[R] problem with installing a local zip file : GFCURE
Dear all, I am trying to install a package called GFCURE from a local zip file. This package fits a cure survival model and has been downloaded from: http://post.queensu.ca/~pengp/software.html The problem is that when I try to install this package from a local zip file using R, I've got the following error message: Error in gzfile(file, r) : cannot open the connection In addition: Warning message: In gzfile(file, r) : cannot open compressed file 'gfcureWinR/DESCRIPTION', probable reason 'No such file or directory' First, I thought it was an internal problem. I then asked some of my colleagues to do the same thing and they had the same error message. I would be very grateful if you can help me on that matter. All the best Marc _ [[elided Hotmail spam]] [[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] problem with installing a local zip file : GFCURE
Dear gabor, Many thanks for your answer. I indeed didn't check the read me text. Bests From: ggrothendi...@gmail.com Date: Tue, 19 May 2009 08:44:13 -0400 Subject: Re: [R] problem with installing a local zip file : GFCURE To: marc_bern...@hotmail.co.uk CC: r-help@r-project.org On Tue, May 19, 2009 at 6:17 AM, marc bernard marc_bern...@hotmail.co.uk wrote: Dear all, I am trying to install a package called GFCURE from a local zip file. This package fits a cure survival model and has been downloaded from: You are assuming its in the form of an R *package* but its not. Unzip it and read the readme.txt file. If you still have problems contact the author. http://post.queensu.ca/~pengp/software.html The problem is that when I try to install this package from a local zip file using R, I've got the following error message: Error in gzfile(file, r) : cannot open the connection In addition: Warning message: In gzfile(file, r) : cannot open compressed file 'gfcureWinR/DESCRIPTION', probable reason 'No such file or directory' First, I thought it was an internal problem. I then asked some of my colleagues to do the same thing and they had the same error message. I would be very grateful if you can help me on that matter. All the best Marc _ [[elided Hotmail spam]] [[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. _ [[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 package to fit mixture or cure survival models
Dear All, I am desperately trying to find any R package that fits a mixture survival models also know as a cure models. These are survival models where the survival function is improper, which also means that a fraction of subjects are expected not to expreience the event. A huge literature has been developed for these type of models but I couldn't find any R package that fits them. Bests Marc _ [[elided Hotmail spam]] [[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] Mixture of survivals or cure models
Dear All, I am desperately trying to find any R package that fits a mixture survival models also know as a cure models. This are survival model where the survival function is improper which also means that a fraction of subjects are expected not to expreience the event. A Huge literature has been developed for thes type of models but I couldn't find any R package that fits this type of models. Bests Marc _ [[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] confidence interval for roc curves
Dear all, I am looking for an R package that allows me to calculate and plot the confidence limits for the roc curve using for example some bootstrapping. I tried ROCR who seems doing such work but i couldn't find the right option to do it. Many thanks Bests Marc _ tarted! [[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] Roc curves confidence intervals
Dear all, I am looking for an R package that allows me to calculate and plot the confidence intervals for the roc curve using for example some bootstrapping. I tried ROCR who seems doing such work but i couldn't find the right option in it. Many thanks Bests Marc _ [[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] NLME: Prediction intervals for random effects
Dear all, nbsp; Is there a function to calculate thenbsp; prediction intervals for random effects in non-linear mixed models? I found a way to do it for linear mixed models but not for non-linearnbsp;mixed one. nbsp; Many thnaks nbsp; Bernard nbsp; nbsp; _ o.fr [[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] prediction intervals for random effects in nlme
Dear all, nbsp; This is a relist of my previous question. I noticed that some charactersnbsp;were nbsp;not displayed in the previous version. nbsp; nbsp; Is there a function to calculate thenbsp; prediction intervals for random effects in non-linear mixed models? I found a way to do it for linear mixed models but not for non-linearnbsp;mixed one. nbsp; Many thanks nbsp; Bernard _ o.fr [[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] Random effects dimension in nlme and P-values
Dear All, I don't know whether this question is appropriate for this list or not. My question is as follows: I am fitting a non-linear mixed model using the SSlogis function. When the parameters xmid and scal are both considered as random (let us say model M1), the p-value for my covariate of interest is greater than 0.05 (non-significant). However, when only the xmid is considered as random (Model M2), the p-value is less than 0.05 and my covariate becomes highly significant. The introduction of random effects of course increases the variability in the fixed effects but does not affect their Bias as I understand. My question is: Is it then legitimate to use the model with only xmid as random effects (model M2 since it gives me significant results)? knowing that the AIC for M1 is lower than that one for M2 meaning that M1 is slightly fitting better the data than M2 Many thanks in advance Bernard, - Une boite mail plus intelligente. [[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] good references on survival analysis
Dear all, I am looking for a good reference on Survival analysis. I am looking for a booking containing both applications and Maths. Explaining different methods in survival analysis Many thanks Bernard - [[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] boxplot and number of observations per box
Dear all, How can I plot the number of observations per box in a boxplot. Many thanks, Bernard - [[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] boxplot and number of observations per box
Dear all, How can I plot the number of observations per box in a boxplot. Many thanks, Bernard - [[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] lme output
Dear all, I noticed the following in the call of lme using msVerbose. fm1 - lme(distance ~ age, data = Orthodont, control = lmeControl(msVerbose=T)) 9 318.073: -0.567886 0.152479 1.98021 10 318.073: -0.567191 0.152472 1.98009 11 318.073: -0.567208 0.152473 1.98010 fm2 - lme(distance ~ age, random =~age, data = Orthodont, lmeControl(msVerbose=T)) 7 318.073: -0.342484 1.75530 4.44650 8 318.073: -0.342507 1.75539 4.44614 9 318.073: -0.342497 1.75539 4.44614 The two model are equivalent and give the same estimates. However, the optimal parameters in the profiled log-likelihood are not the same? why? As I usually thought, the parameters optimised in the profiled likelihood are the log of the precision matrix. The latter can be derived as a Cholesky factorization of the product between the residuals variance and the inverse of the random effects covariance. When I check that it's not the case for model fm1 even if it's equivalent to model fm2. log(chol(((summary(fm1)$sigma)^2)*solve( matrix(getVarCov(fm1), nrow=2 [,1][,2] [1,] -0.3424971 1.492037 [2,] -Inf 1.755388 log(chol(((summary(fm2)$sigma)^2)*solve( matrix(getVarCov(fm2), nrow=2 [,1][,2] [1,] -0.3424971 1.492037 [2,] -Inf 1.755388 In the two mdels, this terms are equals to the optimized parameters in fm2 not in fm1. I am missing something I suppose. Bests, Bernard - [[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] bootstrap for nlme
Dear All, Is there any bootstrap function in nlme for a non linear mixed model. Either a non-parametric or parametric one. Thanks Bernard - [[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] sequence of vectors
Dear All, I wonder if there is any R function to generate a sequence of vectors from existing ones. For example: x 1- c(1,2,3) x2 - c(4,5) x3 - c(6,7,8) The desired output is a list of all 3*2*3 = 18 possible combinations of elements of x1,x2 and x3. One element for example is (1,4,6). Many thanks in advance, Bernard - [[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.
