[R] reference category in binomal glm
Hi all i know this is probably a silly question but im wondering what is the 'reference' category when you run a binomal glm. that is my outcome/DV is 0,1 and i run a regression and get coefficients. do the coefficients refer to the probability to get 0 or 1? thanks so much in advance Z [[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] reference category in binomal glm
Thank you both for your kinds help best z. On Tue, May 27, 2014 at 2:25 PM, Prof Brian Ripley rip...@stats.ox.ac.ukwrote: On 27/05/2014 09:51, Xebar Saram wrote: Hi all i know this is probably a silly question but im wondering what is the 'reference' category when you run a binomal glm. that is my outcome/DV is 0,1 and i run a regression and get coefficients. do the coefficients refer to the probability to get 0 or 1? ?binomial in R-devel says For the âbinomialâ and âquasibinomialâ families the response can be specified in one of three ways: 1. As a factor: âsuccessâ is interpreted as the factor not having the first level (and hence usually of having the second level). 2. As a numerical vector with values between â0â and â1â, interpreted as the proportion of successful cases (with the total number of cases given by the âweightsâ). 3. As a two-column integer matrix. The first column gives the number of successes and the second the number of failures. thanks so much in advance Z [[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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 [[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] R crashes with memory errors on a 256GB machine (and system shoes only 60GB usage)
Hi again and thank you all for the answers i need to add that im a relatively R neewb so i apologize in advance i started R with the --vanilla option and ran gc() this is the output i get: gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 182236 9.8 407500 21.8 35 18.7 Vcells 277896 2.2 786432 6.0 785897 6.0 also this is the memory.profile() memory.profile() NULL symbolpairlist closure environment promise 15611 866952277 3144175 language special builtinchar logical integer 21636 44 63763614574 11089 double complex character ... anylist 782 1 20934 0 08023 expressionbytecode externalptr weakref raw S4 162711272 364 365 831 im running on linux (arch linux) and 'free' shows this: zeltak@zuni ~ â³ free -h total used free sharedbuffers cached Mem: 251G99G 152G66G 249M84G -/+ buffers/cache:14G 237G Swap: 0B 0B 0B im not running any parrallel stuff at all milan: how does one know if the memory is fragmented? thank you all again i really appreciate the help best Z On Thu, Jan 2, 2014 at 10:35 PM, Ben Bolker bbol...@gmail.com wrote: Xebar Saram zeltakc at gmail.com writes: Hi All, I have a terrible issue i cant seem to debug which is halting my work completely. I have R 3.02 installed on a linux machine (arch linux-latest) which I built specifically for running high memory use models. the system is a 16 core, 256 GB RAM machine. it worked well at the start but in the recent days i keep getting errors and crashes regarding memory use, such as cannot create vector size of XXX, not enough memory etc when looking at top (linux system monitor) i see i barley scrape the 60 GB of ram (out of 256GB) i really don't know how to debug this and my whole work is halted due to this so any help would be greatly appreciated I'm very sympathetic, but it will be almost impossible to debug this sort of a problem remotely, without a reproducible example. The only guess that I can make, if you *really* are running *exactly* the same code as you previously ran successfully, is that you might have some very large objects hidden away in a saved workspace in a .RData file that's being loaded automatically ... I would check whether gc(), memory.profile(), etc. give sensible results in a clean R session (R --vanilla). Ben Bolker __ 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.
[R] R crashes with memory errors on a 256GB machine (and system shoes only 60GB usage)
Hi All, I have a terrible issue i cant seem to debug which is halting my work completely. I have R 3.02 installed on a linux machine (arch linux-latest) which I built specifically for running high memory use models. the system is a 16 core, 256 GB RAM machine. it worked well at the start but in the recent days i keep getting errors and crashes regarding memory use, such as cannot create vector size of XXX, not enough memory etc when looking at top (linux system monitor) i see i barley scrape the 60 GB of ram (out of 256GB) i really don't know how to debug this and my whole work is halted due to this so any help would be greatly appreciated Best wishes Z [[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] extracting random intercept
Hi all I am using this model for a time series analysis : lung_new - (glmmPQL(LUNG ~ 1, random = ~ 1 | GUID, family = poisson, data = ts0004lag) Im interested in extracting just the random intercept can anyone point me in the right direction thx zeltak [[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] Extracting random intercept
Hi all I am using this model for a time series analysis : lung_new - (glmmPQL(LUNG ~ 1, random = ~ 1 | GUID, family = poisson, data = ts0004lag) Im interested in extracting just the random intercept can anyone point me in the right direction thx zeltak __ 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] error using predict
Hi I am very new to R (so excuse me in advance if this is pretty trivial) I am using the predict function to get prediction on a dataset from another dataset using the follwoing command: newpredT2003 = predict( object=out.model_T2003, newdata=aodmc_2003 , level = 0 ) yet i get this error: Error in na.fail.default(list(AOD = c(0.092, 0.081, 0.086, 0.085, 0.09, : missing values in object Calls: predict ... model.frame.default - Anonymous - na.fail.default i think its something simple but cant find any info when googling..can anyone point me in the right direction on what needs to be done to fix the errors? thx Ethan __ 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] choosing a random sample by precentage
hi all i have found the follwoing way to choose a random sample by sample size (200): ten_per_T2000 - F_T2000_All[sample(nrow(F_T2000_All), 200), ] but i wondered if there is a way to choose a sample size by precentage (10% etc..) thx ethan __ 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.
