Re: [R] Programming Concepts and Philosophy
On Fri, Jun 20, 2008 at 10:04:46AM -0500, hadley wickham wrote: 2008/6/20 [EMAIL PROTECTED] [EMAIL PROTECTED]: On 20 июн, 11:06, Wacek Kusnierczyk [EMAIL PROTECTED] wrote: the result may be that the more beautiful the code, the more the performance sucks. Sad but true. If you do nothing to your code, in 18 months time its performance will have doubled because computers will have become faster. Your code will not get easier to understand by itself. Very true. And I would like to contribute one of my favorite quotations: It is easier to optimize correct code than to correct optimized code. --Bill Harlan cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Programming Concepts and Philosophy
To quote Jon Bentley (Programming Pearls): The fastest, cheapest, most reliable piece of code is that which isn't there; design as much out of your code as you design in. On Mon, Jun 23, 2008 at 3:57 AM, Philipp Pagel [EMAIL PROTECTED] wrote: On Fri, Jun 20, 2008 at 10:04:46AM -0500, hadley wickham wrote: 2008/6/20 [EMAIL PROTECTED] [EMAIL PROTECTED]: On 20 июн, 11:06, Wacek Kusnierczyk [EMAIL PROTECTED] wrote: the result may be that the more beautiful the code, the more the performance sucks. Sad but true. If you do nothing to your code, in 18 months time its performance will have doubled because computers will have become faster. Your code will not get easier to understand by itself. Very true. And I would like to contribute one of my favorite quotations: It is easier to optimize correct code than to correct optimized code. --Bill Harlan cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Programming Concepts and Philosophy
This is a lot like music- a good musician knows better when not to play than when to (guitar teacher I had 15+ years ago). stephen On Mon, Jun 23, 2008 at 8:33 AM, jim holtman [EMAIL PROTECTED] wrote: To quote Jon Bentley (Programming Pearls): The fastest, cheapest, most reliable piece of code is that which isn't there; design as much out of your code as you design in. On Mon, Jun 23, 2008 at 3:57 AM, Philipp Pagel [EMAIL PROTECTED] wrote: On Fri, Jun 20, 2008 at 10:04:46AM -0500, hadley wickham wrote: 2008/6/20 [EMAIL PROTECTED] [EMAIL PROTECTED]: On 20 иÑн, 11:06, Wacek Kusnierczyk [EMAIL PROTECTED] wrote: the result may be that the more beautiful the code, the more the performance sucks. Sad but true. If you do nothing to your code, in 18 months time its performance will have doubled because computers will have become faster. Your code will not get easier to understand by itself. Very true. And I would like to contribute one of my favorite quotations: It is easier to optimize correct code than to correct optimized code. --Bill Harlan cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Programming Concepts and Philosophy
Simon Blomberg wrote: I try to use a functional programming style. I define functions within functions when it is helpful in terms of information hiding. I avoid writing functions with side-effects as much as possible, so the only communication of the called function with the caller function is through the arguments and the returned value. I try to keep the code as simple and clear as possible (this is one of the things I fail at most). An appropriate amount of comments is also useful, especially when returning to old code after a long break. OOP is useful for really big projects, but I find OOP unnecessarily complicated for small jobs. I found Code Complete, by McConnell (http://www.cc2e.com/) to be very helpful. I'm sure there are other books around with similar tips. Before I switched to R, I used XLisp-Stat. I found learning Lisp to be a really good way to learn good programming practices. Good Lisp code is the closest thing you can get to poetry in computer programming. Lisp Style Design, by Miller and Benson was helpful. I'd like to see an S Style Design. i support this view. i found sicp (structure and interpretation of computer programs, by abelson sussman, a real classic in the field) particularly enlightening, although it certainly is a bit outdated in many respects -- but just a bit. functional programming style is great, but beware -- r will create (afaik, experts please correct me if this is wrong) a deep copy of about any object you send as an argument to a function (if only when it is actually used inside the function), and the result may be that the more beautiful the code, the more the performance sucks. in pure functional programming, a function cannot change any part of the object passed to it as an argument, so there's no need for making a local copy. in r everything can happen as you can deparse the call to a function inside the function body, and you can never tell whether the object you pass to a function will be changed or not, given only the function's signature. vQ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Programming Concepts and Philosophy
On Fri, Jun 20, 2008 at 09:06:24AM +0200, Wacek Kusnierczyk wrote: Simon Blomberg wrote: I try to use a functional programming style. I define functions within functions when it is helpful in terms of information hiding. I avoid writing functions with side-effects as much as possible, so the only communication of the called function with the caller function is through the arguments and the returned value. I try to keep the code as simple and clear as possible (this is one of the things I fail at most). An appropriate amount of comments is also useful, especially when returning to old code after a long break. OOP is useful for really big projects, but I find OOP unnecessarily complicated for small jobs. I found Code Complete, by McConnell (http://www.cc2e.com/) to be very helpful. I'm sure there are other books around with similar tips. Before I switched to R, I used XLisp-Stat. I found learning Lisp to be a really good way to learn good programming practices. Good Lisp code is the closest thing you can get to poetry in computer programming. Lisp Style Design, by Miller and Benson was helpful. I'd like to see an S Style Design. i support this view. i found sicp (structure and interpretation of computer programs, by abelson sussman, a real classic in the field) particularly enlightening, although it certainly is a bit outdated in many respects -- but just a bit. functional programming style is great, but beware -- r will create (afaik, experts please correct me if this is wrong) a deep copy of about any object you send as an argument to a function (if only when it is actually used inside the function), and the result may be that the more beautiful the code, the more the performance sucks. Not necessarily -- R's promise mechanism quite reasonably ensures that copies of parameter objects are only made upon modifying these objects. However, on a more fundamental programming philosophy note, the fact that R does not allow multiple references to one object is a limitation. One of the fundamental principles of good programming is that there should be a one-to-one correspondence between instances in the program and objects in the real world (problem domain etc.), and having no references makes achieving this difficult (and quite impossible for more complex systems). Best regards, Jan -- +- Jan T. Kim ---+ | email: [EMAIL PROTECTED] | | WWW: http://www.cmp.uea.ac.uk/people/jtk | *-= hierarchical systems are for files, not for humans =-* __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Programming Concepts and Philosophy
However, on a more fundamental programming philosophy note, the fact that R does not allow multiple references to one object is a limitation. One of the fundamental principles of good programming is that there should be a one-to-one correspondence between instances in the program and objects in the real world (problem domain etc.), and having no references makes achieving this difficult (and quite impossible for more complex systems). This is a principle of object oriented programming, not good programming in general! Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Programming Concepts and Philosophy
Maybe I missed it, but I haven't seen in this tread mention of Venables and Ripley (2000) S Programming (Springer). I found it interesting and useful, though I have not used it as much as MASS -- partly because it is more specialized and it's coverage is not as broad. Spencer hadley wickham wrote: However, on a more fundamental programming philosophy note, the fact that R does not allow multiple references to one object is a limitation. One of the fundamental principles of good programming is that there should be a one-to-one correspondence between instances in the program and objects in the real world (problem domain etc.), and having no references makes achieving this difficult (and quite impossible for more complex systems). This is a principle of object oriented programming, not good programming in general! Hadley __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Programming Concepts and Philosophy
I read the Wizard Book too. Absolutely classic! I agree about paying attention to performance, of course. Lisp programmers bend over backwards to write tail-recursive functions for similar performance reasons. So you have to pay attention to the language's idiosyncracies. But the time spent coding is usually much longer than the eventual run time. Learning to write well-designed code can do more to save time, even if the run time is slightly longer than optimal. If run time is an issue, then switching to C or Fortran etc. might be the best bet. But even in that case, using R for prototyping code can provide valueable insights. Cheers, Simon. Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician Faculty of Biological and Chemical Sciences The University of Queensland St. Lucia Queensland 4072 Australia T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. - John Tukey. -Original Message- From: Wacek Kusnierczyk [mailto:[EMAIL PROTECTED] Sent: Fri 20/06/2008 5:06 PM To: R help Cc: Simon Blomberg Subject: Re: [R] Programming Concepts and Philosophy Simon Blomberg wrote: I try to use a functional programming style. I define functions within functions when it is helpful in terms of information hiding. I avoid writing functions with side-effects as much as possible, so the only communication of the called function with the caller function is through the arguments and the returned value. I try to keep the code as simple and clear as possible (this is one of the things I fail at most). An appropriate amount of comments is also useful, especially when returning to old code after a long break. OOP is useful for really big projects, but I find OOP unnecessarily complicated for small jobs. I found Code Complete, by McConnell (http://www.cc2e.com/) to be very helpful. I'm sure there are other books around with similar tips. Before I switched to R, I used XLisp-Stat. I found learning Lisp to be a really good way to learn good programming practices. Good Lisp code is the closest thing you can get to poetry in computer programming. Lisp Style Design, by Miller and Benson was helpful. I'd like to see an S Style Design. i support this view. i found sicp (structure and interpretation of computer programs, by abelson sussman, a real classic in the field) particularly enlightening, although it certainly is a bit outdated in many respects -- but just a bit. functional programming style is great, but beware -- r will create (afaik, experts please correct me if this is wrong) a deep copy of about any object you send as an argument to a function (if only when it is actually used inside the function), and the result may be that the more beautiful the code, the more the performance sucks. in pure functional programming, a function cannot change any part of the object passed to it as an argument, so there's no need for making a local copy. in r everything can happen as you can deparse the call to a function inside the function body, and you can never tell whether the object you pass to a function will be changed or not, given only the function's signature. vQ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Programming Concepts and Philosophy
On 20 июн, 11:06, Wacek Kusnierczyk [EMAIL PROTECTED] wrote: the result may be that the more beautiful the code, the more the performance sucks. Sad but true. Andrey __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Programming Concepts and Philosophy
on 06/20/2008 10:04 AM hadley wickham wrote: If you do nothing to your code, in 18 months time its performance will have doubled because computers will have become faster. Your code will not get easier to understand by itself. I suspect a good fortunes candidate... :-) Marc __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Programming Concepts and Philosophy
2008/6/20 hadley wickham [EMAIL PROTECTED]: 2008/6/20 [EMAIL PROTECTED] [EMAIL PROTECTED]: On 20 июн, 11:06, Wacek Kusnierczyk [EMAIL PROTECTED] wrote: the result may be that the more beautiful the code, the more the performance sucks. Sad but true. If you do nothing to your code, in 18 months time its performance will have doubled because computers will have become faster. Your code But that doesn't seem to be true anymore (if we are talking single CPU), and it seems not to have been true for at least a few years (e.g., http://www.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-183.html for instance, their figure 2 in p. 6). will not get easier to understand by itself. No it won't. Best, R. Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ramon Diaz-Uriarte Statistical Computing Team Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz Phone: +34-91-224-6900 ext. 3019 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Programming Concepts and Philosophy
hadley wickham wrote: 2008/6/20 [EMAIL PROTECTED] [EMAIL PROTECTED]: If you do nothing to your code, in 18 months time its performance will have doubled because computers will have become faster. Your code will not get easier to understand by itself. Very nicely put .. and true too! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Programming Concepts and Philosophy
I try to use a functional programming style. I define functions within functions when it is helpful in terms of information hiding. I avoid writing functions with side-effects as much as possible, so the only communication of the called function with the caller function is through the arguments and the returned value. I try to keep the code as simple and clear as possible (this is one of the things I fail at most). An appropriate amount of comments is also useful, especially when returning to old code after a long break. OOP is useful for really big projects, but I find OOP unnecessarily complicated for small jobs. I found Code Complete, by McConnell (http://www.cc2e.com/) to be very helpful. I'm sure there are other books around with similar tips. Before I switched to R, I used XLisp-Stat. I found learning Lisp to be a really good way to learn good programming practices. Good Lisp code is the closest thing you can get to poetry in computer programming. Lisp Style Design, by Miller and Benson was helpful. I'd like to see an S Style Design. Cheers, Simon. On Fri, 2008-06-20 at 14:35 +1200, Murray Jorgensen wrote: I am wondering if people on the list could recommend books that they have found helpful about programming concepts and style? I often find that students write R programs by copying existing code but could really benefit from the understanding of more general programming ideas. An example would be to avoid writing functions which attempt to modify their parameters. Another principle would be not to write programs with numbers used as constants but to assign them to named objects as in n - 120 # number of observations p - 10 # number of variables near the beginning of a program rather than using 10 and 120 throughout the script. This sort of stuff is not specifically R but can be a problem for students with little programming background. I am happy to summarise responses. Murray Jorgensen -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician Faculty of Biological and Chemical Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 http://www.uq.edu.au/~uqsblomb email: S.Blomberg1_at_uq.edu.au Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. - John Tukey. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
