Re: [R] A long digression on packages
Oooops, already missed one: 5. search of the R mailing lists: http://maths.newcastle.edu.au/~rking/R/ ad5. never used this before. Think Google also does an excellent job finding these if you start search with R. Sander. Sander Oom wrote: Maybe some of this confusion about search opportunities and pros/cons could be avoided if the search page on CRAN (http://cran.r-project.org/search.html) would be extended to cover all main search tools! Quickly scanning the discussion, I found these: 1- simply Google: some tips and tricks have been mentioned and would be usefully for most users; 2- R site search (external to CRAN) http://finzi.psych.upenn.edu/search.html; 3- from R prompt: help.search(); 4- browser supported search through local help files: R/doc/html/search/SearchEngine.html. ad1. Google is normally my first source using broad keywords for a method or problem. ad2. just discovered this today! ad3. help.search() provides a simple overview, printing the command with the providing package: help.search(rose) Help files with alias or concept or title matching rose using regular expression matching: hirose(boot)Failure Time of PET Film rose.diag(CircStats)Rose Diagram rose.diag(circular) Rose Diagram windrose(circular) Windrose Generator rosavent(climatol) Wind-rose plot Kinship82(clue) Rosenberg-Kim Kinship Terms Partition Data HolidayDatabase(fCalendar) Holiday Calendars and Utilities conc(ineq) Concentration Measures Type 'help(FOO, package = PKG)' to inspect entry 'FOO(PKG) TITLE'. ad4. when installing all package locally, the results produced by the browser supported search can be overwhelming. Even searching within the results often does not help. If commands were printed along with the providing package would be a good improvement. Then the apparent random order of commands listed might also reveal some order. Hope this is a useful addition to the debate, Sander. Chris Evans wrote: On 5 Jun 2005 at 18:44, Jari Oksanen wrote: There are diverse opinions about netiquette. One of the most basic, in my opinion, is this: if someone posts starts a discussion in a certain forum, you shall not divert it to another forum where it may be hidden by most readers, perhaps even by the originator of the thread. With the greatest of respect for Duncan and the R-devel list, I think Jari has a point here. This is one of the most important issues I've seen raised on this list (R-help) in recent months and I think it may be a structural problem for the development of R, in common with that of much FLOSS s'ware, that there's a separation of users and authors that needs thought. There are no perfect answers but too big a separation and projects go techno and it's hard for those of us who can't code C and who are mere users to help those outstanding people on whom we depend hear what we need: sometimes they are so clever, so specialised in their knowledge, or simply in the realm of genius not the ordinary, that they can't see our problem. I have slowly come to respect that a pretty brusque style from our authorities is the only way to prevent this list being a madhouse but I think that Jim's point may fall into that class that is worth some duplicate bandwidth here. I know I've found the problem Jim highlights very confusing and unhelpful at times. Views, which I didn't know, seem helpful but not a real solution to the key problem: they may tangentially help by ensuring that if your needs fit into a view, it becomes more likely that you'll install the packages you need and a local search may tell you what you need. I've taken the inefficient route which suits me of installing just about every package to make it less likely I'll miss something of use to me. That means my search for kappa and Cohen (with ignore.case=FALSE) turns up at least three implementations of aspects of Cohen's kappa. It may already exist, but a web interface that did a help.search over all the packages in the current release version would be great. (If it does exist, sorry, but I'm no dunce and use R nearly every day and try to read much of r-help every day and don't know it, which may say something!) I think there may be a need for some R improvement and automated updating of what I think is Frank Harrell's function finder: http://biostat.mc.vanderbilt.edu/s/finder/finder.html Though I'm not absolutely sure how fitting your works into something like that could be imposed on developers! Another thing that might help would be for a system by which ordinary users would volunteer to pair up with developers for packages and try to suggest adaptations of the help and such like that might make the packages more user friendly. I wouldn't want to do that for the whole of a huge and vital package like MASS or Hmisc (or base or stats!) but I'm up for pairing with a developer on a smaller package if
Re: [R] A long digression on packages
On 5 Jun 2005 at 18:44, Jari Oksanen wrote: There are diverse opinions about netiquette. One of the most basic, in my opinion, is this: if someone posts starts a discussion in a certain forum, you shall not divert it to another forum where it may be hidden by most readers, perhaps even by the originator of the thread. With the greatest of respect for Duncan and the R-devel list, I think Jari has a point here. This is one of the most important issues I've seen raised on this list (R-help) in recent months and I think it may be a structural problem for the development of R, in common with that of much FLOSS s'ware, that there's a separation of users and authors that needs thought. There are no perfect answers but too big a separation and projects go techno and it's hard for those of us who can't code C and who are mere users to help those outstanding people on whom we depend hear what we need: sometimes they are so clever, so specialised in their knowledge, or simply in the realm of genius not the ordinary, that they can't see our problem. I have slowly come to respect that a pretty brusque style from our authorities is the only way to prevent this list being a madhouse but I think that Jim's point may fall into that class that is worth some duplicate bandwidth here. I know I've found the problem Jim highlights very confusing and unhelpful at times. Views, which I didn't know, seem helpful but not a real solution to the key problem: they may tangentially help by ensuring that if your needs fit into a view, it becomes more likely that you'll install the packages you need and a local search may tell you what you need. I've taken the inefficient route which suits me of installing just about every package to make it less likely I'll miss something of use to me. That means my search for kappa and Cohen (with ignore.case=FALSE) turns up at least three implementations of aspects of Cohen's kappa. It may already exist, but a web interface that did a help.search over all the packages in the current release version would be great. (If it does exist, sorry, but I'm no dunce and use R nearly every day and try to read much of r-help every day and don't know it, which may say something!) I think there may be a need for some R improvement and automated updating of what I think is Frank Harrell's function finder: http://biostat.mc.vanderbilt.edu/s/finder/finder.html Though I'm not absolutely sure how fitting your works into something like that could be imposed on developers! Another thing that might help would be for a system by which ordinary users would volunteer to pair up with developers for packages and try to suggest adaptations of the help and such like that might make the packages more user friendly. I wouldn't want to do that for the whole of a huge and vital package like MASS or Hmisc (or base or stats!) but I'm up for pairing with a developer on a smaller package if anyone thinks that would be helpful. Thoughts for what they're worth. Thanks a million to all developers ... asbestos suit on! Chris -- Chris Evans [EMAIL PROTECTED] Consultant Psychiatrist in Psychotherapy, Rampton Hospital; Research Programmes Director, Nottinghamshire NHS Trust, Hon. SL Institute of Psychiatry *** My views are my own and not representative of those institutions *** __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] A long digression on packages
I haven't followed this thread, but the web interface may exist. (Perhaps help.search() does something that Namazu doesn't do, but I don't think so.) See my .sig below. This is where you get if you click on Search in the R home page. On 06/06/05 11:46, Chris Evans wrote: On 5 Jun 2005 at 18:44, Jari Oksanen wrote: It may already exist, but a web interface that did a help.search over all the packages in the current release version would be great. (If it does exist, sorry, but I'm no dunce and use R nearly every day and try to read much of r-help every day and don't know it, which may say something!) -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron R search page: http://finzi.psych.upenn.edu/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] A long digression on packages
On 6 Jun 2005 at 7:02, Jonathan Baron wrote: I haven't followed this thread, but the web interface may exist. (Perhaps help.search() does something that Namazu doesn't do, but I don't think so.) See my .sig below. This is where you get if you click on Search in the R home page. Not quite: that's wonderful and I use it a lot but it throws up much more from r-project than just the search of the current release packages would in help.search() so it can give you much more than you need ... if there are tuning parameters one can add that will do the necessary, and I'm sure there are, then I'd love to see then and ideally see another search box that applied them for us! But thanks Jonathan! Chris -- Chris Evans [EMAIL PROTECTED] Consultant Psychiatrist in Psychotherapy, Rampton Hospital; Research Programmes Director, Nottinghamshire NHS Trust, Hon. SL Institute of Psychiatry *** My views are my own and not representative of those institutions *** __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] A long digression on packages
On 6/6/2005 6:46 AM, Chris Evans wrote: On 5 Jun 2005 at 18:44, Jari Oksanen wrote: There are diverse opinions about netiquette. One of the most basic, in my opinion, is this: if someone posts starts a discussion in a certain forum, you shall not divert it to another forum where it may be hidden by most readers, perhaps even by the originator of the thread. With the greatest of respect for Duncan and the R-devel list, I think Jari has a point here. This is one of the most important issues I've seen raised on this list (R-help) in recent months and I think it may be a structural problem for the development of R, in common with that of much FLOSS s'ware, that there's a separation of users and authors that needs thought. I don't think the existence of two lists implies separate populations of users versus authors. In fact, I suspect most R users are authors and vice versa (though some authors publish more than others). The point is that when discussing something about the development of R, it makes more sense to do it in the R development list. When asking for help on how to use R, it makes more sense to do it here. If in a few month's time, I want to look up a vaguely remembered discussion about improvements to the package help system, I'll look for it in the R-devel archives. If it took place here, I'd miss it. It may already exist, but a web interface that did a help.search over all the packages in the current release version would be great. (If it does exist, sorry, but I'm no dunce and use R nearly every day and try to read much of r-help every day and don't know it, which may say something!) I don't think a search that is restricted in exactly that way currently exists, but a Google search like kappa site:http://cran.r-project.org/src/contrib/Descriptions might be useful (if you're searching for kappa!). Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] A long digression on packages
On 6 Jun 2005 at 8:38, Jonathan Baron wrote: So use my search engine and unclick all the options except for functions? Do I need a different term? No, I'm being an idiot (as I suspected!) and had looked through your particular search interface and jumped to the big CRAN one. Replying this to R-help list for public helping of humble porridge and in case anyone else is making same mistake. Thanks for a great search facility! BTW, there is a package called ltm for IRT, but my search is not picking it up. I think there is a problem! (It may be fixed by the time you read this.) Yup: ltm has got some of what I want but not all yet!! All power to you on your search interface and thanks again. C -- Chris Evans [EMAIL PROTECTED] Consultant Psychiatrist in Psychotherapy, Rampton Hospital; Research Programmes Director, Nottinghamshire NHS Trust, Hon. SL Institute of Psychiatry *** My views are my own and not representative of those institutions *** __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] A long digression on packages
Maybe some of this confusion about search opportunities and pros/cons could be avoided if the search page on CRAN (http://cran.r-project.org/search.html) would be extended to cover all main search tools! Quickly scanning the discussion, I found these: 1- simply Google: some tips and tricks have been mentioned and would be usefully for most users; 2- R site search (external to CRAN) http://finzi.psych.upenn.edu/search.html; 3- from R prompt: help.search(); 4- browser supported search through local help files: R/doc/html/search/SearchEngine.html. ad1. Google is normally my first source using broad keywords for a method or problem. ad2. just discovered this today! ad3. help.search() provides a simple overview, printing the command with the providing package: help.search(rose) Help files with alias or concept or title matching rose using regular expression matching: hirose(boot)Failure Time of PET Film rose.diag(CircStats)Rose Diagram rose.diag(circular) Rose Diagram windrose(circular) Windrose Generator rosavent(climatol) Wind-rose plot Kinship82(clue) Rosenberg-Kim Kinship Terms Partition Data HolidayDatabase(fCalendar) Holiday Calendars and Utilities conc(ineq) Concentration Measures Type 'help(FOO, package = PKG)' to inspect entry 'FOO(PKG) TITLE'. ad4. when installing all package locally, the results produced by the browser supported search can be overwhelming. Even searching within the results often does not help. If commands were printed along with the providing package would be a good improvement. Then the apparent random order of commands listed might also reveal some order. Hope this is a useful addition to the debate, Sander. Chris Evans wrote: On 5 Jun 2005 at 18:44, Jari Oksanen wrote: There are diverse opinions about netiquette. One of the most basic, in my opinion, is this: if someone posts starts a discussion in a certain forum, you shall not divert it to another forum where it may be hidden by most readers, perhaps even by the originator of the thread. With the greatest of respect for Duncan and the R-devel list, I think Jari has a point here. This is one of the most important issues I've seen raised on this list (R-help) in recent months and I think it may be a structural problem for the development of R, in common with that of much FLOSS s'ware, that there's a separation of users and authors that needs thought. There are no perfect answers but too big a separation and projects go techno and it's hard for those of us who can't code C and who are mere users to help those outstanding people on whom we depend hear what we need: sometimes they are so clever, so specialised in their knowledge, or simply in the realm of genius not the ordinary, that they can't see our problem. I have slowly come to respect that a pretty brusque style from our authorities is the only way to prevent this list being a madhouse but I think that Jim's point may fall into that class that is worth some duplicate bandwidth here. I know I've found the problem Jim highlights very confusing and unhelpful at times. Views, which I didn't know, seem helpful but not a real solution to the key problem: they may tangentially help by ensuring that if your needs fit into a view, it becomes more likely that you'll install the packages you need and a local search may tell you what you need. I've taken the inefficient route which suits me of installing just about every package to make it less likely I'll miss something of use to me. That means my search for kappa and Cohen (with ignore.case=FALSE) turns up at least three implementations of aspects of Cohen's kappa. It may already exist, but a web interface that did a help.search over all the packages in the current release version would be great. (If it does exist, sorry, but I'm no dunce and use R nearly every day and try to read much of r-help every day and don't know it, which may say something!) I think there may be a need for some R improvement and automated updating of what I think is Frank Harrell's function finder: http://biostat.mc.vanderbilt.edu/s/finder/finder.html Though I'm not absolutely sure how fitting your works into something like that could be imposed on developers! Another thing that might help would be for a system by which ordinary users would volunteer to pair up with developers for packages and try to suggest adaptations of the help and such like that might make the packages more user friendly. I wouldn't want to do that for the whole of a huge and vital package like MASS or Hmisc (or base or stats!) but I'm up for pairing with a developer on a smaller package if anyone thinks that would be helpful. Thoughts for what they're worth. Thanks a million to all developers ... asbestos suit on! Chris -- Dr Sander P. Oom Animal, Plant and Environmental
RE: [R] A long digression on packages
From: Chris Evans On 6 Jun 2005 at 7:02, Jonathan Baron wrote: I haven't followed this thread, but the web interface may exist. (Perhaps help.search() does something that Namazu doesn't do, but I don't think so.) See my .sig below. This is where you get if you click on Search in the R home page. Not quite: that's wonderful and I use it a lot but it throws up much more from r-project than just the search of the current release packages would in help.search() so it can give you much more than you need ... if there are tuning parameters one can add that will do the necessary, and I'm sure there are, then I'd love to see then and ideally see another search box that applied them for us! Try something like RSiteSearch(your phrase, restrict=function). The search page itself has more options. But thanks Jonathan! Indeed! Andy Chris -- Chris Evans [EMAIL PROTECTED] Consultant Psychiatrist in Psychotherapy, Rampton Hospital; Research Programmes Director, Nottinghamshire NHS Trust, Hon. SL Institute of Psychiatry *** My views are my own and not representative of those institutions *** __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] A long digression on packages
$.02 (no more): 1. R and its packages are big and diverse, growing rapidly. No simple phrase to describe this, but perhaps the most important contribution to data analysis and statistical practice since Fisher comes close. 2. Ergo lots of diverse information, with little or no way to classify and organize. But this is THE BIG THING in IT today, is it not? -- witness Google, Yahoo search, etc. Everyone says understanding and technology to do this well is in its infancy. So that R and its community struggles too is no surprise. 3. As desirable as efficiency and redundancy reduction is, R's nature and design mitigates against it: core R is centrally controlled (of course!), but the point is **NOT** to restrict contributed packages (core R is the engine and coherent point of entry into all those packages). So the best we can hope for is that package contributors will do their homework before writing to see whether their intended functionality is already there or could be just added to someone else's. Obviously very subjective -- and could be difficult due to terminology variation (different disciplines that use different terms to describe the same statistical functionality). 4. So other than package writers putting as many keywords as they can into their packages for search engines to hit -- and perhaps some limited organization by dedicated workers to organize/bring together obvious stuff like graphics or econometrics or geostatistics, etc. -- it seems that all we can reasonably hope for is to integrate the search functionality into core R and R directory structures. But wait! -- this is exactly what the R team is already doing. Cheers, Bert __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] A long digression on packages
On 6/5/05, Jim Lemon [EMAIL PROTECTED] wrote: There are now about 500 packages on CRAN. Some are focused, covering a particular area well, easy for the prospective user to discover their potential usefulness, while others are less so. CRAN Task Views http://cran.r-project.org/src/contrib/Views/ is one way of addressing CRAN organization. I consider the plotrix package With respect to graphics, the R command: demo(graphics) provides a demonstration of what can be done in R (maybe plotrix should have a demo too?) and the site: http://addictedtor.free.fr/graphiques/ provides examples of what can be done in R using various packages and accepts content contributions. Also the R RSiteSearch function and help.search function are useful for discovery although the latter will only find functions in installed libraries. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] A long digression on packages
Thanks for posting this; I think you raise good points, but they're more appropriate for R-devel, so I've posted my reply there. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] A long digression on packages
On 5 Jun 2005, at 16:47, Duncan Murdoch wrote: Thanks for posting this; I think you raise good points, but they're more appropriate for R-devel, so I've posted my reply there. There are diverse opinions about netiquette. One of the most basic, in my opinion, is this: if someone posts starts a discussion in a certain forum, you shall not divert it to another forum where it may be hidden by most readers, perhaps even by the originator of the thread. cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
