter a bit. I'm purely interested in knowing where subsequent
points will be plotted on the device. However, after using pairs, the
par information (omd, fig, plt, and usr) don't reflect what points
does. For example:
pairs(iris[1:5])
par(xpd = NA)
points(0 - 0.01 * 1:100, 0 - 0.01 * 1:100)
points(0 - 0.01 * 1:100, 1 + 0.01 * 1:100)
points(1 + 0.01 * 1:100, 0 - 0.01 * 1:100)
points(1 + 0.01 * 1:100, 1 + 0.01 * 1:100)
par(c(omd, fig, plt, usr))
The resulting plot shows that the corners of the are approximately
0.05 user coordinate units from the boundaries of the plot region.
According to par, though, there is a margin around the plotting region
that is clearly not symmetric and does not correspond to around 0.05
units.
If we use pairs(iris[1:2]) and repeat the rest, the corners are now
0.02 user coordinate units. par provides the same information as
before.
So:
1. How do I figure out where coordinates I give to points will display
on the figure?
2. More generally (for my own understanding), why does the par
information not do what I expect? Do I have some fundamental
misunderstanding of the arrangement of plotting, figure, display, and
margin regions within the device? Is there a bug in pairs and/or par?
I'm using R 2.5.1, and this behavior occurs on a fresh R console.
Thanks!
Oliver
--
Oliver Soong
Donald Bren School of Environmental Science Management
University of California, Santa Barbara
Santa Barbara, CA 93106-5131
805-893-7044 (office)
610-291-9706 (cell)
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Re: [Rd] LazyLoad changes the class of objects
On 10/17/07, Henrik Bengtsson [EMAIL PROTECTED] wrote: Yes (on the yes), to second Luke. Here is John Chambers' comment when I was bitten by the same bug a while ago: http://tolstoy.newcastle.edu.au/R/devel/02b/0524.html See also Peter Dalgaard's follow up suggesting to wrap up the environment in a list, which will typically be enough. I've been using this trick successfully in the Object class (R.oo package) for several years, where I'm putting the environment in the attributes list of an object, i.e. obj - NA; attr(NA, ..env) - new.env(); It turned out at the time that this was slightly faster to access than using a list element. This has all been discussed before but this trick is not sufficient for defining an environment subclass because it does not respect inheritance. The subclass writer must replicate all methods that act on environments in a subclass for an environment subclass to have them. Inheritance is completely broken. If there were N environment methods the writer of an environment subclass would have to write N methods to support them all. On the other hand, if it worked in a true OO way the subclass writer would not have to write anything. Also suppose a new environment method comes along. In true OO the subclass automatically inherits it but with the trick the subclass writer needs to write a new method always mimicing the parent. This is not how OO is supposed to work. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Withdrawing SaveImage
I noticed this under R 2.7.0 NEWS: o In package installation, SaveImage: yes is defunct and lazyloading is attempted instead. I think its premature to make SaveImage defunct especially when: 1. there is a bug that would be triggered in some packages by automatically using LazyLoad instead of SaveImage: https://stat.ethz.ch/pipermail/r-devel/2007-October/047118.html 2. only last year it was stated on R-devel that there was no intention to withdraw SaveImage: yes http://tolstoy.newcastle.edu.au/R/devel/06/02/4025.html Having SaveImage: yes automatically invoke LazyLoad is really tantamount to withdrawing it. At the very least making SaveImage defunct should be postponed until the bug in #1 is fixed and a period of time has elapsed during which both SaveImage and LazyLoad are available without that bug so that packages affected can gradually move over and have the ability to move back to SaveImage if the move uncovers more R bugs related to this. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Extending deriv3()
If you are modifying it it would also be nice to add
{ to the derivative table so one can write this:
f - function(x) x*x
deriv(body(f), x, func = TRUE)
Currently, one must do:
deriv(body(f)[[2]], x, func = TRUE)
On 10/15/07, Prof Brian Ripley [EMAIL PROTECTED] wrote:
On Mon, 15 Oct 2007, Thomas Yee wrote:
Hello,
I was wondering if the functions deriv3(), deriv() etc. could be extended
to handle psigamma() and its special cases (digamma(), trigamma()
etc.). From the error message it seems that 'psigamma' needs to be
added to the derivatives table.
This might be easy since psigamma() has a deriv argument.
If you look at ?deriv you will see that it only knows about functions *of
one argument* and operators. So it would be easy to add digamma(x) and
psigamma(x) (and I will do so shortly), it would not be so easy to add
psigamma(x, deriv).
Additionally, this error message is also obtained when requesting for
the Hessian of the gamma and lgamma functions:
d3 = deriv(~ gamma(y), namev=y, hessian= TRUE)
d3 = deriv(~ lgamma(y), namev=y, hessian= TRUE)
Another class of special functions worth adding are the Bessel functions.
Well, you can always submit a patch
Note that deriv() in R differs from that in S in being done in C and hence
not being user-extensible. A long time ago that had an advantage: S's
deriv could be very slow and take a lot of memory by the standards of the
early 1990's. Rather than work on adding yet more special cases it would
seem better to work on making it user-extensible.
--
Brian D. Ripley, [EMAIL PROTECTED]
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
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[Rd] LazyLoad changes the class of objects
Consider a package that this DESCRIPTION file: --- Package: tester Version: 0.1-0 Date: 2007-10-12 Title: Prototype object-based programming Author: Gabor Grothendieck Maintainer: Gabor Grothendieck [EMAIL PROTECTED] Description: test LazyLoad: true Depends: R (= 2.6.0) License: GPL2 --- and a single subdirectory R containing tester.R which contains two lines: --- e - new.env() class(e) - c(x, environment) --- Now issue these commands: library(tester) class(tester::e) [1] environment R.version.string # Windows Vista [1] R version 2.6.0 Patched (2007-10-08 r43124) Note that the class of e was changed from what we set it to !!! On the other handn, if we omit LazyLoad: true from the DESCRIPTION file then it retains its original class. # removed LazyLoad: true line from DESCRIPTION and reinstall pkg # now its ok library(tester) class(tester::e) [1] x environment __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Ryacas check
When I do Rcmd check Ryacas on my Windows Vista system under R version 2.6.0 beta (2007-09-23 r42958) it checks out fine but here: http://cran.r-project.org/bin/windows/contrib/checkSummaryWin.html http://cran.r-project.org/bin/windows/contrib/2.5/check/Ryacas-check.log it complains about the XML package even though the XML package *is* declared in the DESCRIPTION file. What is wrong? __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Ryacas check
I don't understand what you are suggesting. I already have Depends: XML in my description file and as indicated in my original post don't get any errors or warnings when I run CHECK on my own system. Its only CRAN that has them. On 9/30/07, Duncan Temple Lang [EMAIL PROTECTED] wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Gabor Grothendieck wrote: When I do Rcmd check Ryacas on my Windows Vista system under R version 2.6.0 beta (2007-09-23 r42958) it checks out fine but here: http://cran.r-project.org/bin/windows/contrib/checkSummaryWin.html http://cran.r-project.org/bin/windows/contrib/2.5/check/Ryacas-check.log it complains about the XML package even though the XML package *is* declared in the DESCRIPTION file. The log says that the XML package refers to a function that cannot be found and so the XML package wasn't loaded. Grab the latest version of the XML package from www.omegahat.org/RSXML/XML_0.93-1.tar.gz. It is usually automatically fetched via CRAN, but we have to figure out why that is not happening currently. What is wrong? __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.7 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFG//Cw9p/Jzwa2QP4RAvjdAJ0aAnMNyjGxO5WdONA7GUUTcIIXBQCfc5eR gWNaJh5gMu5ZmLLDa1Pb1vc= =ZU1N -END PGP SIGNATURE- __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] as.Date.numeric
I noticed that R 2.7.0 will have as.Date.numeric with a second non-optional origin argument. Frankly I would prefer that it default to the Epoch since its a nuisance to specify but at the very least I think that .Epoch should be provided as a builtin variable. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] delayedAssign
Thanks for the explanation.
For lists either: (a) promises should be evaluated as they
enter the list or (b) promises evaluated as they exit the
list (i.e. as they are compared, inspected, etc.). I gather
the intent was (a) but it does not happen that way due to
a bug in R. Originally I thought (b) would then occur but
my surprise was that it does not occur either which is why
I feel its more serious than I had originally thought.
I think its ok if promises only exist in environments and not
lists. Items that would be on my wishlist would be to be able
to do at R level the two mentioned previously
https://stat.ethz.ch/pipermail/r-devel/2007-September/046943.html
and thirdly an ability to get the evaluation environment, not just the
expression,
associated with a promise -- substitute only gets the expression.
Originally I thought I would need some or all of these wish items
and then thought not but am back to the original situation again as I use
them more and realize that they are at least important
for debugging (its very difficult to debug situations involving promises as
there is no way to inspect the evaluation environment so you are never sure
which environment a given promise is evaluating in) and possibly
for writing programs as well.
On 9/27/07, Luke Tierney [EMAIL PROTECTED] wrote:
On Wed, 26 Sep 2007, Gabor Grothendieck wrote:
I thought that perhaps the behavior in the previous post,
while inconsistent with the documentation, was not all that
harmful but I think its related to the following which is a potentially
serious bug.
The previous discussion already established that as.list of an
environment should not return a list with promises in as promises
should not be visible at the R level. (Another loophole that needs
closing is $ for environments). So behavior of results that should not
exist is undefined and I cannot see how any such behavior is a further
bug, serious or otherwise.
z is a list with a single numeric component,
as the dput output verifies,
Except it isn't, as print or str verify, which might be a problem if z
was an input these functions should expect, but it isn't.
yet we cannot compare its first element
to 7 without getting an error message.
Later on we see that its because it thinks that z[[1]] is of type promise
As z[[1]] is in fact of type promise that would seem a fairly
reasonable thing to think at this point ...
and even force(z[[1]]) is of type promise.
which is consistent with what force is documented to do. The
documentation is quite explicit that force does not do what you seem
to be expecting. That documentation is from a time when delay()
existed to produce promises at the R level, which was a nightmare
because of all the peculiarities it introduced, which is why it was
removed.
force is intended for one thing only -- replacing code like this:
# I know the following line look really stupid and you will be
# tempted to remove it for efficiency but DO NOT: it is needed
# to make sure that the formal argument y is evaluated at this
# point.
y - y
with this:
force(y)
which seems much clearer -- at least it suggest you look at the help
page for force to see what it does.
At this point promises should only ever exist in bindings in
environments. If we wanted lazy evaluation constructs more widely
there are really only two sensible options:
The Scheme option where a special function delay creates a deferred
evaluation and another, called force in Scheme, forces the evaluation
but there is no implicit forcing
or
The Haskell option where data structurs are created lazily so
z - list(f(x))
would create a list with a deferred evaluation, but any attempt to
access the value of z would force the evaluation. So printing z,
for example, would force the evaluation but
y - z[[1]]
would not.
It is easy enough to create a Delay/Force pair that behaves like
Scheme's with the tools available in R if that is what you want.
Haskell, and other fully lazy functional languages, are very
interesting but very different animals from R. For some reason you
seem to be expecting some combination of Scheme and Haskell behavior.
Best,
luke
f - function(x) environment()
z - as.list(f(7))
dput(z)
structure(list(x = 7), .Names = x)
z[[1]] == 7
Error in z[[1]] == 7 :
comparison (1) is possible only for atomic and list types
force(z[[1]]) == 7
Error in force(z[[1]]) == 7 :
comparison (1) is possible only for atomic and list types
typeof(z)
[1] list
typeof(z[[1]])
[1] promise
typeof(force(z[[1]]))
[1] promise
R.version.string # Vista
[1] R version 2.6.0 beta (2007-09-23 r42958)
On 9/19/07, Gabor Grothendieck [EMAIL PROTECTED] wrote:
The last two lines of example(delayedAssign) give this:
e - (function(x, y = 1, z) environment())(1+2, y, {cat( HO! ); pi+2})
(le
Re: [Rd] Aggregate factor names
You can do this:
aggregate(iris[-5], iris[5], mean)
On 9/27/07, Mike Lawrence [EMAIL PROTECTED] wrote:
Hi all,
A suggestion derived from discussions amongst a number of R users in
my research group: set the default column names produced by aggregate
() equal to the names of the objects in the list passed to the 'by'
object.
ex. it is annoying to type
with(
my.data
,aggregate(
my.dv
,list(
one.iv = one.iv
,another.iv = another.iv
,yet.another.iv = yet.another.iv
)
,some.function
)
)
to yield a data frame with names = c
('one.iv','another.iv','yet.another.iv','x') when this seems more
economical:
with(
my.data
,aggregate(
my.dv
,list(
one.iv
,another.iv
,yet.another.iv
)
,some.function
)
)
--
Mike Lawrence
Graduate Student, Department of Psychology, Dalhousie University
Website: http://memetic.ca
Public calendar: http://icalx.com/public/informavore/Public
The road to wisdom? Well, it's plain and simple to express:
Err and err and err again, but less and less and less.
- Piet Hein
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Re: [Rd] Aggregate factor names
You can do this too:
aggregate(iris[-5], iris[Species], mean)
or this:
with(iris, aggregate(iris[-5], data.frame(Species), mean))
or this:
attach(iris)
aggregate(iris[-5], data.frame(Species), mean)
The point is that you already don't have to write x = x. The only
reason you are writing it that way is that you are using list instead
of data.frame. Just use data.frame or appropriate indexing as shown.
On 9/27/07, Mike Lawrence [EMAIL PROTECTED] wrote:
Understood, but my point is that the naming I suggest should be the
default. One should not be 'punished' for being explicit in calling
aggregate.
On 27-Sep-07, at 1:06 PM, Gabor Grothendieck wrote:
You can do this:
aggregate(iris[-5], iris[5], mean)
On 9/27/07, Mike Lawrence [EMAIL PROTECTED] wrote:
Hi all,
A suggestion derived from discussions amongst a number of R users in
my research group: set the default column names produced by aggregate
() equal to the names of the objects in the list passed to the 'by'
object.
ex. it is annoying to type
with(
my.data
,aggregate(
my.dv
,list(
one.iv = one.iv
,another.iv = another.iv
,yet.another.iv = yet.another.iv
)
,some.function
)
)
to yield a data frame with names = c
('one.iv','another.iv','yet.another.iv','x') when this seems more
economical:
with(
my.data
,aggregate(
my.dv
,list(
one.iv
,another.iv
,yet.another.iv
)
,some.function
)
)
--
Mike Lawrence
Graduate Student, Department of Psychology, Dalhousie University
Website: http://memetic.ca
Public calendar: http://icalx.com/public/informavore/Public
The road to wisdom? Well, it's plain and simple to express:
Err and err and err again, but less and less and less.
- Piet Hein
__
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--
Mike Lawrence
Graduate Student, Department of Psychology, Dalhousie University
Website: http://memetic.ca
Public calendar: http://icalx.com/public/informavore/Public
The road to wisdom? Well, it's plain and simple to express:
Err and err and err again, but less and less and less.
- Piet Hein
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Re: [Rd] delayedAssign
I thought that perhaps the behavior in the previous post,
while inconsistent with the documentation, was not all that
harmful but I think its related to the following which is a potentially
serious bug. z is a list with a single numeric component,
as the dput output verifies, yet we cannot compare its first element
to 7 without getting an error message.
Later on we see that its because it thinks that z[[1]] is of type promise
and even force(z[[1]]) is of type promise.
f - function(x) environment()
z - as.list(f(7))
dput(z)
structure(list(x = 7), .Names = x)
z[[1]] == 7
Error in z[[1]] == 7 :
comparison (1) is possible only for atomic and list types
force(z[[1]]) == 7
Error in force(z[[1]]) == 7 :
comparison (1) is possible only for atomic and list types
typeof(z)
[1] list
typeof(z[[1]])
[1] promise
typeof(force(z[[1]]))
[1] promise
R.version.string # Vista
[1] R version 2.6.0 beta (2007-09-23 r42958)
On 9/19/07, Gabor Grothendieck [EMAIL PROTECTED] wrote:
The last two lines of example(delayedAssign) give this:
e - (function(x, y = 1, z) environment())(1+2, y, {cat( HO! ); pi+2})
(le - as.list(e)) # evaluates the promises
$x
promise: 0x032b31f8
$y
promise: 0x032b3230
$z
promise: 0x032b3268
which contrary to the comment appears unevaluated. Is the comment
wrong or is it supposed to return an evaluated result but doesn't?
R.version.string # Vista
[1] R version 2.6.0 alpha (2007-09-06 r42791)
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[Rd] Inspecting promises
Is there some way of displaying the expression and evaluation environment associated with a promise? I have found the following: # first run these two commands to set up example e - new.env() delayedAssign(y, x*x, assign.env = e) # method 1. shows expression but not evaluation environment str(as.list(e)) List of 1 $ y: promise to language x * x # method 2. shows expression but not evaluation environment substitute(y, e) x * x which shows two different ways of displaying the expression associated with a promise but neither shows the evaluation environment. The first technique may actually be a bug in R based on previous discussion on r-devel. Is there a way to display both the expression and the evaluation environment associated with a promise. Its a bit difficult to debug code involving promises if you can't inspect the objects you are working with. R.version.string # Vista [1] R version 2.6.0 beta (2007-09-19 r42914) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] warning upon automatic close of connection
I would like to follow up on the annoying warnings which are generated when connections are automatically closed. This is affecting several of my packages and is quite a nuisance. R does not give you a message every time it garbage collects, at least by default. Perhaps there could be a higher level of warnings that issue information on garbage collection, closed connections, etc. or perhaps the user could have control over it but having it as the default is really a nuisance and I hope this warning can be removed. On 9/12/07, Seth Falcon [EMAIL PROTECTED] wrote: Gabor Grothendieck [EMAIL PROTECTED] writes: I noticed that under R 2.6.0 there is a warning about closing the connection in the code from this post: https://stat.ethz.ch/pipermail/r-help/2007-September/140601.html which is evidently related to the following from the NEWS file: o Connections will be closed if there is no R object referring to them. A warning is issued if this is done, either at garbage collection or if all the connection slots are in use. If we use read.table directly it still happens: # use Lines and Lines2 from cited post library(zoo) DF1 - read.table(textConnection(Lines), header = TRUE) DF2 - read.table(textConnection(Lines2), header = TRUE) z1 - zoo(as.matrix(DF1[-1]), as.Date(DF1[,1], %d/%m/%Y)) z2 - zoo(as.matrix(DF2[-1]), as.Date(DF2[,1], %d/%m/%Y)) both - merge(z1, z2) plot(na.approx(both)) R.version.string # Vista [1] R version 2.6.0 alpha (2007-09-06 r42791) Is this annoying warning really necessary? I assume we can get rid of it by explicitly naming and closing the connections but surely there should be a way to avoid the warning without going to those lengths. Up until the change you mention above it really was necessary to name and close all connections. Short scripts run in fresh R sessions may not have had problems with code like you have written above, but longer programs or shorter ones run in a long running R session would run out of connections. Now that connections have weak reference semantics, one can ask whether this behavior should be standard and no warning issued. I would have thought that read.table opens the connection then it would close it itself so no warning would need to be generated. In your example, read.table is _not_ opening the connection. You are passing an open connection which has no symbol bound to it: foo = c = textConnection(foo) c descriptionclass mode text foo textConnection r text opened can readcan write openedyes no But I think passing a closed connection would cause the same sort of issue. It seems that there are two notions of closing a connection: (i) close as the opposite of open, and (ii) clean up the entire connection object. I haven't looked closely at the code here, so I could be wrong, but I'm basing this guess on the following: file(foo) description classmodetext openedcan read foo file r textclosed yes can write yes ## start new R session for (i in 1:75) file(foo) gc() warnings()[1:3] gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 149603 4.0 35 9.4 35 9.4 Vcells 101924 0.8 786432 6.0 486908 3.8 There were 50 or more warnings (use warnings() to see the first 50) warnings()[1:3] $`closing unused connection 76 (foo)` NULL $`closing unused connection 75 (foo)` NULL $`closing unused connection 74 (foo)` NULL -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] delayedAssign
The last two lines of example(delayedAssign) give this:
e - (function(x, y = 1, z) environment())(1+2, y, {cat( HO! ); pi+2})
(le - as.list(e)) # evaluates the promises
$x
promise: 0x032b31f8
$y
promise: 0x032b3230
$z
promise: 0x032b3268
which contrary to the comment appears unevaluated. Is the comment
wrong or is it supposed to return an evaluated result but doesn't?
R.version.string # Vista
[1] R version 2.6.0 alpha (2007-09-06 r42791)
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Re: [Rd] delayedAssign
Also note that earlier in the same example we have:
msg - old
delayedAssign(x, msg)
msg - new!
x #- new!
[1] new!
substitute(x) #- msg
x
R.version.string # Vista
[1] R version 2.6.0 alpha (2007-09-06 r42791)
That is substitute(x) gives x, not msg.
On 9/19/07, Gabor Grothendieck [EMAIL PROTECTED] wrote:
The last two lines of example(delayedAssign) give this:
e - (function(x, y = 1, z) environment())(1+2, y, {cat( HO! ); pi+2})
(le - as.list(e)) # evaluates the promises
$x
promise: 0x032b31f8
$y
promise: 0x032b3230
$z
promise: 0x032b3268
which contrary to the comment appears unevaluated. Is the comment
wrong or is it supposed to return an evaluated result but doesn't?
R.version.string # Vista
[1] R version 2.6.0 alpha (2007-09-06 r42791)
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[Rd] copying promise
1. Is there some way to copy a promise so that the copy has the same expression in its promise as the original. In the following we y is a promise that we want to copy to z. We want z to be a promise based on the expression x since y is a promise based on the expression x. Thus the answer to the code below is desired to be z=2 but its 1, 1 and y in the next three examples so they are not the answer. See examples at end. 2. Is there some way to determine if a variable holds a promise without evaluating it? This code relates to question 1. # example 1 x - 0 delayedAssign(y, x) x - 1 # this forces y which is not what we want z - y x - 2 z # 1 # example 2 # this connects to z to x via y which is not what we want # since if y is forced then z takes its value from that, not x x - 0 delayedAssign(y, x) delayedAssign(z, y) x - 1 y x - 2 z # 1 # example 3 # this attempts to assign the expression underlying promise y to z # which seems closest in spirit to what we want # but it does not work as intended x - 0 delayedAssign(y, x) delayedAssign(z, substitute(y)) x - 1 y x - 2 z # y R.version.string # Vista [1] R version 2.6.0 alpha (2007-09-06 r42791) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Date vs date (long)
On 9/17/07, Terry Therneau [EMAIL PROTECTED] wrote:
Gabor Grothendieck
as.Date(10)
You can define as.Date.numeric in your package and then it will work. zoo
has done that.
library(zoo)
as.Date(10)
This is also a nice idea. Although adding to a package is possible, it is
now very hard to take away, given namespaces. That is, I can't define my
own Math.Date to do away with the creation of timespan objects. Am I
correct? Is it also true that adding methods is hard if one uses version 4
classes?
The rest of Gabor's comments are workarounds for the problem I raised.
But I don't want to have to wrap as.numeric around all of my date
calculations.
You can define as.Date.numeric and Ops.Date, say, using S3 and these
will be added to the whatever is there but won't override the existing
+.Date and -.Date nor would you want them to or else the behavior would
be different depending on whether your package was there or not. Also
namespaces should not be a problem since zoo uses namespaces and
it defined its own as.Date.numeric.
Try this:
Ops.Date - function (e1, e2) {
e - if (missing(e2)) {
NextMethod(.Generic)
}
else if (any(nchar(.Method) == 0)) {
NextMethod(.Generic)
}
else {
e1 - as.numeric(e1)
e2 - as.numeric(e2)
NextMethod(.Generic)
}
e
}
Sys.Date() / Sys.Date()
Sys.Date() + as.numeric(Sys.Date())
as.numeric(Sys.Date()) + as.numeric(Sys.Date())
Sys.Date() + Sys.Date() # error since its intercepted by +.Date
Thus you will have to issue some as.numeric calls but perhaps not too
many.
However, I think its better not to implement Ops.Date as above but
just leave the Date operations the way they are, extend it with
as.Date.numeric like zoo has done and force the user to use as.numeric
in other cases to make it clear from the code that there is conversion
going on. I have done a fair amount of Date manipulation and have not
found the as.numeric to be onerous.
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Re: [Rd] r cmd build
The Writing Extensions manual says to do an R CMD build for releases to CRAN. That's what I have been doing and that does produce a .tar.gz file even though I get a message about hhc.exe. Is that what I should continue to do and ignore the message or should I be using one of the alternatives you mention to create a .tar.gz release file on Vista? On 9/16/07, Duncan Murdoch [EMAIL PROTECTED] wrote: On 15/09/2007 10:27 PM, Gabor Grothendieck wrote: On Windows Vista hhc.exe is not available. One can do this on an install: rcmd install --docs=normal myPackage to avoid the message about hhc.exe; however, rcmd build does not appear to support --docs=normal so one cannot do a build without getting a message about hhc.exe (although the build still proceeds). Are you talking about build --binary? I recommend using install --build instead. AFAIK a non-binary build doesn't make any use of hhc. Another way to do an install or build without getting that message is to indicate in src/gnuwin32/MkRules that you don't want to build CHM help. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] r cmd build
Something should be added to the Writing Extensions manual since one gets this message during the R CMD build on Vista: hhc: not found CHM compile failed: HTML Help Workshop not installed? and one is not really sure if the result is ok or not -- it does say it FAILED. Even better would be to get rid of the message or improve the message. Again, this all refers to doing a build on Vista. On 9/16/07, Uwe Ligges [EMAIL PROTECTED] wrote: Gabor Grothendieck wrote: The Writing Extensions manual says to do an R CMD build for releases to CRAN. That's what I have been doing and that does produce a .tar.gz file even though I get a message about hhc.exe. Is that what I should continue to do and ignore the message or should I be using one of the alternatives you mention to create a .tar.gz release file on Vista? Well, to produce a tar.gz, it is not required to have hhc.exe. It might happen that vignettes are created and therefore the package is installed for this purpose (and hhc is used to produce some help pages - temporarily). When hhc is not found at that place, just ignore it, the resulting .tar.gz should really be fine. Uwe Ligges On 9/16/07, Duncan Murdoch [EMAIL PROTECTED] wrote: On 15/09/2007 10:27 PM, Gabor Grothendieck wrote: On Windows Vista hhc.exe is not available. One can do this on an install: rcmd install --docs=normal myPackage to avoid the message about hhc.exe; however, rcmd build does not appear to support --docs=normal so one cannot do a build without getting a message about hhc.exe (although the build still proceeds). Are you talking about build --binary? I recommend using install --build instead. AFAIK a non-binary build doesn't make any use of hhc. Another way to do an install or build without getting that message is to indicate in src/gnuwin32/MkRules that you don't want to build CHM help. Duncan Murdoch __ 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] r cmd build
On Windows Vista hhc.exe is not available. One can do this on an install: rcmd install --docs=normal myPackage to avoid the message about hhc.exe; however, rcmd build does not appear to support --docs=normal so one cannot do a build without getting a message about hhc.exe (although the build still proceeds). __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Building an R GUI using gWidgets and RGtk2
A fourth approach would be the proto package. It provides a thin layer over environments making use of the prototype (aka object-based) style of programming which is fundamental different relative to class-based programming (although it is powerful enough to encompass class based programming). The gsubfn package uses proto objects as generalizations of replacement strings that hold state from one replacement to the next. An application that may be closer to yours that uses proto is ggplot2 which is a recent grid-based plotting package. The home page is at http://r-proto.googlecode.com . See the paper on prototype programming linked on the home page as well as the package vignette. On 9/14/07, Gerlanc, Daniel [EMAIL PROTECTED] wrote: Hello, I'm developing a GUI in R that will be used to monitor financial portfolio performance. The GUI will be distributed as an R package. So far, I've decided to use the cairoDevice, RGtk2, gWidgets, and gWidgetsRGtk2 packages to develop the GUI. I am trying to decide what would be the best way to structure the GUI would be. I've considered 3 approaches to building the GUI. The first would be to use S4 classes. I would create parent gui object that would store widgets or containers in slots. Other more specialized guis for different purposes would extend this parent gui object. The difficulty in this approach is R's use of pass-by-value. Once the gui object has been created, changing any of the slots of the gui requires returning a new GUI object or saving one off in a higher level environment and editing the slots directly. Editing the slots directly would completely bypass the S4 method dispatch. Another approach would be more functional. I would create variables that are global within the package or in their own environment and define the package function closures within this environment. This could work, but the code could get noisy when calls to have be made to distinguish between local variable assignment within the environment of the functions and assignment within the namespace of the package. The third approach I've been considering is using the R.oo package. I have never used this package before but it appears to provide similar OO features to Java. Because it allows references, it would seem to provide the features I'm looking for from both the S4 and functional approaches. Any comments or suggestions on these different approaches would be appreciated. Thank you. Sincerely, Daniel Gerlanc __ 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] Date vs date
On 9/14/07, Terry Therneau [EMAIL PROTECTED] wrote:
I wrote the date package long ago, and it has been useful. In my current
task
of reunifying the R (Tom Lumley) and Splus (me) code trees for survival, I'm
removing the explicit dependence on 'date' objects from the expected survival
routines so that they better integrate. Comparison of 'date' to 'Date' has
raised a couple of questions.
Clearly Date is more mature -- more options for conversion, better plotting,
etc (a long list of etc). I see three things where date is better. Only the
last of these really matters, and is the point on which I would like comment.
(Well, actually I'd like to talk you all into a change, of course).
1. Since date uses 1/1/1960 as the base, and so does SAS, those of us who
contantly pass files back and forth between those two packages have a slightly
easier time.
There are some other programs that use 1/1/70. See the R Help Desk article
in R News 4/1 that discusses a few origins.
2. as.date(10) works, as.Date(10) does not. Sometimes I have done a
manipluation that the date package does not understand, and I know that the
result is still of the right type, but the package does not. However, this is
fairly rare and I can work around it. (It mostly occurs in processing the rate
tables for expected survival).
You can define as.Date.numeric in your package and then it will work. zoo
has done that.
library(zoo)
as.Date(10)
Some other things you can do:
today - Sys.Date()
Epoch - today - as.numeric(today)
Epoch + 10 # similar to as.Date(10)
3. temp - as.Date('1990/1/1') - as.date('1953/2/5')
sqrt(temp)
Error in Math.difftime(temp3) : sqrtnot defined for difftime objects
Minor bug: no space before the word 'not'
Major: this shouldn't fail.
People will do things with time intervals that you have not thought of.
Fitting
a growth curve that uses a square root, for instance. I firmly believe that
the
superior behavior in the face of something unexpected is to assume that the
user
knows what they are doing, and return a numeric.
I recognize that assume the user knows what they are doing is an anathema
to the more zealous OO types, but in designing a class I have found that they
often know more than me!
4. Variation on #3 above
(as.Date('2007-9-14') - as.Date('1953-3-10')) / 365.25
Time difference of 54.51335 days
No, I am not 54.5 days old. Both hair color and knee creaking most
definitely proclaim otherwise, I am sorry to say. Time difference / number
should be a number.
Note that you can write:
x - Sys.Date()
y - x + 1
as.numeric(x-y)
as.numeric(x) - as.numeric(y)
5. This is only amusing. Im not saying that as.Date should necessarily
work,
but the format is certainly not ambiguous. (Not standard, but not ambiguous).
Not important to fix, not something that date does any better.
as.Date('09Sep2007')
Error in fromchar(x) : character string is not in a standard unambiguous
format
as.Date(09Sep2007, %d%b%Y)
Terry Therneau
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Re: [Rd] Building an R GUI using gWidgets and RGtk2
On 9/14/07, Gabor Grothendieck [EMAIL PROTECTED] wrote:
On 9/14/07, Gerlanc, Daniel [EMAIL PROTECTED] wrote:
Hello,
I'm developing a GUI in R that will be used to monitor financial
portfolio performance. The GUI will be distributed as an R package. So
far, I've decided to use the cairoDevice, RGtk2, gWidgets, and
gWidgetsRGtk2 packages to develop the GUI. I am trying to decide what
would be the best way to structure the GUI would be.
I've considered 3 approaches to building the GUI. The first would be to
use S4 classes. I would create parent gui object that would store
widgets or containers in slots. Other more specialized guis for
different purposes would extend this parent gui object. The
difficulty in this approach is R's use of pass-by-value. Once the gui
object has been created, changing any of the slots of the gui requires
returning a new GUI object or saving one off in a higher level
environment and editing the slots directly. Editing the slots directly
would completely bypass the S4 method dispatch.
Another approach would be more functional. I would create variables
that are global within the package or in their own environment and
define the package function closures within this environment. This
could work, but the code could get noisy when calls to have be made to
distinguish between local variable assignment within the environment of
the functions and assignment within the namespace of the package.
The third approach I've been considering is using the R.oo package. I
have never used this package before but it appears to provide similar OO
features to Java. Because it allows references, it would seem to
provide the features I'm looking for from both the S4 and functional
approaches.
Any comments or suggestions on these different approaches would be
appreciated.
Thank you.
Sincerely,
Daniel Gerlanc
A fourth approach would be the proto package. It provides a thin
layer over environments making use of the prototype (aka object-based)
style of programming which is fundamental different relative to
class-based programming (although it is powerful enough to encompass
class based programming). The gsubfn package uses proto objects
as generalizations of replacement strings that hold state from one replacement
to the next. An application that may be closer to yours that uses proto
is ggplot2 which is a recent grid-based plotting package. The home page is at
http://r-proto.googlecode.com .
See the paper on prototype programming linked on the home page as well
as the package vignette.
Just to illustrate this further here is a simple example of gWidgets and
proto. In this example we create a proto object, p, that corresponds to
an ok/cancel dialogue labelled Hello and that prints Hello when OK is
pressed. The components of p are go, msg and handler. msg is
a character string, go is a method and handler is a function (to be
a method it would have to pass the proto object as its first arg).
q is created as a child of p so q gets components via
delegation from p. q overrides msg which was Hello in p but is Bye
in q. q acts the same as p except the label is Bye and q prints Bye when
OK is pressed. Note that we pass the proto object to the handler via
the action= argument. Here we used a dot (.) to denote the current
object but you could use this or self or any variable name you prefer.
library(proto)
library(gWidgets)
p - proto(go = function(.) {
w = gwindow()
g = ggroup(container = w)
g.i = ggroup(horizontal=FALSE, container = g)
glabel(.$msg, container = g.i, expand = TRUE)
g.i.b = ggroup(container = g.i)
addSpring(g.i.b)
gbutton(ok, handler = with(., handler), action = ., container = g.i.b)
gbutton(cancel, handler = function(h, ...) dispose(w),
container = g.i.b)
},
msg = Hello,
handler = function(h, ...) {
cat(\n, h$action$msg, \n)
dispose(h$obj)
}
)
p$go() # press ok and Hello is printed
q - p$proto(msg = Bye) # q is child of p overriding msg
q$go() # press ok and Bye is printed
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