[Rd] data(lh) time serie parameters
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 Best, Jean sessionInfo() R version 2.6.2 (2008-02-08) i386-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 -- Jean R. Lobry([EMAIL PROTECTED]) Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I, 43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE allo : +33 472 43 27 56 fax: +33 472 43 13 88 http://pbil.univ-lyon1.fr/members/lobry/ __ 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
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
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/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] callCC in 2.7.0
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/ __ 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
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/ __ 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
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/ __ 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
Re: [Rd] callCC in 2.7.0
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/ __ 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
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/ __ 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
Re: [Rd] callCC in 2.7.0
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 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
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