[Rd] inconsistency in ?factor
In the almost current development version (2009-05-22 r48594) and also in
https://svn.r-project.org/R/trunk/src/library/base/man/factor.Rd
?factor contains (compare the formulations marked by ^^)
\section{Warning}{
The interpretation of a factor depends on both the codes and the
\code{"levels"} attribute. Be careful only to compare factors with
the same set of levels (in the same order).
^
\section{Comparison operators and group generic methods}{
...
Only \code{==} and \code{!=} can be used for factors: a factor can
only be compared to another factor with an identical set of levels
(not necessarily in the same ordering) or to a character vector.
In the development version 2009-05-22 r48594, the latter formulation
"not necessarily in the same ordering" is correct.
f1 <- factor(c("a", "b", "c", "c", "b", "a", "a"), levels=c("a", "b", "c"))
f2 <- factor(c("a", "b", "c", "c", "b", "a", "c"), levels=c("c", "b", "a"))
f1 == f2 # [1] TRUE TRUE TRUE TRUE TRUE TRUE FALSE
The first formulation "Be careful to compare ... levels in the same order" may
be just a warning against a potential problem if the levels have different
order,
however this is not clear.
Petr.
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Re: [Rd] inconsistency in ?factor
G'day Petr,
On Mon, 25 May 2009 09:04:14 +0200
Petr Savicky wrote:
> The first formulation "Be careful to compare ... levels in the same
> order" may be just a warning against a potential problem if the
> levels have different order, however this is not clear.
Well, the first statement is a remark on comparison in general while
the second statement is specific to "comparison operators and generic
methods". There are other ways of comparing objects; note:
R> f1 <- factor(c("a", "b", "c", "c", "b", "a"), levels=c("a", "b", "c"))
R> f2 <- factor(c("a", "b", "c", "c", "b", "a"), levels=c("c", "b", "a"))
R> f1==f2
[1] TRUE TRUE TRUE TRUE TRUE TRUE
R> identical(f1,f2)
[1] FALSE
R> all.equal(f1,f2)
[1] "Attributes: < Component 2: 2 string mismatches >"
Just my 2c.
Cheers,
Berwin
=== Full address =
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Dept of Statistics and Applied Probability+65 6516 6650 (self)
Faculty of Science FAX : +65 6872 3919
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Re: [Rd] [R] step by step debugger in R?
On May 24, 2009, at 10:18 AM, Romain Francois wrote: Robert Gentleman wrote: Hi, I stripped the cc's as I believe that all read this list. Romain Francois wrote: [moving this to r-devel] Robert Gentleman wrote: Hi, Romain Francois wrote: Duncan Murdoch wrote: On 5/22/2009 10:59 AM, Michael wrote: Really I think if there is a Visual Studio strength debugger, our collective time spent in developing R code will be greatly reduced. If someone who knows how to write a debugger plugin for Eclipse wants to help, we could have that fairly easily. All the infrastructure is there; it's the UI part that's missing. Duncan Murdoch [I've copied Mark Bravington and Robert Gentleman to the list as they are likely to have views here, and I am not sure they monitor R- help] Hello, Making a front-end to debugging was one of the proposed google summer of code for this year [1], it was not retained eventually, but I am still motivated. Pretty much all infrastructure is there, and some work has been done __very recently__ in R's debugging internals (ability to step up). As I see it, the ability to call some sort of hook each time the debugger waits for input would make it much easier for someone to write I have still not come to an understanding of what this is supposed to do? When you have the browser prompt you can call any function or code you want to. There is no need for something special to allow you to do that. Sure. What I have in mind is something that gets __automatically__ called, similar to the task callback but happening right before the user is given the browser prompt. I am trying to understand the scenario you have in mind. Is it that the user is running R directly and your debugger is essentially a helper function that gets updated etc as R runs? yes. there are now several ui toolkits that could be use to give some sort of graphical representation of what is being debugged. I agree with you that and IDE should command R and not the other way around, but I am not (yet) here talking about a fully featured IDE, but simply a debugger. I need to read more about embedding R (as in section 8 of WRE). I know you can supply your own implementation of the REPL, but I am not sure this includes the one that goes on once trapped into the browser. Yes - it would be quite useless otherwise ;) there are many examples of GUIs that use it (including the built-in ones [Windows, MAc, ..] or external ones e.g JGR). Cheers, S For example littler ships its own REPL, but this does not seem to fool/deal with browser: $ r -e "print(1:10); browser(); print(1:5) " [1] 1 2 3 4 5 6 7 8 9 10 Called from: NULL c [1] 1 2 3 4 5 Not sure this is an omission of Jeffrey and Dirk or something else. If so, then I don't think that works very well and given the constraints we have with R I don't think it will be able to solve many of the problems that an IDE should. The hook you want will give you some functionality, but no where near enough. In the long run, I do agree. In the short run, I'd prefer taking the bus to the airport rather than walk. Let me suggest instead that the IDE should be running the show. It should initialize an instance of R, but it controls all communication and hence controls what is rendered on the client side. If that is what you mean by embedding R, then yes that is what is needed. There is no way that I can see to support most of the things that IDE type debuggers support without the IDE controlling the communication with R. And if I am wrong about what your debugger will look like please let me know. best wishes Robert front-ends. A recent post of mine (patch included) [2] on R-devel suggested a custom prompt for browser which would do the trick, but I now think that a hook would be more appropriate. Without something similar to that, there is no way that I know of for making a front-end, unless maybe if you embed R ... (please let me know how I am wrong) I think you are wrong. I can't see why it is needed. The external debugger has lots of options for handling debugging. It can rewrite code (see examples in trace for how John Chambers has done this to support tracing at a location), which is AFAIK a pretty standard approach to writing debuggers. It can figure out where the break point is (made a bit easier by allowing it to put in pieces of text in the call to browser). These are things the internal debugger can't do. Thanks. I'll have another look into that. There is also the debug package [3,4] which does __not__ work with R internals but rather works with instrumenting tricks at the R level. debug provides a tcl/tk front-end. It is my understanding that it does not work using R internals (do_browser, ...) because it was not possible at the time, and I believe this is still not possible today, but I might be wrong. I'd prefer to be w
Re: [Rd] inconsistency in ?factor
On Mon, May 25, 2009 at 03:58:06PM +0800, Berwin A Turlach wrote:
> Well, the first statement is a remark on comparison in general while
> the second statement is specific to "comparison operators and generic
> methods". There are other ways of comparing objects; note:
>
> R> f1 <- factor(c("a", "b", "c", "c", "b", "a"), levels=c("a", "b", "c"))
> R> f2 <- factor(c("a", "b", "c", "c", "b", "a"), levels=c("c", "b", "a"))
> R> f1==f2
> [1] TRUE TRUE TRUE TRUE TRUE TRUE
> R> identical(f1,f2)
> [1] FALSE
> R> all.equal(f1,f2)
> [1] "Attributes: < Component 2: 2 string mismatches >"
I see. We have to distinguish comparison of the objects and their components.
Let me propose the following formulation
Two factors may be identical only if they have the same set of
levels (in the same order).
instead of
Be careful only to compare factors with the same set of
levels (in the same order).
Petr.
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Re: [Rd] qbinom (PR#13711)
> "PS" == Petr Savicky
> on Sat, 23 May 2009 18:22:26 +0200 writes:
PS> On Wed, May 20, 2009 at 11:10:11PM +0200, wolfgang.re...@gmail.com
wrote:
PS> ...
>> Strange behavior of qbinom:
>>
>> > qbinom(0.01, 5016279, 1e-07)
>> [1] 0
>> > qbinom(0.01, 5016279, 2e-07)
>> [1] 16
>> > qbinom(0.01, 5016279, 3e-07)
>> [1] 16
>> > qbinom(0.01, 5016279, 4e-07)
>> [1] 16
>> > qbinom(0.01, 5016279, 5e-07)
>> [1] 0
>>
PS> There is a bug in function do_search() in file src/nmath/qbinom.c. This
PS> function contains a cycle
PS> for(;;) {
PS> if(y == 0 ||
PS> (*z = pbinom(y - incr, n, pr, /*l._t.*/TRUE, /*log_p*/FALSE)) < p)
PS> return y;
PS> y = fmax2(0, y - incr);
PS> }
PS> When this cycle stops, *z contains pbinom(y - incr, ...), but is used
PS> as if it is pbinom(y, ...) for the resulting y.
PS> In the example qbinom(p=0.01, size=5016279, prob=4e-07), we get at
PS> some step y=15 as a result of a search left with incr=50, so we have
PS> *z=pbinom(-35, ...)=0. Hence, y=15 is treated as too low and is
increased
PS> to 16. Since 16 is detected to be sufficient, the search stops with
y=16,
PS> which is wrong.
[]
Thanks to Wolfgang and Petr,
Petr's analysis of the problem seems right on spot to me,
and I'm currently testing the patch (and will also add some
regression tests along Petr's example)
which will make it into R-patched (to be R 2.9.1 in a while) and
R-devel.
Gratefully,
Martin Maechler, ETH Zurich
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Re: [Rd] (PR#13705) [wishlist, patch] make row() and col() preserve dimnames
On Sun, 17 May 2009, goodr...@fas.harvard.edu wrote: Full_Name: Ben Goodrich Version: 2.9.0 OS: Linux (Debian unstable) Submission from: (NULL) (128.103.220.16) row(x), col(x), and functions that call them like lower.tri(x) and upper.tri(x) do not retain the rownames or colnames of x in the matrix that is returned. Example from R version 2.9.0 : x <- matrix(1:9, nrow = 3, ncol = 3) rownames(x) <- LETTERS[1:3] colnames(x) <- letters[1:3] dimnames(row(x)) # NULL dimnames(col(x)) # NULL Is there anyone for whom the expected behavior is to drop the dimnames of x ? It is not consistent with other functions of matrices. I suspect everyone who reads the help page carefully. This is not a 'function of a matrix' x but of dim(x) for a 'matrix-like' object. The help page makes this clear to me (I am not the author), so I think you have misread it. There is no question of 'drop the dimames' nor 'retaining the rownames': it is a new object, an integer matrix whatever x was. These functions are mainly for use in programming, and need to be efficient -- so adding dimnames that will never be needed by all the existing code is a non-trivial overhead. By default, row(x) already returns the row numbers of x (and similarly for col()), so how would seeing integers in the rownames be helpful? Without patch: row(x) [,1] [,2] [,3] [1,]111 [2,]222 [3,]333 With patch: row(x) a b c A 1 1 1 B 2 2 2 C 3 3 3 Patch: Index: src/library/base/R/matrix.R === --- src/library/base/R/matrix.R (revision 48553) +++ src/library/base/R/matrix.R (working copy) @@ -104,8 +104,9 @@ labs <- rownames(x, do.NULL=FALSE, prefix="") res <- factor(.Internal(row(dim(x))), labels=labs) dim(res) <- dim(x) -res -} else .Internal(row(dim(x))) +} else res <- .Internal(row(dim(x))) +dimnames(res) <- dimnames(x) +res } Lots of issues here: dimnames() is generic and may not be compatible with the object produced, so checks are needed. And for efficiency this should be done in the C-level code that creates the object if done at all. col <- function(x, as.factor=FALSE) @@ -114,8 +115,9 @@ labs <- colnames(x, do.NULL=FALSE, prefix="") res <- factor(.Internal(col(dim(x))), labels=labs) dim(res) <- dim(x) -res -} else .Internal(col(dim(x))) +} else res <- .Internal(col(dim(x))) +dimnames(res) <- dimnames(x) +res } crossprod <- function(x, y=NULL) .Internal(crossprod(x,y)) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] step by step debugger in R?
Simon Urbanek wrote:
[snip]
I need to read more about embedding R (as in section 8 of WRE). I
know you can supply your own implementation of the REPL, but I am not
sure this includes the one that goes on once trapped into the browser.
Yes - it would be quite useless otherwise ;) there are many examples
of GUIs that use it (including the built-in ones [Windows, MAc, ..] or
external ones e.g JGR).
Cheers,
S
Hi Simon,
Do you mean the rReadConsole callback ? I managed to make some minor
modifications to the rtest.java example that comes with JRI to somewhat
emulate automatically call some code (ls.str()) in this example at the
browser prompt, before giving the prompt to the user.
static boolean browse_first = true ;
public String rReadConsole(Rengine re, String prompt, int
addToHistory) {
System.out.print(prompt);
if( prompt.startsWith( "Browse[") ){
if( browse_first ){
System.out.println( "\n re.eval( \"
print( ls.str() )\" ); " ) ;
re.eval( "print( ls.str() )" ) ;
browse_first = false ;
System.out.println( "\n return
\"ls.str()\"" ) ;
return "ls.str()\n" ;
} else{
browse_first = true ;
}
}
...
}
It seems to work and could get me somewhere, although it has a "it
works, but it does not feel right" taste. Basically the code pretends
the user typed "ls.str\n" at the browse prompt, so that the R evaluator
evaluates it, and then comes back to the browse prompt.
There is also the re.eval( "print( ls.str() )" ) part which was my first
attempt, but apparently this gets evaluated in the global environment,
which is no good. I can get around that by returning some sort of
"record the sys.frames and sys.calls somewhere and do something with
them" function, but I was wondering if you meant something else.
Romain
Here is the transcript of a simple session of ./run rtest (with the
small adjustement above)
> f <- function( x= 5) browser()
rBusy(1)
rBusy(0)
> f()
rBusy(1)
Called from: f()
rBusy(0)
Browse[1]>
re.eval( " print( ls.str() )" );
a : chr "hello"
b : 'data.frame':3 obs. of 2 variables:
$ a: num 1.2 2.3 4.5
$ b: num 1.4 2.6 4.2
bool : logi [1:3] TRUE FALSE FALSE
f : function (x = 5)
iris : 'data.frame':150 obs. of 5 variables:
$ Sepal.Length: num 5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
$ Sepal.Width : num 3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
$ Petal.Length: num 1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
$ Petal.Width : num 0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
$ Species : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1 1
1 1 1 1 1 ...
return "ls.str()"
rBusy(1)
x : num 5
rBusy(0)
Browse[1]>
rBusy(0)
>
--
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[Rd] "interpolator constructor"; was "Scope problem?"
Hi Barry,
this is just a side-remark, probably not at all something you
were interested in, but to be put along this thread in the list
archives, in case some readers are side-tracked there ...
> "BaRow" == Barry Rowlingson
> on Fri, 22 May 2009 17:28:42 +0100 writes:
BaRow> I've just spent today trying to fix a Heisenbug...
BaRow> this function returns a linear interpolator function:
BaRow> interpOne <- function(xl,yl){
BaRow> f = function(data){
BaRow> t = (data-min(xl))/(max(xl)-min(xl))
BaRow> return(min(yl)+t*(max(yl)-min(yl)))
BaRow> }
BaRow> return(f)
BaRow> }
>> k=interpOne(c(0,1),c(4,5))
>> k(0.5)
BaRow> [1] 4.5
Note that "base R" has already two such functions,
namely
splinefun()
and approxfun(),
both returning a *function* as in your examples.
Best,
Martin Maechler, ETH Zurich
BaRow> and this function uses the above to return a function that returns a
BaRow> piece-wise linear interpolator function:
BaRow> mr <- function(){
BaRow> parts = list()
BaRow> ranges = rbind(c(0,1),c(1,2),c(2,3))
BaRow> domains = rbind(c(3,4),c(5,6),c(2,8))
BaRow> for(i in 1:length(ranges[,1])){
BaRow> parts[[i]] = interpOne(ranges[i,],domains[i,])
BaRow> }
BaRow> f = function(d){
BaRow> pos = sum(d>ranges[,1])
BaRow> cat("using pos = ",pos,"\n")
BaRow> return(parts[[pos]](d))
BaRow> }
BaRow> return(f)
BaRow> }
BaRow> m = mr()
BaRow> The 'ranges' and 'domains' vectors describe the pieces. But this
doesn't work:
>> m(0.5)
BaRow> using pos = 1
BaRow> [1] -7
BaRow> - but it should be 3.5 (since 0.5 is in the first piece, and that
BaRow> then interpolates between 3 and 4). What about the other pieces:
>> m(1.5)
BaRow> using pos = 2
BaRow> [1] -1
>> m(2.5)
BaRow> using pos = 3
BaRow> [1] 5
BaRow> - which looks like it's using the last set of range/domain pairs each
BaRow> time. Curious, I thought.
BaRow> So I thought I'd evaluate the functions as they are created in the
BaRow> list to see what's going on. Change the loop to print out:
BaRow> for(i in 1:length(ranges[,1])){
BaRow> parts[[i]] = interpOne(ranges[i,],domains[i,])
BaRow> cat("part ",i," at zero = ",parts[[i]](0),"\n")
BaRow> }
BaRow> and try:
>> m=mr()
BaRow> part 1 at zero = 3
BaRow> part 2 at zero = 4
BaRow> part 3 at zero = -10
BaRow> looks good, those are the intercepts of my pieces... but now:
>> m(0.5)
BaRow> using pos = 1
BaRow> [1] 3.5
>> m(1.5)
BaRow> using pos = 2
BaRow> [1] 5.5
>> m(2.5)
BaRow> using pos = 3
BaRow> [1] 5
BaRow> Woah! It's now working! Trying to observe the thing changes it? A
Heisenbug!
BaRow> I can only think it's my misunderstanding of some aspect of R's
BaRow> scoping and evaluation rules. Does evaluating the functions within
BaRow> that loop cause a copy of some environment to be made, or a 'lazy
BaRow> evaluation' to be evaluated? Or a 'promise' to be fulfilled? I don't
BaRow> really understand those terms, I'd just hoped functions ran in the
BaRow> environment they were created in. Seems sometimes they do, sometimes
BaRow> they dont... What's going on?
BaRow> R 2.9.0 on Ubuntu.
BaRow> Barry
BaRow> __
BaRow> R-devel@r-project.org mailing list
BaRow> https://stat.ethz.ch/mailman/listinfo/r-devel
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Re: [Rd] [R] step by step debugger in R?
On May 25, 2009, at 4:54 PM, Romain Francois wrote:
Simon Urbanek wrote:
[snip]
I need to read more about embedding R (as in section 8 of WRE). I
know you can supply your own implementation of the REPL, but I am
not sure this includes the one that goes on once trapped into the
browser.
Yes - it would be quite useless otherwise ;) there are many
examples of GUIs that use it (including the built-in ones [Windows,
MAc, ..] or external ones e.g JGR).
Cheers,
S
Hi Simon,
Do you mean the rReadConsole callback ? I managed to make some minor
modifications to the rtest.java example that comes with JRI to
somewhat emulate automatically call some code (ls.str()) in this
example at the browser prompt, before giving the prompt to the user.
static boolean browse_first = true ; public String
rReadConsole(Rengine re, String prompt, int addToHistory) {
System.out.print(prompt);
if( prompt.startsWith( "Browse[") ){
if( browse_first ){
System.out.println( "\n re.eval( \"
print( ls.str() )\" ); " ) ;
re.eval( "print( ls.str() )" ) ;
browse_first = false ;
System.out.println( "\n return
\"ls.str()\"" ) ;
return "ls.str()\n" ;
} else{
browse_first = true ;
}
}
...
}
It seems to work and could get me somewhere, although it has a "it
works, but it does not feel right" taste. Basically the code
pretends the user typed "ls.str\n" at the browse prompt, so that the
R evaluator evaluates it, and then comes back to the browse prompt.
There is also the re.eval( "print( ls.str() )" ) part which was my
first attempt, but apparently this gets evaluated in the global
environment, which is no good. I can get around that by returning
some sort of "record the sys.frames and sys.calls somewhere and do
something with them" function, but I was wondering if you meant
something else.
Well, it's entirely up to you - the REPL is working. I wasn't
suggesting you have to use JRI for the debugger, I was just pointing
out that browsing is treated as a regular prompt on the REPL, so any
embedding has access to it.
The JRI eval() command has nothing to do with this directly - you can
evaluate in any environment, just not specifying anything will throw
you in the global environment - it's really up to you (it just
abstracts out the direct access to parse and eval part of R - you can
(ab)use it any way you see fit).
Cheers,
Simon
Romain
Here is the transcript of a simple session of ./run rtest (with the
small adjustement above)
> f <- function( x= 5) browser()
rBusy(1)
rBusy(0)
> f()
rBusy(1)
Called from: f()
rBusy(0)
Browse[1]>
re.eval( " print( ls.str() )" );
a : chr "hello"
b : 'data.frame':3 obs. of 2 variables:
$ a: num 1.2 2.3 4.5
$ b: num 1.4 2.6 4.2
bool : logi [1:3] TRUE FALSE FALSE
f : function (x = 5) iris : 'data.frame':150 obs. of 5 variables:
$ Sepal.Length: num 5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
$ Sepal.Width : num 3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
$ Petal.Length: num 1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
$ Petal.Width : num 0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
$ Species : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1
1 1 1 1 1 1 ...
return "ls.str()"
rBusy(1)
x : num 5
rBusy(0)
Browse[1]>
rBusy(0)
>
--
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Independent R Consultant
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
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Re: [Rd] [R] step by step debugger in R?
Simon Urbanek wrote:
On May 25, 2009, at 4:54 PM, Romain Francois wrote:
Simon Urbanek wrote:
[snip]
I need to read more about embedding R (as in section 8 of WRE). I
know you can supply your own implementation of the REPL, but I am
not sure this includes the one that goes on once trapped into the
browser.
Yes - it would be quite useless otherwise ;) there are many
examples of GUIs that use it (including the built-in ones [Windows,
MAc, ..] or external ones e.g JGR).
Cheers,
S
Hi Simon,
Do you mean the rReadConsole callback ? I managed to make some minor
modifications to the rtest.java example that comes with JRI to
somewhat emulate automatically call some code (ls.str()) in this
example at the browser prompt, before giving the prompt to the user.
static boolean browse_first = true ; public String
rReadConsole(Rengine re, String prompt, int addToHistory) {
System.out.print(prompt);
if( prompt.startsWith( "Browse[") ){
if( browse_first ){
System.out.println( "\n re.eval( \"
print( ls.str() )\" ); " ) ;
re.eval( "print( ls.str() )" ) ;
browse_first = false ;
System.out.println( "\n return
\"ls.str()\"" ) ;
return "ls.str()\n" ;
} else{
browse_first = true ;
}
}
...
}
It seems to work and could get me somewhere, although it has a "it
works, but it does not feel right" taste. Basically the code pretends
the user typed "ls.str\n" at the browse prompt, so that the R
evaluator evaluates it, and then comes back to the browse prompt.
There is also the re.eval( "print( ls.str() )" ) part which was my
first attempt, but apparently this gets evaluated in the global
environment, which is no good. I can get around that by returning
some sort of "record the sys.frames and sys.calls somewhere and do
something with them" function, but I was wondering if you meant
something else.
Thank you for these comments. It confirms what I was thinking.
Well, it's entirely up to you - the REPL is working. I wasn't
suggesting you have to use JRI for the debugger, I was just pointing
out that browsing is treated as a regular prompt on the REPL, so any
embedding has access to it.
I understand that. It was the quickest way for me to get an example
going. java/JRI is one option, but there are others (Qt, ...)
The JRI eval() command has nothing to do with this directly - you can
evaluate in any environment, just not specifying anything will throw
you in the global environment - it's really up to you (it just
abstracts out the direct access to parse and eval part of R - you can
(ab)use it any way you see fit).
... and I surely will.
Romain
Cheers,
Simon
Romain
Here is the transcript of a simple session of ./run rtest (with the
small adjustement above)
> f <- function( x= 5) browser()
rBusy(1)
rBusy(0)
> f()
rBusy(1)
Called from: f()
rBusy(0)
Browse[1]>
re.eval( " print( ls.str() )" );
a : chr "hello"
b : 'data.frame':3 obs. of 2 variables:
$ a: num 1.2 2.3 4.5
$ b: num 1.4 2.6 4.2
bool : logi [1:3] TRUE FALSE FALSE
f : function (x = 5) iris : 'data.frame':150 obs. of 5 variables:
$ Sepal.Length: num 5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
$ Sepal.Width : num 3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
$ Petal.Length: num 1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
$ Petal.Width : num 0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
$ Species : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1
1 1 1 1 1 1 ...
return "ls.str()"
rBusy(1)
x : num 5
rBusy(0)
Browse[1]>
rBusy(0)
>
--
Romain Francois
Independent R Consultant
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
--
Romain Francois
Independent R Consultant
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
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[Rd] Fwd: [R] size of point symbols
Dear all,
Having received no answer in r-help I'm trying r-devel (hoping this is
not a stupid question).
I don't understand the rationale behind the absolute sizes of the point
symbols, and I couldn't find it documented (I got lost in the C code
graphics.c and gave up). The example below uses
Grid to check the size of the symbols against a square of 10mm x 10mm.
checkOneSymbol <- function(pch=0){
gTree(children=gList(
rectGrob(0.5, 0.5, width=unit(10, "mm"), height=unit(10,
"mm"),
gp=gpar(lty=2, fill=NA, col=alpha("black", 0.5))),
pointsGrob(0.5, 0.5, size=unit(10, "mm"),pch=pch,
gp=gpar(col=alpha("red", 0.5)))
))
}
all.symbols <- lapply(0:23, checkOneSymbol)
pdf("symbols.pdf", height=1.2/2.54, width=24.2/2.54)
vp <- viewport(width=0.5, height=0.5, name="main")
pushViewport(vp)
pushViewport(viewport(layout=grid.layout(1, 24,
widths=unit(10, "mm"),
heights=unit(10, "mm"),
just="center")))
for(ii in 0:23){
pushViewport(viewport(layout.pos.col=ii+1, layout.pos.row=1))
grid.draw(all.symbols[[ii+1]])
upViewport(1)
}
dev.off()
What dictates the size of each symbol? (in other words, why is pch=21
a circle of radius given in inches, while pch=2 is a triangle of base
length specified in mm and offset vertically?, etc.)
I'm trying to develop a new symbol for the ggplot2 package where the
size is to be accurately mapped onto the data either in linear size or
area. I was expecting a similar idea behind the choice of base
symbols. Is this documented?
Best regards,
baptiste
_
Baptiste Auguié
School of Physics
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
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[Rd] Vista authorization issues (PR#13718)
Full_Name: David Kesling Version: 2.9.0 OS: Windows Vista & XP sp2 Submission from: (NULL) (65.166.169.237) I upgraded to 2.9.0 on my desktop (XP) and my laptop (Vista Home Basic). The XP machine (with both Tinn-R and JGR) is running just fine... very happy. The laptop is NOT doing too well. I've had to activate the XP-compatability mode AND run Rgui as administrator... and there still seem to be issues. Tinn-R, even after reinstallation, will not properly communicate with Rgui. JGR can't even FIND R 2.9. Again, 2.9 seems to run fine under XP and, with much struggling, under Vista. But registry issues on the Vista platform have broken Tinn-R and JGR IDEs. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Fwd: [R] size of point symbols
I don't know where you get your claims from. R graphics is handled
internally in inches, with a device-specific mapping to pixels/points
etc (which is documented for each device on its help page). This has
to be done carefully, as pixels may not be square.
What the meaning of pch=1:23 is in terms of coordinates is not
documented except via the sources. The source is function GESymbol in
file src/main/engine.c, so for example pch = 2 is
case 2: /* S triangle - point up */
xc = RADIUS * GSTR_0;
r = toDeviceHeight(TRC0 * xc, GE_INCHES, dd);
yc = toDeviceHeight(TRC2 * xc, GE_INCHES, dd);
xc = toDeviceWidth(TRC1 * xc, GE_INCHES, dd);
xx[0] = x; yy[0] = y+r;
xx[1] = x+xc; yy[1] = y-yc;
xx[2] = x-xc; yy[2] = y-yc;
gc->fill = R_TRANWHITE;
GEPolygon(3, xx, yy, gc, dd);
break;
which as you see is in inches, not mm as you asserted. The first line
sets xc to 0.375 inches for cex=1, for example.
You need to take the stroke width (as set by lty) into account when
assessing the visual size of symbols
On Mon, 25 May 2009, baptiste auguie wrote:
Dear all,
Having received no answer in r-help I'm trying r-devel (hoping this is not a
stupid question).
I don't understand the rationale behind the absolute sizes of the point
symbols, and I couldn't find it documented (I got lost in the C code
graphics.c and gave up).
You are expected to study the sources for yourself. That's part of
the price of R.
There is a manual, 'R Internals', that would have explained to you
that graphics.c is part of base graphics and hence not of grid
graphics.
The example below uses
Grid to check the size of the symbols against a square of 10mm x 10mm.
checkOneSymbol <- function(pch=0){
gTree(children=gList(
rectGrob(0.5, 0.5, width=unit(10, "mm"), height=unit(10,
"mm"),
gp=gpar(lty=2, fill=NA, col=alpha("black", 0.5))),
pointsGrob(0.5, 0.5, size=unit(10, "mm"),pch=pch,
gp=gpar(col=alpha("red", 0.5)))
))
}
all.symbols <- lapply(0:23, checkOneSymbol)
pdf("symbols.pdf", height=1.2/2.54, width=24.2/2.54)
vp <- viewport(width=0.5, height=0.5, name="main")
pushViewport(vp)
pushViewport(viewport(layout=grid.layout(1, 24,
widths=unit(10, "mm"),
heights=unit(10, "mm"),
just="center")))
for(ii in 0:23){
pushViewport(viewport(layout.pos.col=ii+1, layout.pos.row=1))
grid.draw(all.symbols[[ii+1]])
upViewport(1)
}
dev.off()
What dictates the size of each symbol? (in other words, why is pch=21
a circle of radius given in inches, while pch=2 is a triangle of base
length specified in mm and offset vertically?, etc.)
I'm trying to develop a new symbol for the ggplot2 package where the size is
to be accurately mapped onto the data either in linear size or area. I was
expecting a similar idea behind the choice of base symbols. Is this
documented?
Best regards,
baptiste
_
Baptiste Auguié
School of Physics
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595__
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