Re: [R] read.csv.sql() to select from a large csv file
On Fri, Nov 23, 2012 at 5:05 PM, Juliane Struve
juliane_str...@yahoo.co.uk wrote:
Rui, Anthony, and Gabor,
I got this to work in the end:
for(i in length(Names_EastCoast){
name - Names_EastCoast[i]
sql - paste(select * from file where ID =
',name,',sep = )
Data - read.csv.sql(filename,sql = sql)
}
loops through all individuals in the csv file.
That sets i to the length of Names_EastCoast and then runs the query only once.
I think you want:
for(nam in Names_EastCoast) {
Data - fn$read.csv.sql(filename,
sql = 'select * from file where ID = $nam ')
# ... process Data ...
}
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
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Re: [R] qbinom
On Dec 1, 2012, at 01:00 , David Winsemius wrote: On Nov 30, 2012, at 1:05 PM, jaybell wrote: sorry, I repost the question again Why? This was already answered. a=c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9) b=c(0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1) cor(a,b)= -1 pa=qbinom(a, 1, 0.5) pb=qbinom(b, 1, 0.5) cor(pa,pb)=-0.8 but when pa=qbinom(a,10,0.5) pb=qbinom(b,10,0.5) cor(pa,pb) becomes -1 again What part of plot the values was difficult to understand? (Actually, list the values might be more informative in this case: pa [1] 0 0 0 0 0 1 1 1 1 pb [1] 1 1 1 1 0 0 0 0 0 Notice that pb != 1-pa when size=1.) -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ 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] segfault debugging
Thank you so far. Here is an excerpt from the gdb session after a crash: Program received signal SIGSEGV, Segmentation fault. 0xb7509a6b in Rf_allocVector () from /usr/lib/R/lib/libR.so (gdb) backtrace #0 0xb7509a6b in Rf_allocVector () from /usr/lib/R/lib/libR.so #1 0xb744b64c in ?? () from /usr/lib/R/lib/libR.so #2 0xb74c58bf in ?? () from /usr/lib/R/lib/libR.so #3 0xb74c9c62 in Rf_eval () from /usr/lib/R/lib/libR.so #4 0xb74ce60f in Rf_applyClosure () from /usr/lib/R/lib/libR.so #5 0xb74c9f29 in Rf_eval () from /usr/lib/R/lib/libR.so #6 0xb7503002 in Rf_ReplIteration () from /usr/lib/R/lib/libR.so #7 0xb7503298 in ?? () from /usr/lib/R/lib/libR.so #8 0xb7503812 in run_Rmainloop () from /usr/lib/R/lib/libR.so #9 0xb7503839 in Rf_mainloop () from /usr/lib/R/lib/libR.so #10 0x08048768 in main () #11 0xb728de46 in __libc_start_main (main=0x8048730 main, argc=8, ubp_av=0xbfdb7824, init=0x80488a0 __libc_csu_init, fini=0x8048890 __libc_csu_fini, rtld_fini=0xb7784590, stack_end=0xbfdb781c) at libc-start.c:228 #12 0x08048791 in _start () It seems to me that the error is in frame #0. Does it mean that there is a bug in libR.so? What can I do next? Greetings Donatella __ 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.
[R] Getting all possible contingency tables
Hello all, Let say I have 2-way contingency table: Tab - matrix(c(8, 10, 12, 6), nr = 2) and the Chi-squared test could not reject the independence: chisq.test(Tab) Pearson's Chi-squared test with Yates' continuity correction data: Tab X-squared = 1.0125, df = 1, p-value = 0.3143 However I want to get all possible contingency tables under this independence scenario (one of them would obviously be the given table as, we could not reject the independence), and for each such table I want to calculate the Ch-sq statistic. Can somebody help me how to generate all such tables? Thanks and regards, __ 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] segfault debugging
On 12-12-01 6:56 AM, Donatella Quagli wrote: Thank you so far. Here is an excerpt from the gdb session after a crash: Program received signal SIGSEGV, Segmentation fault. 0xb7509a6b in Rf_allocVector () from /usr/lib/R/lib/libR.so (gdb) backtrace #0 0xb7509a6b in Rf_allocVector () from /usr/lib/R/lib/libR.so #1 0xb744b64c in ?? () from /usr/lib/R/lib/libR.so #2 0xb74c58bf in ?? () from /usr/lib/R/lib/libR.so #3 0xb74c9c62 in Rf_eval () from /usr/lib/R/lib/libR.so #4 0xb74ce60f in Rf_applyClosure () from /usr/lib/R/lib/libR.so #5 0xb74c9f29 in Rf_eval () from /usr/lib/R/lib/libR.so #6 0xb7503002 in Rf_ReplIteration () from /usr/lib/R/lib/libR.so #7 0xb7503298 in ?? () from /usr/lib/R/lib/libR.so #8 0xb7503812 in run_Rmainloop () from /usr/lib/R/lib/libR.so #9 0xb7503839 in Rf_mainloop () from /usr/lib/R/lib/libR.so #10 0x08048768 in main () #11 0xb728de46 in __libc_start_main (main=0x8048730 main, argc=8, ubp_av=0xbfdb7824, init=0x80488a0 __libc_csu_init, fini=0x8048890 __libc_csu_fini, rtld_fini=0xb7784590, stack_end=0xbfdb781c) at libc-start.c:228 #12 0x08048791 in _start () It seems to me that the error is in frame #0. Does it mean that there is a bug in libR.so? What can I do next? It means that the error was detected when trying to do a memory allocation. That could be a bug in R, but more likely something else has damaged the memory management system structures, e.g. a function writing to memory that it doesn't own. Bugs like this are hard to track down, because the damage could have occurred a long time before it showed up, and small changes to your script could affect it. I would try to narrow it down to a single statement in your script. You might be able to deduce that from the last line printed before the crash. If you don't have any printing, you could try adding some, but as I mentioned above, that might make the bug behave differently. Another approach is to cut off statements at the end of your script. That probably won't affect the bug until you cut off the statement that actually triggered it (but it might, which is why this kind of bug is so frustrating to track down). If you find the bad statement, then look at calls to external code in it, or recently executed before it. See if any of them look like they contain errors. Common errors are to write to an array without allocating it, or to write beyond the bounds of an array, or (in .Call() code) to allocate something and then fail to protect it from garbage collection. You could also figure out what the problem is that caused the seg fault in frame 0. It might be because some particular variable contains a garbage value. Then in a new run, you can ask gdb to break when that memory location takes on the garbage value. This is usually effective if you really can identify the bad value, but doing that can be hard, especially when you aren't familiar with how things normally work. Good luck! Duncan Murdoch __ 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] Getting all possible contingency tables
Are you basically asking for all possible permutations of the table? If so see ?permn in the combinat package. John Kane Kingston ON Canada -Original Message- From: bogaso.christo...@gmail.com Sent: Sat, 01 Dec 2012 18:10:15 +0545 To: r-help@r-project.org Subject: [R] Getting all possible contingency tables Hello all, Let say I have 2-way contingency table: Tab - matrix(c(8, 10, 12, 6), nr = 2) and the Chi-squared test could not reject the independence: chisq.test(Tab) Pearson's Chi-squared test with Yates' continuity correction data: Tab X-squared = 1.0125, df = 1, p-value = 0.3143 However I want to get all possible contingency tables under this independence scenario (one of them would obviously be the given table as, we could not reject the independence), and for each such table I want to calculate the Ch-sq statistic. Can somebody help me how to generate all such tables? Thanks and regards, __ 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. FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more! __ 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.
[R] cubic spline
Hallo, I'm facing a problem and I would really appreciate your support. I have to translate some Matalb code in R that I don't know very well but I would like to. I have to interpolate 5 point with a cubic spline function and then I expect my function returns the Y value as output a specific X value inside the evaluation range. Let's suppose that: 1- *X = [-10, -5, 0, 5, 10]* 2 - *Y = [12, 10, 8, 7, 6]* 3 - *I have to interpolate with a cubic spline assuming x=11* In Matlab I used this function: *y = interp1(X, Y, x, cubic); * How can I do the same in R? Many thanks in advance for your reply and support! Kindly Steve -- View this message in context: http://r.789695.n4.nabble.com/cubic-spline-tp4651537.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] How to built a pivot table of value
Hi R users Imagine the table base: p=c(d,d,b,b,a,a) q=c(v1,v2,v1,v2,v1,v2) r=c(5,2,4,8,9,7) base=data.frame(p,q,r) base p q r 1 d v1 5 2 d v2 2 3 b v1 4 4 b v2 8 5 a v1 9 6 a v2 7 How programming R to get this result: v1 v2 a 97 b 48 d 52 I tried the function table but the result is divided in several matrix: table(base$p,base$q,base$r) , , = 2 v1 v2 a 0 0 b 0 0 d 0 1 , , = 4 v1 v2 a 0 0 b 1 0 d 0 0 , , = 5 v1 v2 a 0 0 b 0 0 d 1 0 , , = 7 v1 v2 a 0 1 b 0 0 d 0 0 , , = 8 v1 v2 a 0 0 b 0 1 d 0 0 , , = 9 v1 v2 a 1 0 b 0 0 d 0 0 SIncerely yours -- View this message in context: http://r.789695.n4.nabble.com/How-to-built-a-pivot-table-of-value-tp4651539.html Sent from the R help mailing list archive at Nabble.com. __ 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] cubic spline
Hi Steve, Check the splint function in the fields package. HTH, Jorge.- On Sat, Dec 1, 2012 at 11:09 PM, Steve Stephenson wrote: Hallo, I'm facing a problem and I would really appreciate your support. I have to translate some Matalb code in R that I don't know very well but I would like to. I have to interpolate 5 point with a cubic spline function and then I expect my function returns the Y value as output a specific X value inside the evaluation range. Let's suppose that: 1- *X = [-10, -5, 0, 5, 10]* 2 - *Y = [12, 10, 8, 7, 6]* 3 - *I have to interpolate with a cubic spline assuming x=11* In Matlab I used this function: *y = interp1(X, Y, x, cubic); * How can I do the same in R? Many thanks in advance for your reply and support! Kindly Steve -- View this message in context: http://r.789695.n4.nabble.com/cubic-spline-tp4651537.html Sent from the R help mailing list archive at Nabble.com. __ 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. [[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] How to built a pivot table of value
Hi, One way could be with(base, tapply(r, list(p, q), sum)) HTH, Jorge.- On Sat, Dec 1, 2012 at 11:37 PM, CE.KA wrote: Hi R users Imagine the table base: p=c(d,d,b,b,a,a) q=c(v1,v2,v1,v2,v1,v2) r=c(5,2,4,8,9,7) base=data.frame(p,q,r) base p q r 1 d v1 5 2 d v2 2 3 b v1 4 4 b v2 8 5 a v1 9 6 a v2 7 How programming R to get this result: v1 v2 a 97 b 48 d 52 I tried the function table but the result is divided in several matrix: table(base$p,base$q,base$r) , , = 2 v1 v2 a 0 0 b 0 0 d 0 1 , , = 4 v1 v2 a 0 0 b 1 0 d 0 0 , , = 5 v1 v2 a 0 0 b 0 0 d 1 0 , , = 7 v1 v2 a 0 1 b 0 0 d 0 0 , , = 8 v1 v2 a 0 0 b 0 1 d 0 0 , , = 9 v1 v2 a 1 0 b 0 0 d 0 0 SIncerely yours -- View this message in context: http://r.789695.n4.nabble.com/How-to-built-a-pivot-table-of-value-tp4651539.html Sent from the R help mailing list archive at Nabble.com. __ 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. [[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] Getting all possible contingency tables
Thanks John for your reply. However still not clear how I should proceed. My goal is to generate all possible contingency tables. Basically I want to see the distribution of Chi-squared Statistic under independence (NULL). So I was thinking if I can generate all possible permutation of integer numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is there any R function to do that? Thanks and regards, On 01-12-2012 18:39, John Kane wrote: Are you basically asking for all possible permutations of the table? If so see ?permn in the combinat package. John Kane Kingston ON Canada -Original Message- From: bogaso.christo...@gmail.com Sent: Sat, 01 Dec 2012 18:10:15 +0545 To: r-help@r-project.org Subject: [R] Getting all possible contingency tables Hello all, Let say I have 2-way contingency table: Tab - matrix(c(8, 10, 12, 6), nr = 2) and the Chi-squared test could not reject the independence: chisq.test(Tab) Pearson's Chi-squared test with Yates' continuity correction data: Tab X-squared = 1.0125, df = 1, p-value = 0.3143 However I want to get all possible contingency tables under this independence scenario (one of them would obviously be the given table as, we could not reject the independence), and for each such table I want to calculate the Ch-sq statistic. Can somebody help me how to generate all such tables? Thanks and regards, __ 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. FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more! __ 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] How to built a pivot table of value
On 01-12-2012, at 13:37, CE.KA wrote: Hi R users Imagine the table base: p=c(d,d,b,b,a,a) q=c(v1,v2,v1,v2,v1,v2) r=c(5,2,4,8,9,7) base=data.frame(p,q,r) base p q r 1 d v1 5 2 d v2 2 3 b v1 4 4 b v2 8 5 a v1 9 6 a v2 7 How programming R to get this result: v1 v2 a 97 b 48 d 52 xtabs(r~p+q,data=base) Output - q p v1 v2 a 9 7 b 4 8 d 5 2 Berend __ 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] How to built a pivot table of value
One way, using the plyr package would be: library(plyr) dcast(base, p ~ q) John Kane Kingston ON Canada -Original Message- From: ce.kay...@yahoo.fr Sent: Sat, 1 Dec 2012 04:37:02 -0800 (PST) To: r-help@r-project.org Subject: [R] How to built a pivot table of value Hi R users Imagine the table base: p=c(d,d,b,b,a,a) q=c(v1,v2,v1,v2,v1,v2) r=c(5,2,4,8,9,7) base=data.frame(p,q,r) base p q r 1 d v1 5 2 d v2 2 3 b v1 4 4 b v2 8 5 a v1 9 6 a v2 7 How programming R to get this result: v1 v2 a 97 b 48 d 52 I tried the function table but the result is divided in several matrix: table(base$p,base$q,base$r) , , = 2 v1 v2 a 0 0 b 0 0 d 0 1 , , = 4 v1 v2 a 0 0 b 1 0 d 0 0 , , = 5 v1 v2 a 0 0 b 0 0 d 1 0 , , = 7 v1 v2 a 0 1 b 0 0 d 0 0 , , = 8 v1 v2 a 0 0 b 0 1 d 0 0 , , = 9 v1 v2 a 1 0 b 0 0 d 0 0 SIncerely yours -- View this message in context: http://r.789695.n4.nabble.com/How-to-built-a-pivot-table-of-value-tp4651539.html Sent from the R help mailing list archive at Nabble.com. __ 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. GET FREE SMILEYS FOR YOUR IM EMAIL - Learn more at http://www.inbox.com/smileys Works with AIM®, MSN® Messenger, Yahoo!® Messenger, ICQ®, Google Talk™ and most webmails __ 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] Getting all possible contingency tables
R can usually do almost anything but if the function exists I am not aware of it. Sorry. I did misunderstand what you were doing. John Kane Kingston ON Canada -Original Message- From: bogaso.christo...@gmail.com Sent: Sat, 01 Dec 2012 19:33:09 +0545 To: jrkrid...@inbox.com Subject: Re: [R] Getting all possible contingency tables Thanks John for your reply. However still not clear how I should proceed. My goal is to generate all possible contingency tables. Basically I want to see the distribution of Chi-squared Statistic under independence (NULL). So I was thinking if I can generate all possible permutation of integer numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is there any R function to do that? Thanks and regards, On 01-12-2012 18:39, John Kane wrote: Are you basically asking for all possible permutations of the table? If so see ?permn in the combinat package. John Kane Kingston ON Canada -Original Message- From: bogaso.christo...@gmail.com Sent: Sat, 01 Dec 2012 18:10:15 +0545 To: r-help@r-project.org Subject: [R] Getting all possible contingency tables Hello all, Let say I have 2-way contingency table: Tab - matrix(c(8, 10, 12, 6), nr = 2) and the Chi-squared test could not reject the independence: chisq.test(Tab) Pearson's Chi-squared test with Yates' continuity correction data: Tab X-squared = 1.0125, df = 1, p-value = 0.3143 However I want to get all possible contingency tables under this independence scenario (one of them would obviously be the given table as, we could not reject the independence), and for each such table I want to calculate the Ch-sq statistic. Can somebody help me how to generate all such tables? Thanks and regards, __ 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. FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more! FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! __ 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] Getting all possible contingency tables
Christopher: Don't do this! If I understand you correctly, you want FIsher's exact test. This is already available in R, using far smarter algorithms then you would. See: ?fisher.test -- Bert On Sat, Dec 1, 2012 at 5:48 AM, Christofer Bogaso bogaso.christo...@gmail.com wrote: Thanks John for your reply. However still not clear how I should proceed. My goal is to generate all possible contingency tables. Basically I want to see the distribution of Chi-squared Statistic under independence (NULL). So I was thinking if I can generate all possible permutation of integer numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is there any R function to do that? Thanks and regards, On 01-12-2012 18:39, John Kane wrote: Are you basically asking for all possible permutations of the table? If so see ?permn in the combinat package. John Kane Kingston ON Canada -Original Message- From: bogaso.christo...@gmail.com Sent: Sat, 01 Dec 2012 18:10:15 +0545 To: r-help@r-project.org Subject: [R] Getting all possible contingency tables Hello all, Let say I have 2-way contingency table: Tab - matrix(c(8, 10, 12, 6), nr = 2) and the Chi-squared test could not reject the independence: chisq.test(Tab) Pearson's Chi-squared test with Yates' continuity correction data: Tab X-squared = 1.0125, df = 1, p-value = 0.3143 However I want to get all possible contingency tables under this independence scenario (one of them would obviously be the given table as, we could not reject the independence), and for each such table I want to calculate the Ch-sq statistic. Can somebody help me how to generate all such tables? Thanks and regards, __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/**posting-guide.htmlhttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __**__ FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/**photosharinghttp://www.inbox.com/photosharingto find out more! __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm [[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] How to built a pivot table of value
On 01-12-2012, at 14:56, John Kane wrote: One way, using the plyr package would be: library(plyr) dcast(base, p ~ q) Shouldn't that be library(reshape2) ? Berend John Kane Kingston ON Canada -Original Message- From: ce.kay...@yahoo.fr Sent: Sat, 1 Dec 2012 04:37:02 -0800 (PST) To: r-help@r-project.org Subject: [R] How to built a pivot table of value Hi R users Imagine the table base: p=c(d,d,b,b,a,a) q=c(v1,v2,v1,v2,v1,v2) r=c(5,2,4,8,9,7) base=data.frame(p,q,r) base p q r 1 d v1 5 2 d v2 2 3 b v1 4 4 b v2 8 5 a v1 9 6 a v2 7 How programming R to get this result: v1 v2 a 97 b 48 d 52 I tried the function table but the result is divided in several matrix: table(base$p,base$q,base$r) , , = 2 v1 v2 a 0 0 b 0 0 d 0 1 , , = 4 v1 v2 a 0 0 b 1 0 d 0 0 , , = 5 v1 v2 a 0 0 b 0 0 d 1 0 , , = 7 v1 v2 a 0 1 b 0 0 d 0 0 , , = 8 v1 v2 a 0 0 b 0 1 d 0 0 , , = 9 v1 v2 a 1 0 b 0 0 d 0 0 SIncerely yours -- View this message in context: http://r.789695.n4.nabble.com/How-to-built-a-pivot-table-of-value-tp4651539.html Sent from the R help mailing list archive at Nabble.com. __ 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. GET FREE SMILEYS FOR YOUR IM EMAIL - Learn more at http://www.inbox.com/smileys Works with AIM®, MSN® Messenger, Yahoo!® Messenger, ICQ®, Google Talk™ and most webmails __ 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. __ 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] Getting all possible contingency tables
Thanks Bert for your reply. I am trying to understand/visualize the Sample Chi-Squared Statistic's Null distribution. Therefore I need all possible Contingency tables under Independence case. What could be better way to visualize that? Thanks and regards, On 01 December 2012 20:03:00, Bert Gunter wrote: Christopher: Don't do this! If I understand you correctly, you want FIsher's exact test. This is already available in R, using far smarter algorithms then you would. See: ?fisher.test -- Bert On Sat, Dec 1, 2012 at 5:48 AM, Christofer Bogaso bogaso.christo...@gmail.com mailto:bogaso.christo...@gmail.com wrote: Thanks John for your reply. However still not clear how I should proceed. My goal is to generate all possible contingency tables. Basically I want to see the distribution of Chi-squared Statistic under independence (NULL). So I was thinking if I can generate all possible permutation of integer numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is there any R function to do that? Thanks and regards, On 01-12-2012 18:39, John Kane wrote: Are you basically asking for all possible permutations of the table? If so see ?permn in the combinat package. John Kane Kingston ON Canada -Original Message- From: bogaso.christo...@gmail.com mailto:bogaso.christo...@gmail.com Sent: Sat, 01 Dec 2012 18:10:15 +0545 To: r-help@r-project.org mailto:r-help@r-project.org Subject: [R] Getting all possible contingency tables Hello all, Let say I have 2-way contingency table: Tab - matrix(c(8, 10, 12, 6), nr = 2) and the Chi-squared test could not reject the independence: chisq.test(Tab) Pearson's Chi-squared test with Yates' continuity correction data: Tab X-squared = 1.0125, df = 1, p-value = 0.3143 However I want to get all possible contingency tables under this independence scenario (one of them would obviously be the given table as, we could not reject the independence), and for each such table I want to calculate the Ch-sq statistic. Can somebody help me how to generate all such tables? Thanks and regards, R-help@r-project.org mailto:R-help@r-project.org mailing list https://stat.ethz.ch/mailman/__listinfo/r-help https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/__posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/__photosharing http://www.inbox.com/photosharing to find out more! R-help@r-project.org mailto:R-help@r-project.org mailing list https://stat.ethz.ch/mailman/__listinfo/r-help https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/__posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ 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] segfault debugging
On 12/01/2012 04:51 AM, Duncan Murdoch wrote: On 12-12-01 6:56 AM, Donatella Quagli wrote: Thank you so far. Here is an excerpt from the gdb session after a crash: Program received signal SIGSEGV, Segmentation fault. 0xb7509a6b in Rf_allocVector () from /usr/lib/R/lib/libR.so (gdb) backtrace #0 0xb7509a6b in Rf_allocVector () from /usr/lib/R/lib/libR.so #1 0xb744b64c in ?? () from /usr/lib/R/lib/libR.so #2 0xb74c58bf in ?? () from /usr/lib/R/lib/libR.so #3 0xb74c9c62 in Rf_eval () from /usr/lib/R/lib/libR.so #4 0xb74ce60f in Rf_applyClosure () from /usr/lib/R/lib/libR.so #5 0xb74c9f29 in Rf_eval () from /usr/lib/R/lib/libR.so #6 0xb7503002 in Rf_ReplIteration () from /usr/lib/R/lib/libR.so #7 0xb7503298 in ?? () from /usr/lib/R/lib/libR.so #8 0xb7503812 in run_Rmainloop () from /usr/lib/R/lib/libR.so #9 0xb7503839 in Rf_mainloop () from /usr/lib/R/lib/libR.so #10 0x08048768 in main () #11 0xb728de46 in __libc_start_main (main=0x8048730 main, argc=8, ubp_av=0xbfdb7824, init=0x80488a0 __libc_csu_init, fini=0x8048890 __libc_csu_fini, rtld_fini=0xb7784590, stack_end=0xbfdb781c) at libc-start.c:228 #12 0x08048791 in _start () It seems to me that the error is in frame #0. Does it mean that there is a bug in libR.so? What can I do next? It means that the error was detected when trying to do a memory allocation. That could be a bug in R, but more likely something else has damaged the memory management system structures, e.g. a function writing to memory that it doesn't own. Bugs like this are hard to track down, because the damage could have occurred a long time before it showed up, and small changes to your script could affect it. I would try to narrow it down to a single statement in your script. You might be able to deduce that from the last line printed before the crash. If you don't have any printing, you could try adding some, but as I mentioned above, that might make the bug behave differently. Another approach is to cut off statements at the end of your script. That probably won't affect the bug until you cut off the statement that actually triggered it (but it might, which is why this kind of bug is so frustrating to track down). If you find the bad statement, then look at calls to external code in it, or recently executed before it. See if any of them look like they contain errors. Common errors are to write to an array without allocating it, or to write beyond the bounds of an array, or (in .Call() code) to allocate something and then fail to protect it from garbage collection. You could also figure out what the problem is that caused the seg fault in frame 0. It might be because some particular variable contains a garbage value. Then in a new run, you can ask gdb to break when that memory location takes on the garbage value. This is usually effective if you really can identify the bad value, but doing that can be hard, especially when you aren't familiar with how things normally work. valgrind is usually effective for this R -d valgrind -f myscript.R but it requires an operating system where it is available (e.g., linux) and a quick (say less than 10's of seconds) way of reproducing the bug (because valgrind slows evaluation alot). So the first step is really to narrow down your large script to something that is easier to re-run., e.g., saving the important R objects to a file shortly before the problem section of your script, then reproducing the problem by loading those and evaluating a few steps of the code. The bug can still be intermittent; valgrind will likely spot the problem. Martin Good luck! Duncan Murdoch __ 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. -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 __ 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] How to built a pivot table of value
Blast, you're right. I tend to load both at the same time and confused the two. It should be reshape2 John Kane Kingston ON Canada -Original Message- From: b...@xs4all.nl Sent: Sat, 1 Dec 2012 15:20:13 +0100 To: jrkrid...@inbox.com Subject: Re: [R] How to built a pivot table of value On 01-12-2012, at 14:56, John Kane wrote: One way, using the plyr package would be: library(plyr) dcast(base, p ~ q) Shouldn't that be library(reshape2) ? Berend John Kane Kingston ON Canada -Original Message- From: ce.kay...@yahoo.fr Sent: Sat, 1 Dec 2012 04:37:02 -0800 (PST) To: r-help@r-project.org Subject: [R] How to built a pivot table of value Hi R users Imagine the table base: p=c(d,d,b,b,a,a) q=c(v1,v2,v1,v2,v1,v2) r=c(5,2,4,8,9,7) base=data.frame(p,q,r) base p q r 1 d v1 5 2 d v2 2 3 b v1 4 4 b v2 8 5 a v1 9 6 a v2 7 How programming R to get this result: v1 v2 a 97 b 48 d 52 I tried the function table but the result is divided in several matrix: table(base$p,base$q,base$r) , , = 2 v1 v2 a 0 0 b 0 0 d 0 1 , , = 4 v1 v2 a 0 0 b 1 0 d 0 0 , , = 5 v1 v2 a 0 0 b 0 0 d 1 0 , , = 7 v1 v2 a 0 1 b 0 0 d 0 0 , , = 8 v1 v2 a 0 0 b 0 1 d 0 0 , , = 9 v1 v2 a 1 0 b 0 0 d 0 0 SIncerely yours -- View this message in context: http://r.789695.n4.nabble.com/How-to-built-a-pivot-table-of-value-tp4651539.html Sent from the R help mailing list archive at Nabble.com. __ 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. GET FREE SMILEYS FOR YOUR IM EMAIL - Learn more at http://www.inbox.com/smileys Works with AIM®, MSN® Messenger, Yahoo!® Messenger, ICQ®, Google Talk™ and most webmails __ 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. GET FREE SMILEYS FOR YOUR IM EMAIL - Learn more at http://www.inbox.com/smileys Works with AIM®, MSN® Messenger, Yahoo!® Messenger, ICQ®, Google Talk™ and most webmails __ 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] cubic spline
Hi Jorge, many thanks for your suggestion! I tried the function you mentioned and it looks working!! Now I have just to check that splint (R) and interp1 (Matlab) functions provide me the same results. Kind regards! Steve -- View this message in context: http://r.789695.n4.nabble.com/cubic-spline-tp4651537p4651555.html Sent from the R help mailing list archive at Nabble.com. __ 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] Getting all possible contingency tables
You will need to be clear about whether you are conditioning on the marginal totals as well as on the overall total. As stated, you are only asking for the overall total (36) to be fixed. In that case, one possible (and by no means unique) approach would be to: [A]: Choose any four random integers a,b,c,d that add up to 36 (even there, you still have to make a choice about what distribution to adopt for the random integers). [B]: Place the results into the 2x2 matrix; then evaluate chi-squared. [C]: Repeat until you have enough cases. Example (using equiprobable multinomial to generate 4 random integers) Tab - matrix(rmultinom(1,36,c(1,1,1,1)/4), nrow=2) A more specific choice would be to fix the row and column probablilties (but not the sample row and column totals), e.g.: P.row1 - 0.25 ; P.row2 - 1 - P.row1 P.col1 - 0.50 ; P.col2 - 1 - P.col1 Then, adopting the hypothesis of independence between rows and columns: P11 - P.row1*P.col1 P21 - P.row2*P.col1 P12 - P.row1*P.col2 P22 - P.row2*P.col2 Tab - matrix(rmultinom(1,36,c(P11,P21,P12,P22)), nrow=2) On the other hand, if you want to also fix the sample row margins and column margins, then your sampled table needs to be generated using a hypergeometric distribution, (which is the basis of the fisher.test mentioned by Bert Gunter). Since explaining how to do this is a bit mjore complicated than the above, please first confirm what constraints (e.g. only total count; row-margins only; col-margins only; both row- col-margins) you wich to impose. Hoping this helps, Ted. On 01-Dec-2012 14:28:24 Christofer Bogaso wrote: Thanks Bert for your reply. I am trying to understand/visualize the Sample Chi-Squared Statistic's Null distribution. Therefore I need all possible Contingency tables under Independence case. What could be better way to visualize that? Thanks and regards, On 01 December 2012 20:03:00, Bert Gunter wrote: Christopher: Don't do this! If I understand you correctly, you want FIsher's exact test. This is already available in R, using far smarter algorithms then you would. See: ?fisher.test -- Bert On Sat, Dec 1, 2012 at 5:48 AM, Christofer Bogaso bogaso.christo...@gmail.com mailto:bogaso.christo...@gmail.com wrote: Thanks John for your reply. However still not clear how I should proceed. My goal is to generate all possible contingency tables. Basically I want to see the distribution of Chi-squared Statistic under independence (NULL). So I was thinking if I can generate all possible permutation of integer numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is there any R function to do that? Thanks and regards, On 01-12-2012 18:39, John Kane wrote: Are you basically asking for all possible permutations of the table? If so see ?permn in the combinat package. John Kane Kingston ON Canada -Original Message- From: bogaso.christo...@gmail.com mailto:bogaso.christo...@gmail.com Sent: Sat, 01 Dec 2012 18:10:15 +0545 To: r-help@r-project.org mailto:r-help@r-project.org Subject: [R] Getting all possible contingency tables Hello all, Let say I have 2-way contingency table: Tab - matrix(c(8, 10, 12, 6), nr = 2) and the Chi-squared test could not reject the independence: chisq.test(Tab) Pearson's Chi-squared test with Yates' continuity correction data: Tab X-squared = 1.0125, df = 1, p-value = 0.3143 However I want to get all possible contingency tables under this independence scenario (one of them would obviously be the given table as, we could not reject the independence), and for each such table I want to calculate the Ch-sq statistic. Can somebody help me how to generate all such tables? Thanks and regards, - E-Mail: (Ted Harding) ted.hard...@wlandres.net Date: 01-Dec-2012 Time: 16:00:16 This message was sent by XFMail __ 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] segfault debugging
valgrind is usually effective for this R -d valgrind -f myscript.R And adding the R command gctorture(TRUE) to the top of your script lets valgrind do a better job of find memory misuse. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Martin Morgan Sent: Saturday, December 01, 2012 6:54 AM To: Duncan Murdoch Cc: r-help@r-project.org; Donatella Quagli Subject: Re: [R] segfault debugging On 12/01/2012 04:51 AM, Duncan Murdoch wrote: On 12-12-01 6:56 AM, Donatella Quagli wrote: Thank you so far. Here is an excerpt from the gdb session after a crash: Program received signal SIGSEGV, Segmentation fault. 0xb7509a6b in Rf_allocVector () from /usr/lib/R/lib/libR.so (gdb) backtrace #0 0xb7509a6b in Rf_allocVector () from /usr/lib/R/lib/libR.so #1 0xb744b64c in ?? () from /usr/lib/R/lib/libR.so #2 0xb74c58bf in ?? () from /usr/lib/R/lib/libR.so #3 0xb74c9c62 in Rf_eval () from /usr/lib/R/lib/libR.so #4 0xb74ce60f in Rf_applyClosure () from /usr/lib/R/lib/libR.so #5 0xb74c9f29 in Rf_eval () from /usr/lib/R/lib/libR.so #6 0xb7503002 in Rf_ReplIteration () from /usr/lib/R/lib/libR.so #7 0xb7503298 in ?? () from /usr/lib/R/lib/libR.so #8 0xb7503812 in run_Rmainloop () from /usr/lib/R/lib/libR.so #9 0xb7503839 in Rf_mainloop () from /usr/lib/R/lib/libR.so #10 0x08048768 in main () #11 0xb728de46 in __libc_start_main (main=0x8048730 main, argc=8, ubp_av=0xbfdb7824, init=0x80488a0 __libc_csu_init, fini=0x8048890 __libc_csu_fini, rtld_fini=0xb7784590, stack_end=0xbfdb781c) at libc-start.c:228 #12 0x08048791 in _start () It seems to me that the error is in frame #0. Does it mean that there is a bug in libR.so? What can I do next? It means that the error was detected when trying to do a memory allocation. That could be a bug in R, but more likely something else has damaged the memory management system structures, e.g. a function writing to memory that it doesn't own. Bugs like this are hard to track down, because the damage could have occurred a long time before it showed up, and small changes to your script could affect it. I would try to narrow it down to a single statement in your script. You might be able to deduce that from the last line printed before the crash. If you don't have any printing, you could try adding some, but as I mentioned above, that might make the bug behave differently. Another approach is to cut off statements at the end of your script. That probably won't affect the bug until you cut off the statement that actually triggered it (but it might, which is why this kind of bug is so frustrating to track down). If you find the bad statement, then look at calls to external code in it, or recently executed before it. See if any of them look like they contain errors. Common errors are to write to an array without allocating it, or to write beyond the bounds of an array, or (in .Call() code) to allocate something and then fail to protect it from garbage collection. You could also figure out what the problem is that caused the seg fault in frame 0. It might be because some particular variable contains a garbage value. Then in a new run, you can ask gdb to break when that memory location takes on the garbage value. This is usually effective if you really can identify the bad value, but doing that can be hard, especially when you aren't familiar with how things normally work. valgrind is usually effective for this R -d valgrind -f myscript.R but it requires an operating system where it is available (e.g., linux) and a quick (say less than 10's of seconds) way of reproducing the bug (because valgrind slows evaluation alot). So the first step is really to narrow down your large script to something that is easier to re-run., e.g., saving the important R objects to a file shortly before the problem section of your script, then reproducing the problem by loading those and evaluating a few steps of the code. The bug can still be intermittent; valgrind will likely spot the problem. Martin Good luck! Duncan Murdoch __ 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. -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do
Re: [R] Getting all possible contingency tables
My goal is to generate all possible contingency tables. Basically I want to see the distribution of Chi-squared Statistic under independence (NULL). So I was thinking if I can generate all possible permutation of integer numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is there any R function to do that? I think R *can* do this (thanks to Robin Hankin): library(partitions) str(parts(36)) 'partition' int [1:36, 1:17977] 36 0 0 0 0 0 0 0 0 0 ... I'm not quite clear on how you're going to take these results and turn them into possible tables, but I guess you do ... You might also be interested in the simulate.p.value option to chisq.test and the randomizer (which preserves row and column totals): from the code of chisq.test, tmp - .Call(C_chisq_sim, sr, sc, B, E) -Original Message- From: bogaso.christofer at gmail.com Let say I have 2-way contingency table: Tab - matrix(c(8, 10, 12, 6), nr = 2) and the Chi-squared test could not reject the independence: chisq.test(Tab) Pearson's Chi-squared test with Yates' continuity correction data: Tab X-squared = 1.0125, df = 1, p-value = 0.3143 However I want to get all possible contingency tables under this independence scenario (one of them would obviously be the given table as, we could not reject the independence), and for each such table I want to calculate the Ch-sq statistic. Can somebody help me how to generate all such tables? __ 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] cubic spline
On Dec 1, 2012, at 5:09 AM, Steve Stephenson wrote: Hallo, I'm facing a problem and I would really appreciate your support. I have to translate some Matalb code in R that I don't know very well but I would like to. I have to interpolate 5 point with a cubic spline function and then I expect my function returns the Y value as output a specific X value inside the evaluation range. Let's suppose that: 1- *X = [-10, -5, 0, 5, 10]* 2 - *Y = [12, 10, 8, 7, 6]* 3 - *I have to interpolate with a cubic spline assuming x=11* In Matlab I used this function: *y = interp1(X, Y, x, cubic); * How can I do the same in R? Many thanks in advance for your reply and support! splinefun( x = c(-10, -5, 0, 5, 10), y = c(12, 10, 8, 7, 6), method=natural)(11) [1] 5.785714 -- David Winsemius, MD Alameda, CA, USA __ 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] Getting all possible contingency tables
On Dec 1, 2012, at 7:28 AM, Christofer Bogaso wrote: Thanks Bert for your reply. I am trying to understand/visualize the Sample Chi-Squared Statistic's Null distribution. Therefore I need all possible Contingency tables under Independence case. What could be better way to visualize that? In your quest for enlightenment, consider looking at the example in: ?r2dtable -- David. Thanks and regards, On 01 December 2012 20:03:00, Bert Gunter wrote: Christopher: Don't do this! If I understand you correctly, you want FIsher's exact test. This is already available in R, using far smarter algorithms then you would. See: ?fisher.test -- Bert On Sat, Dec 1, 2012 at 5:48 AM, Christofer Bogaso bogaso.christo...@gmail.com mailto:bogaso.christo...@gmail.com wrote: Thanks John for your reply. However still not clear how I should proceed. My goal is to generate all possible contingency tables. Basically I want to see the distribution of Chi-squared Statistic under independence (NULL). So I was thinking if I can generate all possible permutation of integer numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is there any R function to do that? Thanks and regards, On 01-12-2012 18:39, John Kane wrote: Are you basically asking for all possible permutations of the table? If so see ?permn in the combinat package. John Kane Kingston ON Canada -Original Message- From: bogaso.christo...@gmail.com mailto:bogaso.christo...@gmail.com Sent: Sat, 01 Dec 2012 18:10:15 +0545 To: r-help@r-project.org mailto:r-help@r-project.org Subject: [R] Getting all possible contingency tables Hello all, Let say I have 2-way contingency table: Tab - matrix(c(8, 10, 12, 6), nr = 2) and the Chi-squared test could not reject the independence: chisq.test(Tab) Pearson's Chi-squared test with Yates' continuity correction data: Tab X-squared = 1.0125, df = 1, p-value = 0.3143 However I want to get all possible contingency tables under this independence scenario (one of them would obviously be the given table as, we could not reject the independence), and for each such table I want to calculate the Ch-sq statistic. Can somebody help me how to generate all such tables? Thanks and regards, David Winsemius, MD Alameda, CA, USA __ 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] segfault debugging
On 1 Dec 2012, at 16:09, William Dunlap wdun...@tibco.com wrote: valgrind is usually effective for this R -d valgrind -f myscript.R And adding the R command gctorture(TRUE) to the top of your script lets valgrind do a better job of find memory misuse. That makes things even slower: it really only helps when PROTECT is used incorrectly (including not used): this error looks more like a memory over-run. Note that valgrind is really only effective for under/over-run errors involving memory allocated by R if the build of R is instrumented (see 'Writing R Extensions'). Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Martin Morgan Sent: Saturday, December 01, 2012 6:54 AM To: Duncan Murdoch Cc: r-help@r-project.org; Donatella Quagli Subject: Re: [R] segfault debugging On 12/01/2012 04:51 AM, Duncan Murdoch wrote: On 12-12-01 6:56 AM, Donatella Quagli wrote: Thank you so far. Here is an excerpt from the gdb session after a crash: Program received signal SIGSEGV, Segmentation fault. 0xb7509a6b in Rf_allocVector () from /usr/lib/R/lib/libR.so (gdb) backtrace #0 0xb7509a6b in Rf_allocVector () from /usr/lib/R/lib/libR.so #1 0xb744b64c in ?? () from /usr/lib/R/lib/libR.so #2 0xb74c58bf in ?? () from /usr/lib/R/lib/libR.so #3 0xb74c9c62 in Rf_eval () from /usr/lib/R/lib/libR.so #4 0xb74ce60f in Rf_applyClosure () from /usr/lib/R/lib/libR.so #5 0xb74c9f29 in Rf_eval () from /usr/lib/R/lib/libR.so #6 0xb7503002 in Rf_ReplIteration () from /usr/lib/R/lib/libR.so #7 0xb7503298 in ?? () from /usr/lib/R/lib/libR.so #8 0xb7503812 in run_Rmainloop () from /usr/lib/R/lib/libR.so #9 0xb7503839 in Rf_mainloop () from /usr/lib/R/lib/libR.so #10 0x08048768 in main () #11 0xb728de46 in __libc_start_main (main=0x8048730 main, argc=8, ubp_av=0xbfdb7824, init=0x80488a0 __libc_csu_init, fini=0x8048890 __libc_csu_fini, rtld_fini=0xb7784590, stack_end=0xbfdb781c) at libc-start.c:228 #12 0x08048791 in _start () It seems to me that the error is in frame #0. Does it mean that there is a bug in libR.so? What can I do next? It means that the error was detected when trying to do a memory allocation. That could be a bug in R, but more likely something else has damaged the memory management system structures, e.g. a function writing to memory that it doesn't own. Bugs like this are hard to track down, because the damage could have occurred a long time before it showed up, and small changes to your script could affect it. I would try to narrow it down to a single statement in your script. You might be able to deduce that from the last line printed before the crash. If you don't have any printing, you could try adding some, but as I mentioned above, that might make the bug behave differently. Another approach is to cut off statements at the end of your script. That probably won't affect the bug until you cut off the statement that actually triggered it (but it might, which is why this kind of bug is so frustrating to track down). If you find the bad statement, then look at calls to external code in it, or recently executed before it. See if any of them look like they contain errors. Common errors are to write to an array without allocating it, or to write beyond the bounds of an array, or (in .Call() code) to allocate something and then fail to protect it from garbage collection. You could also figure out what the problem is that caused the seg fault in frame 0. It might be because some particular variable contains a garbage value. Then in a new run, you can ask gdb to break when that memory location takes on the garbage value. This is usually effective if you really can identify the bad value, but doing that can be hard, especially when you aren't familiar with how things normally work. valgrind is usually effective for this R -d valgrind -f myscript.R but it requires an operating system where it is available (e.g., linux) and a quick (say less than 10's of seconds) way of reproducing the bug (because valgrind slows evaluation alot). So the first step is really to narrow down your large script to something that is easier to re-run., e.g., saving the important R objects to a file shortly before the problem section of your script, then reproducing the problem by loading those and evaluating a few steps of the code. The bug can still be intermittent; valgrind will likely spot the problem. Martin Good luck! Duncan Murdoch __ 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. --
[R] screen if a value is within range
Dear all, could you please give me some pointers on how I could make R screen for a value if it falls within a certain range? I looked at the subset function, but is not doing it, perhaps because I only have 1 value to screen? aptreciate the input ex: a -16.5 I would like to screen to see if a is within the range of 15 to 20, (which it is:-)), and I would like the code to return a value of 1 if a is within the specified range or 0 if it is not. Apreciate the insights, Andras [[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] screen if a value is within range
15 a a 20
Wrap it in a function if you like:
in_interval - function(x, interval){
stopifnot(length(interval) == 2L)
interval[1] x x interval[2]
}
in_interval(a, c(15, 20))
Cheers,
Michael
On Sat, Dec 1, 2012 at 4:50 PM, Andras Farkas motyoc...@yahoo.com wrote:
could you please give me some pointers on how I could make R screen for a
value if it falls within a certain range?
I looked at the subset function, but is not doing it, perhaps because I only
have 1 value to screen?
aptreciate the input
ex:
a -16.5
I would like to screen to see if a is within the range of 15 to 20, (which it
is:-)), and I would like the code to return a value of 1 if a is within the
specified range or 0 if it is not.
__
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] segfault debugging
On Nov 30, 2012, at 10:02 AM, Donatella Quagli wrote: Hello everybody, I have written a script with two inline cfunctions. The script crashes from time to time with: *** caught segfault *** address 0x10, cause 'memory not mapped' The crashs happen within R code after the cfunctions were executed. Nevertheless I think that the pointers in my cfunctions are not used correctly. I tried to find some examples for debugging tools. I found something like R -d gdb. But I could not find an example how to use it with #!/usr/bin/Rscript. And I cannot source the script within a running R session because I must run it with some args. Can anybody tell me as a non nerd step by step what I can do to locate the problem? Can you recommend tools? If so how are they used with Rscript? I think you may have difficulty defending your non-nerd claim if you are writing cfunctions in R. That said, you may want to look at a very recent SO answer by Hadley Wickham on StackOverflow: http://stackoverflow.com/questions/13661065/r-superimpose-histogram-fits-in-one-plot (I'm less nerdy than you, but it does appear that Hadley's code demonstrates efforts at checking for available memory and you may benefit from a worked example in Rcpp.) -- David Winsemius, MD Alameda, CA, USA __ 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] screen if a value is within range
On 12/1/2012 10:50 AM, Andras Farkas wrote: Dear all, could you please give me some pointers on how I could make R screen for a value if it falls within a certain range? I looked at the subset function, but is not doing it, perhaps because I only have 1 value to screen? aptreciate the input ex: a -16.5 I would like to screen to see if a is within the range of 15 to 20, (which it is:-)), and I would like the code to return a value of 1 if a is within the specified range or 0 if it is not. Apreciate the insights, Andras [[alternative HTML version deleted]] a = 16.5 ans = (a = 15 a = 20) ans [1] TRUE Rob __ 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] screen if a value is within range
On Dec 1, 2012, at 9:55 AM, R. Michael Weylandt wrote:
15 a a 20
Wrap it in a function if you like:
in_interval - function(x, interval){
stopifnot(length(interval) == 2L)
interval[1] x x interval[2]
}
in_interval(a, c(15, 20))
Could just use the findInterval function:
findInterval(x, c(15,20) ) == 1
findInterval returns a numeric vector indicating which bin(s) the
argument vector element(s) fall(s) into. Items below the lower bound
get a zero which means if the result is used as an index the there
will be no item chosen for that value. Items above the maximal
boundary get a value of n+1 where n is the number of bins. (Very
useful function.)
--
David.
Cheers,
Michael
On Sat, Dec 1, 2012 at 4:50 PM, Andras Farkas motyoc...@yahoo.com
wrote:
could you please give me some pointers on how I could make R screen
for a value if it falls within a certain range?
I looked at the subset function, but is not doing it, perhaps
because I only have 1 value to screen?
aptreciate the input
ex:
a -16.5
I would like to screen to see if a is within the range of 15 to 20,
(which it is:-)), and I would like the code to return a value of 1
if a is within the specified range or 0 if it is not.
__
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.
David Winsemius, MD
Alameda, CA, USA
__
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] protentially serious R error
Congratulations, you've reached the First Circle of the R Inferno. Only 8 more to go http://www.burns-stat.com/pages/Tutor/R_inferno.pdf -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Ben Bolker Sent: Friday, November 30, 2012 7:19 PM To: r-h...@stat.math.ethz.ch Subject: Re: [R] protentially serious R error Cutting and pasting from the R posting guide -- I think this advice has special force when responding to FAQ 7.31 questions (I've seen several within the last few days, and at least two were answered by three different people: When responding to a very simple question, use the following algorithm: compose your response type 4*runif(1) at the R prompt, and wait this many hours check for new posts to R-help; if no similar suggestion, post your response (This is partly in jest, but if you know immediately why it is suggested, you probably should use it! Also, it's a nice idea to replace 4 by the number of years you have been using R or S-plus.) __ 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. __ 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] Reading .gsheet within R
Thank you Henrik the others that have commented. Accessing the actual online data is what I would need, but apparently this is not yet feasible… Luca Il giorno 01/dic/2012, alle ore 04:53, Henrik Bengtsson h...@biostat.ucsf.edu ha scritto: On Fri, Nov 30, 2012 at 9:43 AM, Luca Meyer lucam1...@gmail.com wrote: Hello R-experts, I would like to know if there is a solution to read files with extension .gsheet directly into R - see http://www.fileinfo.com/extension/gsheet for more info on this file format. AFAIK, those files (*.gsheet, *.gdoc, *.gslides) are just tiny JSON files containing references to the online/cloud resource (specifying the url and the resource_id). There are several packages on CRAN for parsing JSON files. Accessing the actual online data is a different story... My $0.02 /Henrik Thank you, Luca Mr. Luca Meyer www.lucameyer.com R 2.15.1 Mac OS X 10.8.2 [[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. __ 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] segfault debugging
While it is true that valgrind is most effective when R is built with special flags, it can be useful without the special build. Also, gctorture(TRUE) does make it run very slowly, but I have seen it show things that only sporadically show up otherwise. E.g., with an optimized 64-bit Linux build of R-2.15.2 we get: % R --debugger=valgrind --quiet ==19559== Memcheck, a memory error detector ==19559== Copyright (C) 2002-2011, and GNU GPL'd, by Julian Seward et al. ==19559== Using Valgrind-3.7.0 and LibVEX; rerun with -h for copyright info ==19559== Command: /opt/sw/R/R-2.15.2.atlas1/lib/R/bin/exec/R --quiet ... gctorture(TRUE) library(gam) Loading required package: splines Loaded gam 1.06.2 g - gam(mpg~lo(hp,span=.4,degree=2)+gear, data=mtcars) ==19559== Conditional jump or move depends on uninitialised value(s) ==19559==at 0x4F4CA5D: R_gc_internal (memory.c:1510) ==19559==by 0x4F4EDDD: Rf_allocVector (memory.c:2355) ==19559==by 0x4FC94D0: do_lazyLoadDBfetch (serialize.c:2517) ==19559==by 0x4F12E8E: Rf_eval (eval.c:497) ... ==19559== Use of uninitialised value of size 8 ==19559==at 0x4F4CA5F: R_gc_internal (memory.c:1510) ==19559==by 0x4F4EDDD: Rf_allocVector (memory.c:2355) ==19559==by 0x4FC94D0: do_lazyLoadDBfetch (serialize.c:2517) ==19559==by 0x4F12E8E: Rf_eval (eval.c:497) ... ==19559== Invalid read of size 1 ==19559==at 0x4F4CA5F: R_gc_internal (memory.c:1510) ==19559==by 0x4F4EDDD: Rf_allocVector (memory.c:2355) ==19559==by 0x4FC94D0: do_lazyLoadDBfetch (serialize.c:2517) ==19559==by 0x4F12E8E: Rf_eval (eval.c:497) ... *** caught segfault *** address 0x3010, cause 'memory not mapped' ==19559== Conditional jump or move depends on uninitialised value(s) ==19559==at 0x4F4CA5D: R_gc_internal (memory.c:1510) ==19559==by 0x4F4EB19: Rf_cons (memory.c:2076) ==19559==by 0x4F4ECEE: Rf_allocList (memory.c:2481) ==19559==by 0x4EFD094: R_GetTraceback (errors.c:1307) ... Without the gctorture(TRUE) there is no complaint from valgrind, although I've seen evidence of memory corruption later. (Without valgrind but with gctorture(TRUE) there is no complaint on the first call to gam() but R dies on a repeated call.) Perhaps if I used a valgrind-enabled build of R it would localize the problem to C or Fortran code behind lo(degree=2). Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: Brian Ripley [mailto:rip...@stats.ox.ac.uk] Sent: Saturday, December 01, 2012 8:45 AM To: William Dunlap Cc: Martin Morgan; Duncan Murdoch; r-help@r-project.org; Donatella Quagli Subject: Re: [R] segfault debugging On 1 Dec 2012, at 16:09, William Dunlap wdun...@tibco.com wrote: valgrind is usually effective for this R -d valgrind -f myscript.R And adding the R command gctorture(TRUE) to the top of your script lets valgrind do a better job of find memory misuse. That makes things even slower: it really only helps when PROTECT is used incorrectly (including not used): this error looks more like a memory over-run. Note that valgrind is really only effective for under/over-run errors involving memory allocated by R if the build of R is instrumented (see 'Writing R Extensions'). Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Martin Morgan Sent: Saturday, December 01, 2012 6:54 AM To: Duncan Murdoch Cc: r-help@r-project.org; Donatella Quagli Subject: Re: [R] segfault debugging On 12/01/2012 04:51 AM, Duncan Murdoch wrote: On 12-12-01 6:56 AM, Donatella Quagli wrote: Thank you so far. Here is an excerpt from the gdb session after a crash: Program received signal SIGSEGV, Segmentation fault. 0xb7509a6b in Rf_allocVector () from /usr/lib/R/lib/libR.so (gdb) backtrace #0 0xb7509a6b in Rf_allocVector () from /usr/lib/R/lib/libR.so #1 0xb744b64c in ?? () from /usr/lib/R/lib/libR.so #2 0xb74c58bf in ?? () from /usr/lib/R/lib/libR.so #3 0xb74c9c62 in Rf_eval () from /usr/lib/R/lib/libR.so #4 0xb74ce60f in Rf_applyClosure () from /usr/lib/R/lib/libR.so #5 0xb74c9f29 in Rf_eval () from /usr/lib/R/lib/libR.so #6 0xb7503002 in Rf_ReplIteration () from /usr/lib/R/lib/libR.so #7 0xb7503298 in ?? () from /usr/lib/R/lib/libR.so #8 0xb7503812 in run_Rmainloop () from /usr/lib/R/lib/libR.so #9 0xb7503839 in Rf_mainloop () from /usr/lib/R/lib/libR.so #10 0x08048768 in main () #11 0xb728de46 in __libc_start_main (main=0x8048730 main, argc=8, ubp_av=0xbfdb7824, init=0x80488a0 __libc_csu_init, fini=0x8048890 __libc_csu_fini, rtld_fini=0xb7784590, stack_end=0xbfdb781c) at libc-start.c:228 #12 0x08048791 in _start () It seems to me that the error is in frame #0. Does it mean that there is a bug in libR.so? What can I do next? It means that the error
Re: [R] Fw: quantreg installation and conflicts with R 2.15.2
On 30.11.2012 22:10, Brian S Cade wrote: Just noticed that I get a similar error about object 'kronecker' in Matrix package when trying to load lme4. So this is a more pervasive problem. Probably you have a mixture of packages for various versions of R around. So after checking if all required packages are really installed, please run update.packages(checkBuilt=TRUE) Uwe Ligges Brian Brian S. Cade, PhD U. S. Geological Survey Fort Collins Science Center 2150 Centre Ave., Bldg. C Fort Collins, CO 80526-8818 email: brian_c...@usgs.gov tel: 970 226-9326 - Forwarded by Brian S Cade/BRD/USGS/DOI on 11/30/2012 02:07 PM - From: Brian S Cade/BRD/USGS/DOI To: R-help@r-project.org Date: 11/30/2012 01:16 PM Subject: quantreg installation and conflicts with R 2.15.2 I recently lost the partitions on my hard drive (second time in 6 months) so I had to have our IT folks image all my files over to a new drive. I completely reinstalled R (now 2.15.2) and all my libraries to my computer (Dell Latitude running Windows 7). A few of my previous workspaces (created with R 2.14.1) can't be restored, reporting an error similar to the one I get when I try to load quantreg package which requires SparseM (see below). So, not only will quantreg not load but some of my workspaces can't be restored when being loaded (see below). Not sure about what this is about. I asked Roger Koenker, the package maintainer, but he is on travel and won't have chance to seriously investigate this for awhile. So I thought I would put it out to the R community and see if anyone has any suggestions about why this conflict might be occurring. library(quantreg) Loading required package: SparseM Error : object ?kronecker? is not exported by 'namespace:methods' Error: package ?SparseM? could not be loaded or Error: object ?kronecker? is not exported by 'namespace:methods' During startup - Warning message: unable to restore saved data in C:\CADESTUFF\DATA\BarryNoon\.RData Brian Brian S. Cade, PhD U. S. Geological Survey Fort Collins Science Center 2150 Centre Ave., Bldg. C Fort Collins, CO 80526-8818 email: brian_c...@usgs.gov tel: 970 226-9326 [[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. __ 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] SVM using R
On 30.11.2012 05:08, vivek kumar singh wrote: HI All, I am very new to R tool. Can some one please suggest me some tutorial links for understanding SVM using R. After reading some textbook about the SVM, go ahead and look for ?svm in package e1071. Best, Uwe Ligges Regards, Vivek __ 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. __ 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] How to repeat replication
On 30.11.2012 08:23, Kamontip Srihaset wrote: Dear all, I generate data under IRT mdel. I conducted 1000 replications. When I run, some replication was not fit with my model. So, replications were fit model were less than 1000 replication. If I want its run until 1000 replicaions. How shouldI write functin. Show us your (reduced but reproducible) code and we may be able to help. Please read the positng guide. Uwe Ligges Thank you, Kamontip [[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. __ 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] [R-pkgs] New package: gRain - gRAphical Independence Networks
On 29.11.2012 20:46, fkh wrote: I am trying to use your package gRain using your book on graphical models in R to do predictions, I have 38 columns of vectors all factors and built a bayesian network using iamb() function, then I used the following command to make a grpahNEL (However, I have 38 nodes and 106 edges) using BN-iamb(data1) BN.gr-as(amat(BN),graphNEL) Then when I am using the following command to make a grain object I got the following errors, any thoughts? Thanks a lot for your help in advance. BN.grain-grain(BN.gr,data=data1) Error in function (classes, fdef, mtable) : unable to find an inherited method for function nodes, for signature graphNEL, missing Are you aware you posted to the mailing list rather than to the package maintainer? Uwe Ligges -- View this message in context: http://r.789695.n4.nabble.com/R-pkgs-New-package-gRain-gRAphical-Independence-Networks-tp846943p4651338.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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] deleting data of a given date range.
On 29.11.2012 17:37, arun wrote: Hi, You haven't given any example dataset. So,not sure about the format of the date column. set.seed(5) dat1-data.frame(Date1=c(10/25/2009,11/25/2009,12/25/2009,5/10/2010,8/10/2010,9/25/2011,11/28/2011,5/3/2012),col2=sample(1:15,8,replace=TRUE)) dat1$Date1-as.Date(dat1$Date1,format=%m/%d/%Y) #change your date column format if it is not matching to this example. dat2-dat1[format(dat1$Date1,%Y)!=2009,] dat2 # Date1 col2 #4 2010-05-105 #5 2010-08-102 #6 2011-09-25 11 #7 2011-11-288 #8 2012-05-03 13 A.K. Or just use comparison operators on Date objects, so it is also possible to specify arbitrary ranges. Uwe Ligges - Original Message - From: siddanth911 siddanth.srivast...@mu-sigma.com To: r-help@r-project.org Cc: Sent: Thursday, November 29, 2012 6:10 AM Subject: [R] deleting data of a given date range. hey, I have a huge dataset with over 30 rows which contains data about something from 2009-2012. does anyone know how i can delete all the rows which contain data from 2009 and only have data from 2010-2012??? is there a particular function i can use on the date column so that all data from 2009 can be deleted??? -- View this message in context: http://r.789695.n4.nabble.com/deleting-data-of-a-given-date-range-tp4651272.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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. __ 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] NA return to NLM routine
On 30.11.2012 23:55, Mac Gaulin wrote:
Hello,
I am trying to understand a small quirk I came across in R. The
following code results in an error:
k - c(2, 1, 1, 5, 5)
f - c(1, 1, 1, 3, 2)
loglikelihood - function(theta,k,f){
if( theta1 theta0 )
return(-1*sum(log(choose(k,f))+f*log(theta)+(k-f)*log(1-theta)))
return(NA)
}
nlm(loglikelihood ,0.5, k, f )
Running this code results in:
Error in nlm(logliklihood, 0.5, k, f) :
invalid function value in 'nlm' optimizer
However if the line return(NA) is changed to return(-NA) or even
return(1*NA) or return(1/0), the code works. Is this expected
behavior? The nlm help file says not NA or not NaN are acceptable
values but I don't understand what that means.
Your function must return finite numbers, that means infinite numbers,
NA nor NaN are not allowed and you experienced what happens if you do that.
Please see ?constrOptim or other appropriate functions for constrained
optimization problems.
Uwe Ligges
Thank you for your time,
Mac Gaulin
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Re: [R] CreateThread failure since R 2.15.2 (32-bit)
On 30.11.2012 12:27, Martin Studer wrote: Dear R users developers, I coming across the following issue since R 2.15.2 32-bit (running on Windows XP 32.bit; some output left out for conciseness): Works for me. Which Java version are you using is this? Perhaps Java changes the environment so that your version of ls fails. Is it the one from Rtools? Uwe Ligges setInternet2(TRUE) require(rJava) .jinit() getCRANmirrors() system(ls , intern = TRUE) Error in system(ls, intern = TRUE) : CreateThread failed My details are as follows: sessionInfo() R version 2.15.2 (2012-10-26) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=German_Switzerland.1252 LC_CTYPE=German_Switzerland.1252 LC_MONETARY=German_Switzerland.1252 [4] LC_NUMERIC=CLC_TIME=German_Switzerland.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rJava_0.9-3 The failure appears since R 2.15.2, i.e. also with R 2.15.2patched and with R-Devel. It does, however, not appear with e.g. R 2.15.1 or R 2.14.2. Also, I don't get the issue with R 2.15.2 64-bit (running on Windows 7 Professional 64-bit). Also note that the issue seems related to rJava in that running the same without the rJava part (and therefore without initializing a JVM instance) runs fine: setInternet2(TRUE) getCRANmirrors() system(ls , intern = TRUE) Any ideas on what the issue might be? Thanks Best regards, Martin __ 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. __ 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] protentially serious R error
That applies to the OP (Xiaofeng, aka liuxf), of course. Ben himself is a guardian of all Circles (loc.cit.). With regard to Ben's quote from the Posting Guide, it occurs to me that the more years one has been using R, the more rapdily one should (or should be able to) answer a question. The implication of the Posting Guide is that the time it should take one to respond to a question is inversely proportional to one's experience of using R. This is turn could imply that some users, with the longest experience, may never respond (since, by the time their response is due, adequate responses have probably already been furnished by others, somewhat less experienced). There may be some empirical evidence for this. :) Best wishes to all, Ted. On 01-Dec-2012 17:54:50 David L Carlson wrote: Congratulations, you've reached the First Circle of the R Inferno. Only 8 more to go http://www.burns-stat.com/pages/Tutor/R_inferno.pdf -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Ben Bolker Sent: Friday, November 30, 2012 7:19 PM To: r-h...@stat.math.ethz.ch Subject: Re: [R] protentially serious R error Cutting and pasting from the R posting guide -- I think this advice has special force when responding to FAQ 7.31 questions (I've seen several within the last few days, and at least two were answered by three different people: When responding to a very simple question, use the following algorithm: compose your response type 4*runif(1) at the R prompt, and wait this many hours check for new posts to R-help; if no similar suggestion, post your response (This is partly in jest, but if you know immediately why it is suggested, you probably should use it! Also, it's a nice idea to replace 4 by the number of years you have been using R or S-plus.) __ 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. __ 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. - E-Mail: (Ted Harding) ted.hard...@wlandres.net Date: 01-Dec-2012 Time: 19:30:19 This message was sent by XFMail __ 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] cubic spline
David Winsemius dwinsem...@comcast.net on Sat, 1 Dec 2012 09:25:42 -0700 writes: On Dec 1, 2012, at 5:09 AM, Steve Stephenson wrote: Hallo, I'm facing a problem and I would really appreciate your support. I have to translate some Matalb code in R that I don't know very well but I would like to. I have to interpolate 5 point with a cubic spline function and then I expect my function returns the Y value as output a specific X value inside the evaluation range. Let's suppose that: 1- *X = [-10, -5, 0, 5, 10]* 2 - *Y = [12, 10, 8, 7, 6]* 3 - *I have to interpolate with a cubic spline assuming x=11* In Matlab I used this function: *y = interp1(X, Y, x, cubic); * How can I do the same in R? Many thanks in advance for your reply and support! splinefun( x = c(-10, -5, 0, 5, 10), y = c(12, 10, 8, 7, 6), method=natural)(11) [1] 5.785714 Yes, indeed, or simple spline() but definitely *no* need to use a function from an extra CRAN package .. as someone else ``erronously'' suggested. Note that spline() and splinefun() together with approx() and approxfun() are among the several hundred functions that were already part of pre-alpha R, i.e., before R had a version number or *any* packages ... and yes, the README then started with the two lines | R Source Code (Tue Jun 20 14:33:47 NZST 1995) | Copyright 1993, 1994, 1995 by Robert Gentleman and Ross Ihaka and it would be *really* *really* great if people did not add stuff to their packages that has been part of R for longer than they have even heard of R. Martin Maechler, ETH Zurich __ 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.
[R] reading json tables
I'm trying to read two data sets in json format from a single .js file.
I've tried fromJSON()
in both RJSONIOIO and RJSON packages, but they require that the lines be
pre-parsed somehow in ways I don't understand. Can someone help?
wheat - readLines(http://mbostock.github.com/protovis/ex/wheat.js;)
str(wheat)
chr [1:70] var wheat = [ { year: 1565, wheat: 41, wages: 5 }, ...
The wheat.js file looks like this and defines two tables: wheat and
monarch:
var wheat = [
{ year: 1565, wheat: 41, wages: 5 },
{ year: 1570, wheat: 45, wages: 5.05 },
{ year: 1575, wheat: 42, wages: 5.08 },
{ year: 1580, wheat: 49, wages: 5.12 },
{ year: 1585, wheat: 41.5, wages: 5.15 },
{ year: 1590, wheat: 47, wages: 5.25 },
{ year: 1595, wheat: 64, wages: 5.54 },
{ year: 1600, wheat: 27, wages: 5.61 },
{ year: 1605, wheat: 33, wages: 5.69 },
{ year: 1610, wheat: 32, wages: 5.78 },
{ year: 1615, wheat: 33, wages: 5.94 },
{ year: 1620, wheat: 35, wages: 6.01 },
...
{ year: 1800, wheat: 79, wages: 28.5 },
{ year: 1805, wheat: 81, wages: 29.5 },
{ year: 1810, wheat: 99, wages: 30 },
{ year: 1815, wheat: 78 }, // TODO
{ year: 1820, wheat: 54 },
{ year: 1821, wheat: 54 }
];
var monarch = [
{ name: Elizabeth, start: 1565, end: 1603 },
{ name: James I, start: 1603, end: 1625 },
{ name: Charles I, start: 1625, end: 1649 },
{ name: Cromwell, start: 1649, end: 1660, commonwealth: true },
{ name: Charles II, start: 1660, end: 1685 },
{ name: James II, start: 1685, end: 1689 },
{ name: WM, start: 1689, end: 1702 },
{ name: Anne, start: 1702, end: 1714 },
{ name: George I, start: 1714, end: 1727 },
{ name: George II, start: 1727, end: 1760 },
{ name: George III, start: 1760, end: 1820 },
{ name: George IV, start: 1820, end: 1821 }
];
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. Chair, Quantitative Methods
York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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Re: [R] reading json tables
Hi Michael
The problem is that the content of the .js file is not JSON,
but actual JavaScript code.
You could use something like the following
tt = readLines(http://mbostock.github.com/protovis/ex/wheat.js;)
txt = c([, gsub(;, ,, gsub(var [a-zA-Z]+ = , , tt)), ])
tmp = paste(txt, collapse = \n)
tmp = gsub(([a-zA-Z]+):, '\\1:', tmp)
o = fromJSON(tmp)
data = structure(o[1:2], names = c(wheat, monarch))
Basically, this
removes the 'var variable name =' part
replaces the ; with a , to separate elements
quotes the names of the fields, e.g. year, wheat, wages
puts the two global data objects into a top-level array ([]) container
This isn't ideal (as the regular expressions are not sufficiently specific
and could modify the actual values incorrectly). However, it does the job
for this particular file.
On 12/1/12 12:47 PM, Michael Friendly wrote:
I'm trying to read two data sets in json format from a single .js file. I've
tried fromJSON()
in both RJSONIOIO and RJSON packages, but they require that the lines be
pre-parsed somehow in ways I don't understand. Can someone help?
wheat - readLines(http://mbostock.github.com/protovis/ex/wheat.js;)
str(wheat)
chr [1:70] var wheat = [ { year: 1565, wheat: 41, wages: 5 }, ...
The wheat.js file looks like this and defines two tables: wheat and monarch:
var wheat = [
{ year: 1565, wheat: 41, wages: 5 },
{ year: 1570, wheat: 45, wages: 5.05 },
{ year: 1575, wheat: 42, wages: 5.08 },
{ year: 1580, wheat: 49, wages: 5.12 },
{ year: 1585, wheat: 41.5, wages: 5.15 },
{ year: 1590, wheat: 47, wages: 5.25 },
{ year: 1595, wheat: 64, wages: 5.54 },
{ year: 1600, wheat: 27, wages: 5.61 },
{ year: 1605, wheat: 33, wages: 5.69 },
{ year: 1610, wheat: 32, wages: 5.78 },
{ year: 1615, wheat: 33, wages: 5.94 },
{ year: 1620, wheat: 35, wages: 6.01 },
...
{ year: 1800, wheat: 79, wages: 28.5 },
{ year: 1805, wheat: 81, wages: 29.5 },
{ year: 1810, wheat: 99, wages: 30 },
{ year: 1815, wheat: 78 }, // TODO
{ year: 1820, wheat: 54 },
{ year: 1821, wheat: 54 }
];
var monarch = [
{ name: Elizabeth, start: 1565, end: 1603 },
{ name: James I, start: 1603, end: 1625 },
{ name: Charles I, start: 1625, end: 1649 },
{ name: Cromwell, start: 1649, end: 1660, commonwealth: true },
{ name: Charles II, start: 1660, end: 1685 },
{ name: James II, start: 1685, end: 1689 },
{ name: WM, start: 1689, end: 1702 },
{ name: Anne, start: 1702, end: 1714 },
{ name: George I, start: 1714, end: 1727 },
{ name: George II, start: 1727, end: 1760 },
{ name: George III, start: 1760, end: 1820 },
{ name: George IV, start: 1820, end: 1821 }
];
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] NA return to NLM routine
On 30-11-2012, at 23:55, Mac Gaulin wrote:
Hello,
I am trying to understand a small quirk I came across in R. The
following code results in an error:
k - c(2, 1, 1, 5, 5)
f - c(1, 1, 1, 3, 2)
loglikelihood - function(theta,k,f){
if( theta1 theta0 )
return(-1*sum(log(choose(k,f))+f*log(theta)+(k-f)*log(1-theta)))
return(NA)
}
nlm(loglikelihood ,0.5, k, f )
Running this code results in:
Error in nlm(logliklihood, 0.5, k, f) :
invalid function value in 'nlm' optimizer
if you do
a - NA
str(a)
you'll see that a is a logical. And that is an invalid value for the function
to return.
When you do things such as NA+0 or -NA you get a numeric value NA and that is a
non-finite value which is why you get the warning..
Instead of NA you could return something like .Machine$double.xmax .
Or use constrOptim as advised.
Berend
However if the line return(NA) is changed to return(-NA) or even
return(1*NA) or return(1/0), the code works. Is this expected
behavior? The nlm help file says not NA or not NaN are acceptable
values but I don't understand what that means.
Thank you for your time,
Mac Gaulin
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Re: [R] Getting all possible contingency tables
I believe you are looking for a detailed construction of Fisher's Exact Test. I have an example with code in my book and R package. The book discussion is Section 15.2 of Heiberger, Richard M., and Burt Holland (2004). Statistical Analysis and Data Display: An Intermediate Course with Examples in S-Plus, R, and SAS. Springer--Verlag, New York. http://springer.com/0-387-40270-5 Table 15.2 shows the full set of tables for the example. The package is HH install.packages(HH) The code to construct Table 15.2 is in file library/HH/scripts/Ch15-twtb.r Search for the line: ## study the construction of the Fisher Exact test and read through to the end of the glasses example. Rich On Sat, Dec 1, 2012 at 7:25 AM, Christofer Bogaso bogaso.christo...@gmail.com wrote: Hello all, Let say I have 2-way contingency table: Tab - matrix(c(8, 10, 12, 6), nr = 2) and the Chi-squared test could not reject the independence: chisq.test(Tab) Pearson's Chi-squared test with Yates' continuity correction data: Tab X-squared = 1.0125, df = 1, p-value = 0.3143 However I want to get all possible contingency tables under this independence scenario (one of them would obviously be the given table as, we could not reject the independence), and for each such table I want to calculate the Ch-sq statistic. Can somebody help me how to generate all such tables? Thanks and regards, __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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] cubic spline
Martin Maechler maechler at stat.math.ethz.ch writes: [snip] but definitely *no* need to use a function from an extra CRAN package .. as someone else ``erronously'' suggested. Note that spline() and splinefun() together with approx() and approxfun() are among the several hundred functions that were already part of pre-alpha R, i.e., before R had a version number or *any* packages ... and yes, the README then started with the two lines | R Source Code (Tue Jun 20 14:33:47 NZST 1995) | Copyright 1993, 1994, 1995 by Robert Gentleman and Ross Ihaka and it would be *really* *really* great if people did not add stuff to their packages that has been part of R for longer than they have even heard of R. Martin Maechler, ETH Zurich To be fair, the 'fields' package has a pretty long history too -- I think it may have been ported from an S-PLUS 'package' (or whatever the correct terminology is) that existed quite a while ago. I think it was the FUNFITS module. From http://lib.stat.cmu.edu/S/: funfits FUNFITS is a comprehensive S-Plus module for fitting functions and nonlinear time series, including multivariate splines, Kriging and neural networks. Contributed by Doug Nychka (nyc...@ucar.edu). [25/Apr/96] [24/Mar/97][24/Sep/99] (3 kbytes). The actual compressed tar file is available as funfits23.tar.gz in the S collection. Access this file via FTP, or the WWW, but not e-mail. (596k). Older version avaulable at funfits.tar.Z A quick look at funfits.tar.Z suggests that 'splint' existed in that version, in 1996 -- so respectably old. __ 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.
[R] x axis labels
Hi, I have a problem with plotting my data as a histogram using barplot2. I am plotting the x axis using axis(). I want to label only every fifth bar and not all of them as they get too busy but I don't know how to do it. I was trying to set the labels for the axis using at=seq(min value, max value, by=5) but that leads to labels not being under the right bars but just sort of spread around. Does anyone know how to do it properly? Thanks in advance, Barbara -- View this message in context: http://r.789695.n4.nabble.com/x-axis-labels-tp4651589.html Sent from the R help mailing list archive at Nabble.com. __ 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] How to built a pivot table of value
HI, You can also also ?reshape() res-reshape(base,v.names=r,idvar=p,timevar=q,direction=wide) res[order(res$p),] A.K. - Original Message - From: CE.KA ce.kay...@yahoo.fr To: r-help@r-project.org Cc: Sent: Saturday, December 1, 2012 7:37 AM Subject: [R] How to built a pivot table of value Hi R users Imagine the table base: p=c(d,d,b,b,a,a) q=c(v1,v2,v1,v2,v1,v2) r=c(5,2,4,8,9,7) base=data.frame(p,q,r) base p q r 1 d v1 5 2 d v2 2 3 b v1 4 4 b v2 8 5 a v1 9 6 a v2 7 How programming R to get this result: v1 v2 a 9 7 b 4 8 d 5 2 I tried the function table but the result is divided in several matrix: table(base$p,base$q,base$r) , , = 2 v1 v2 a 0 0 b 0 0 d 0 1 , , = 4 v1 v2 a 0 0 b 1 0 d 0 0 , , = 5 v1 v2 a 0 0 b 0 0 d 1 0 , , = 7 v1 v2 a 0 1 b 0 0 d 0 0 , , = 8 v1 v2 a 0 0 b 0 1 d 0 0 , , = 9 v1 v2 a 1 0 b 0 0 d 0 0 SIncerely yours -- View this message in context: http://r.789695.n4.nabble.com/How-to-built-a-pivot-table-of-value-tp4651539.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ 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.
[R] Daily Time Series, patterns.
Hi. I would like to ask You for help: I am new in R and i use R for forecasting, i have problem. I am trying to build daily time series: My data looks like this: Date| quantity ... 2012-11-01 | 142 2012-11-02 | 156 2012-11-05 | 151 2012-11-06 | 121 2012-11-07 | 118 2012-11-08 | 119 2012-11-11 | 160 ... My goal in general is to build time series, and to find 7-day patterns, decompose data and forecast. I dont know how tu use dates to build daily time series (to convert that dates, that would be good for time series functions), notice that there is missing data on certain days (like weekends, or days when warehouse was closed, so there was no releases) so I cant just use rep function to build replacement for dates like 1-5, start from... How would You do this? Sorry for my english, if there is something more to explain, just tell me. -- View this message in context: http://r.789695.n4.nabble.com/Daily-Time-Series-patterns-tp4651569.html Sent from the R help mailing list archive at Nabble.com. __ 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] Daily Time Series, patterns.
Hi Arun, thx for Your reply. thats interesting, but its not what I mean. I know that there is some patterns in data, example: the highest value of the sale is on Monday, and the smallest on Wednesday and so on, there might be trend also I am trying to build forecasting model that will include patterns like that, for example forecast to next 5 days. So i think I can say that is weekly sesonality, i believe the metod to make correct model is to decompose time series like there. http://otexts.com/fppfigs/elecequip_stl.png http://otexts.com/fppfigs/elecequip_stl.png Do You think I am right? In any case, I have big problem to do this in R. -- View this message in context: http://r.789695.n4.nabble.com/Daily-Time-Series-patterns-tp4651569p4651591.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] Simulation in R
Hello! How can I do 100 simulations of length 17 from bivariate bivariate normal distribution, if I know all 5 parameters? -- View this message in context: http://r.789695.n4.nabble.com/Simulation-in-R-tp4651578.html Sent from the R help mailing list archive at Nabble.com. __ 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.
[R] How to re-combine values based on an index?
I am able to split my df into two like so: dataset - trainset index - 1:nrow(dataset) testindex - sample(index, trunc(length(index)*30/100)) trainset - dataset[-testindex,] testset - dataset[testindex,-1] So I have the index information, how could I re-combine the data using that back into a single df? I tried what I thought might work, but failed with: newdataset[testindex] = testset[testindex] object 'dataset' not found newdataset[-testindex] = trainset[-testindex] object 'dataset' not found Brian __ 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] Simulation in R
look at functions replicate and mvrnorm functions (the later in the MASS package). On Sat, Dec 1, 2012 at 12:02 PM, mboricgs mbori...@hotmail.com wrote: Hello! How can I do 100 simulations of length 17 from bivariate bivariate normal distribution, if I know all 5 parameters? -- View this message in context: http://r.789695.n4.nabble.com/Simulation-in-R-tp4651578.html Sent from the R help mailing list archive at Nabble.com. __ 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. -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com [[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] How to re-combine values based on an index?
newdataset[testindex] = testset[testindex] object 'dataset' not found Is that really what R printed? I get newdataset[testindex] = testset[testindex] Error in newdataset[testindex] = testset[testindex] : object 'newdataset' not found but perhaps you have a different problem. Copy and paste (and read) the error message you got. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Brian Feeny Sent: Saturday, December 01, 2012 8:04 PM To: r-help@r-project.org Subject: [R] How to re-combine values based on an index? I am able to split my df into two like so: dataset - trainset index - 1:nrow(dataset) testindex - sample(index, trunc(length(index)*30/100)) trainset - dataset[-testindex,] testset - dataset[testindex,-1] So I have the index information, how could I re-combine the data using that back into a single df? I tried what I thought might work, but failed with: newdataset[testindex] = testset[testindex] object 'dataset' not found newdataset[-testindex] = trainset[-testindex] object 'dataset' not found Brian __ 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. __ 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] How to re-combine values based on an index?
Thank you for your response, here is a better example of what I am trying to do: data(iris) index_setosa - which(iris$Species == setosa) iris_setosa - data.frame() iris_setosa[index_setosa,] -iris[index_setosa,] iris_others - data.frame() iris_others[-index_setosa,] - iris[-index_setosa,] So the idea would be that iris_setosa is a dataframe of size 150, with 50 observations of setosa, using their original same indices, and 100 observations of NA. Likewise iris_others would be 100 observations of species besides setosa, using their original indices, and there would be 50 NA's. The above doesn't work. When I execute it, I am left with iris_setosa having 0 columns, I wish it to have all the original columns of iris. That said, once I get past the above (being able to split them out and keep original indices), I wish to be able to combine iris_setosa and iris_others so that iris_combined is a data frame with no NA's and all the original data. Does this make sense? So I am basically taking a dataframe, splitting it based on some criteria, and working on the two split dataframes separately, and then I wish to recombine. Brian So at this point, I have iris_setosa a dataframe of size On Dec 1, 2012, at 11:34 PM, William Dunlap wrote: newdataset[testindex] = testset[testindex] object 'dataset' not found Is that really what R printed? I get newdataset[testindex] = testset[testindex] Error in newdataset[testindex] = testset[testindex] : object 'newdataset' not found but perhaps you have a different problem. Copy and paste (and read) the error message you got. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Brian Feeny Sent: Saturday, December 01, 2012 8:04 PM To: r-help@r-project.org Subject: [R] How to re-combine values based on an index? I am able to split my df into two like so: dataset - trainset index - 1:nrow(dataset) testindex - sample(index, trunc(length(index)*30/100)) trainset - dataset[-testindex,] testset - dataset[testindex,-1] So I have the index information, how could I re-combine the data using that back into a single df? I tried what I thought might work, but failed with: newdataset[testindex] = testset[testindex] object 'dataset' not found newdataset[-testindex] = trainset[-testindex] object 'dataset' not found Brian __ 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. __ 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] How to re-combine values based on an index?
Hi, ?merge(), ?rbind(), or ?join() from library(plyr) set.seed(5) trainset-data.frame(ID=1:10,col2=runif(10,0,1)) dataset - trainset trainset-dataset[-testindex,] testset-dataset[testindex,] merge(testset,trainset,by=c(ID,col2),all=TRUE) # ID col2 #1 1 0.2002145 #2 2 0.6852186 #3 3 0.9168758 #4 4 0.2843995 #5 5 0.1046501 #6 6 0.7010575 #7 7 0.5279600 #8 8 0.8079352 #9 9 0.9565001 #10 10 0.1104530 You can also do this as: newdataset-data.frame(ID=rep(NA,nrow(dataset)),col2=rep(NA,nrow(dataset))) newdataset[testindex,]-testset newdataset[-testindex,]-trainset head(newdataset) # ID col2 #1 1 0.2002145 #2 2 0.6852186 #3 3 0.9168758 #4 4 0.2843995 #5 5 0.1046501 #6 6 0.7010575 A.K. - Original Message - From: Brian Feeny bfe...@mac.com To: r-help@r-project.org Cc: Sent: Saturday, December 1, 2012 11:04 PM Subject: [R] How to re-combine values based on an index? I am able to split my df into two like so: dataset - trainset index - 1:nrow(dataset) testindex - sample(index, trunc(length(index)*30/100)) trainset - dataset[-testindex,] testset - dataset[testindex,-1] So I have the index information, how could I re-combine the data using that back into a single df? I tried what I thought might work, but failed with: newdataset[testindex] = testset[testindex] object 'dataset' not found newdataset[-testindex] = trainset[-testindex] object 'dataset' not found Brian __ 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. __ 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] How to re-combine values based on an index?
On 02-12-2012, at 06:06, Brian Feeny wrote: Thank you for your response, here is a better example of what I am trying to do: data(iris) index_setosa - which(iris$Species == setosa) iris_setosa - data.frame() iris_setosa[index_setosa,] -iris[index_setosa,] iris_others - data.frame() iris_others[-index_setosa,] - iris[-index_setosa,] Change you example to make it actually do something data(iris) index_setosa - which(iris$Species == setosa) iris_setosa -iris[index_setosa,] head(iris_setosa) # iris_others - data.frame() # iris_others[-index_setosa,] - iris[-index_setosa,] iris_others - iris[-index_setosa,] head(iris_others) tail(iris_others) The head() and tail() calls are for checking. Combine the two like this z - rbind(iris_setosa,iris_others) head(z) tail(z) Berend So the idea would be that iris_setosa is a dataframe of size 150, with 50 observations of setosa, using their original same indices, and 100 observations of NA. Likewise iris_others would be 100 observations of species besides setosa, using their original indices, and there would be 50 NA's. The above doesn't work. When I execute it, I am left with iris_setosa having 0 columns, I wish it to have all the original columns of iris. That said, once I get past the above (being able to split them out and keep original indices), I wish to be able to combine iris_setosa and iris_others so that iris_combined is a data frame with no NA's and all the original data. Does this make sense? So I am basically taking a dataframe, splitting it based on some criteria, and working on the two split dataframes separately, and then I wish to recombine. Brian So at this point, I have iris_setosa a dataframe of size On Dec 1, 2012, at 11:34 PM, William Dunlap wrote: newdataset[testindex] = testset[testindex] object 'dataset' not found Is that really what R printed? I get newdataset[testindex] = testset[testindex] Error in newdataset[testindex] = testset[testindex] : object 'newdataset' not found but perhaps you have a different problem. Copy and paste (and read) the error message you got. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Brian Feeny Sent: Saturday, December 01, 2012 8:04 PM To: r-help@r-project.org Subject: [R] How to re-combine values based on an index? I am able to split my df into two like so: dataset - trainset index - 1:nrow(dataset) testindex - sample(index, trunc(length(index)*30/100)) trainset - dataset[-testindex,] testset - dataset[testindex,-1] So I have the index information, how could I re-combine the data using that back into a single df? I tried what I thought might work, but failed with: newdataset[testindex] = testset[testindex] object 'dataset' not found newdataset[-testindex] = trainset[-testindex] object 'dataset' not found Brian __ 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. __ 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. __ 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.
