[R] [R-pkgs] package JMbayes -- version 0.5-0
*** Apologies for cross posting *** Dear Colleagues, Dear R-users, I would like to announce the release of the new version of package JMbayes available from CRAN (http://CRAN.R-project.org/package=JMbayes). This package fits joint models for longitudinal and time-to-event data under a Bayesian approach using MCMC. These models are applicable in mainly two settings. First, when focus is on the survival outcome and we wish to account for the effect of an endogenous (aka internal) time-dependent covariates measured with error. Second, when focus is on the longitudinal outcome and we wish to correct for nonrandom dropout. Some basic features of the new version: * The MCMC in now implemented with efficient custom-made code and no longer relies on JAGS, OpenBUGS or WinBUGS. * The user can now specify her own density function for the longitudinal responses using argument 'densLong' (default is the normal pdf). Among others, this allows to fit joint models with categorical and left-censored longitudinal responses and robust joint models with Student's-t error terms. In addition, using the 'df.RE' argument, the user can also change the distribution of the random effects from multivariate normal to a multivariate Student's-t with prespecified degrees of freedom. * The user has now the option to define custom transformation functions for the terms of the longitudinal submodel that enter into the linear predictor of the survival submodel (argument 'transFun'). For example, interactions terms, nonlinear terms (polynomials, splines), etc. * The baseline hazard is now only estimated using B-splines (penalized (default) or regression). * Dynamic predictions: - function survfitJM.JMbayes(), which computes dynamic survival probabilities, is now faster; - the new generic function aucJM() calculates time-dependent AUCs for joint models; - the new generic function dynCJM() calculates a dynamic discrimination index (weighted average of time-dependent AUCs) for joint models; - the new generic function prederrJM() calculates prediction errors for joint models; - the new function bma.combine() combines predictions using Bayesian model averaging; posterior model weights can be calculated using logLik.JMbayes() and marglogLik(). * a method has been added for the xtable() generic from package xtable for producing a LaTeX table with the results of the joint model. * Backward-incompatible version; the aforementioned changes require refitting joint models that have been fitted with previous versions. As always, any kind of feedback (e.g., questions, suggestions, bug-reports, etc.) is more than welcome. Kind regards, Dimitris -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ 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] Counting various elemnts in a vactor
try this: df - c(F, C, F, B, D, A, D, D, A, F, D, F, B, C) tab - table(df) tab rep(names(tab), 100 * tab) I hope it helps. Best, Dimitris On 3/26/2013 9:12 AM, Katherine Gobin wrote: Dear R forum I have a vector say as given below df = c(F, C, F, B, D, A, D, D, A, F, D, F, B, C) I need to find (1) how many times each element occurs? e.g. in above vector F occurs 4 times, C occurs 2 times etc. (2) Depending on the number of occurrences, I need to repeat the element 100 times of the occurrences e.g. I need to repeat F 6 * 100 = 600 times, C 2*100 = 200 times. I can manage the second part i.e. repeating but I am not able to count the number of times the element is appearing in a given vector. Kindly guide Katherine [[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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ __ 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] transpose lists
two possibilities are: lis - list(c(12.1,0.1,12.0,1.1), c(3.44,3.00,33.10,23.00)) # 1st m - do.call(rbind, lis) split(m, col(m)) # 2nd lapply(seq_along(lis[[1]]), function (i) sapply(lis, [, i)) I hope it helps. Best, Dimitris On 3/8/2013 11:06 AM, ishi soichi wrote: Thanks. The result should be a list of lists like... x [[1]] [1] 12.10 3.44 [[2]] [1] 0.1 3.0 [[3]] [1] 12.0 33.1 [[4]] [1] 1.1 23.0 lapply(x, t) doesn't do the job, I think. ishida 2013/3/8 PIKAL Petr petr.pi...@precheza.cz Hi -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of ishi soichi Sent: Friday, March 08, 2013 10:50 AM To: r-help Subject: [R] transpose lists Can you think of a function that transposes a list like What shall be the result of transposed list? Something like lapply(x, t) Regards Petr x [[1]] [1] 12.1 0.1 12.0 1.1 [[2]] [1] 3.44 3.00 33.10 23.00 ? ishida [[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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ __ 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] Script for conditional sums of vectors
try this: a - c(1,1,1,1,1,1,2,2,2,2,2,2) b - c(1,1,1,2,3,4,1,1,2,2,3,4) c - c(400,200,300,100,500,300,200,100,500,400,200,100) DF - data.frame(a, b, c) with(DF, tapply(c, list(a, b), sum)) I hope it helps. Best, Dimitris On 2/4/2013 10:29 AM, Benjamin Gillespie wrote: Hi guys, I hope you can help me with this (probably) simple query: I have a data frame: -- a=c(1,1,1,1,1,1,2,2,2,2,2,2) b=c(1,1,1,2,3,4,1,1,2,2,3,4) c=c(400,200,300,100,500,300,200,100,500,400,200,100) data=data.frame(a=a,b=b,c=c) -- And I would like to get the following output: -- b a 1 2 3 4 1 900 100 500 300 2 300 900 200 100 -- The values in the output represent the sum of values c in data frame data, for each a and b combination. For example, where a = 1 and b = 1, the output is 400+200+300 = 900. Please would anyone be able to provide a script to create my desired output? Many thanks in advance, Ben Gillespie Research Postgraduate School of Geography University of Leeds Leeds LS2 9JT __ 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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ __ 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 create a random matrix with conditions
You didn't say how you want these variables to be distributed, but in case you want a multivariate normal, then have a look at function mvrnorm() from package MASS, and especially at the 'empirical' argument, e.g., library(MASS) # assumed covariance matrix V - cbind(c(2, 1), c(1, 1.2)) V x1 - mvrnorm(1000, c(0,0), V, empirical = FALSE) var(x1) x2 - mvrnorm(1000, c(0,0), V, empirical = TRUE) var(x2) I hope it helps. Best, Dimitris On 1/28/2013 7:11 AM, Simon Givoli wrote: Hi! I want to create a random matrix with 15 variables, each variable having 1000 observations. Between each two variables, I want to define a specific (*not *random) correlations between them, but still saving the randomness of each variable (mean=zero, s.d=1). How can I do this in R? thanks, Simon [[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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ __ 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] problems with coercing a factor to be numeric
Check R FAQ 7.10: How do I convert factors to numeric? I hope it helps. Best, Dimitris On 1/23/2013 10:33 AM, Francesco Sarracino wrote: Dear R listers, I am trying to compute the mean of a dummy variable that is encoded as a factor. However, even though the levels of my factor are 0 - 1, when I compute the mean (after coercing the factor to be numeric), R changes 0 into 1 and 1 into yes, thus altering my expected result. Please, consider the following working example: pp - rep(0:1, 10) pp - factor(pp, levels=(0:1), labels=c(no,yes)) mean(pp) #this won't work because the argument is not numeric or logical mean(as.integer(pp)) # this computes the average, but not on the range 0-1, but 1-2. Indeed, the result is 1.5 and not 0.5 as expected. What am I doing wrong? Thanks in advance for your kind support, f. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ __ 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] problems with coercing a factor to be numeric
check also pp - rep(0:1, 10) pp - factor(pp, levels=(0:1), labels=c(no,yes)) unclass(pp) unclass(pp) - 1 Best, Dimitris On 1/23/2013 10:48 AM, Francesco Sarracino wrote: Dear Dimitris, thanks for your quick reply. I've tried the solutions proposed in 7.10 How do I convert factors to numeric? as.numeric(as.character(pp)) and as.numeric(levels(pp))[as.integer(pp)] However, whatever I do, I get Warning message: NAs introduced by coercion and the output is a vector of NA. Any ideas? f. On 23 January 2013 10:39, D. Rizopoulos d.rizopou...@erasmusmc.nl mailto:d.rizopou...@erasmusmc.nl wrote: Check R FAQ 7.10: How do I convert factors to numeric? I hope it helps. Best, Dimitris On 1/23/2013 10:33 AM, Francesco Sarracino wrote: Dear R listers, I am trying to compute the mean of a dummy variable that is encoded as a factor. However, even though the levels of my factor are 0 - 1, when I compute the mean (after coercing the factor to be numeric), R changes 0 into 1 and 1 into yes, thus altering my expected result. Please, consider the following working example: pp - rep(0:1, 10) pp - factor(pp, levels=(0:1), labels=c(no,yes)) mean(pp) #this won't work because the argument is not numeric or logical mean(as.integer(pp)) # this computes the average, but not on the range 0-1, but 1-2. Indeed, the result is 1.5 and not 0.5 as expected. What am I doing wrong? Thanks in advance for your kind support, f. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 tel:%2B31%2F%280%2910%2F7043478 Fax: +31/(0)10/7043014 tel:%2B31%2F%280%2910%2F7043014 Web: http://www.erasmusmc.nl/biostatistiek/ -- Francesco Sarracino, Ph.D. https://sites.google.com/site/fsarracino/ -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ __ 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] Concatenate two lists, list by list
you just need: mapply(c, Part1$dataset, Part2$dataset, SIMPLIFY = FALSE) I hope it helps. Best, Dimitris On 1/23/2013 11:01 AM, Alaios wrote: Thanks a lot Petr, for the answer unfortunately that would convert everything to a matrix num [1:32002, 1:3] 0 0 0 0 0 0 0 0 0 0 ... but if you check below you can see that I Want those to form a list. Regards Alex From: PIKAL Petr petr.pi...@precheza.cz Sent: Tuesday, January 22, 2013 11:51 AM Subject: RE: [R] Concatenate two lists, list by list Hi Maybe you could use mapply mapply(c, Part1$dataset,Part2$dataset) Regards Petr -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Alaios Sent: Tuesday, January 22, 2013 11:26 AM To: R help Subject: [R] Concatenate two lists, list by list Dear all, I would like to concatenate the lists below str(Part2$dataset) List of 3 $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... str(Part1$dataset) List of 3 $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... I tried concatenating those with: str(cbind(Part1$datase,Part2$dataset)) List of 6 $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... - attr(*, dim)= int [1:2] 3 2 but I want something different. To concatenate those into a list by list operation so I will end up with something looking like that str(concatenatedLists) List of 3 $ : num [1:32002] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:32002] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:32002] 0 0 0 0 0 0 0 0 0 0 ... - attr(*, dim)= int [1:2] 3 2 Is there anything that can do that in R? Regards Alex [[alternative HTML version deleted]] [[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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ __ 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] Concatenate two lists, list by list
In this example, I get the following: lis1 - replicate(3, rnorm(5), simplify = FALSE) lis2 - replicate(3, rnorm(5), simplify = FALSE) lis1 lis2 mapply(c, lis1, lis2, SIMPLIFY = FALSE) Best, Dimitris On 1/23/2013 11:58 AM, Alaios wrote: Thanks a lot. Unfortunately that did not help either. num [1:32003, 1:3] 0 0 0 0 0 0 0 0 0 0 ... - attr(*, dimnames)=List of 2 ..$ : chr [1:32003] ... ..$ : NULL but I want to get List of 3 $ : num [1:32002] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:32002] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:32002] 0 0 0 0 0 0 0 0 0 0 ... - attr(*, dim)= int [1:2] 3 2 I am sorry that I can not find reproducible example to show you Alex *From:* D. Rizopoulos d.rizopou...@erasmusmc.nl *To:* Alaios ala...@yahoo.com *Cc:* PIKAL Petr petr.pi...@precheza.cz; R help R-help@r-project.org *Sent:* Wednesday, January 23, 2013 11:08 AM *Subject:* Re: [R] Concatenate two lists, list by list you just need: mapply(c, Part1$dataset, Part2$dataset, SIMPLIFY = FALSE) I hope it helps. Best, Dimitris On 1/23/2013 11:01 AM, Alaios wrote: Thanks a lot Petr, for the answer unfortunately that would convert everything to a matrix num [1:32002, 1:3] 0 0 0 0 0 0 0 0 0 0 ... but if you check below you can see that I Want those to form a list. Regards Alex From: PIKAL Petr petr.pi...@precheza.cz mailto:petr.pi...@precheza.cz Sent: Tuesday, January 22, 2013 11:51 AM Subject: RE: [R] Concatenate two lists, list by list Hi Maybe you could use mapply mapply(c, Part1$dataset,Part2$dataset) Regards Petr -Original Message- From: r-help-boun...@r-project.org mailto:r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org http://project.org/] On Behalf Of Alaios Sent: Tuesday, January 22, 2013 11:26 AM To: R help Subject: [R] Concatenate two lists, list by list Dear all, I would like to concatenate the lists below str(Part2$dataset) List of 3 $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... str(Part1$dataset) List of 3 $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... I tried concatenating those with: str(cbind(Part1$datase,Part2$dataset)) List of 6 $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:16001] 0 0 0 0 0 0 0 0 0 0 ... - attr(*, dim)= int [1:2] 3 2 but I want something different. To concatenate those into a list by list operation so I will end up with something looking like that str(concatenatedLists) List of 3 $ : num [1:32002] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:32002] 0 0 0 0 0 0 0 0 0 0 ... $ : num [1:32002] 0 0 0 0 0 0 0 0 0 0 ... - attr(*, dim)= int [1:2] 3 2 Is there anything that can do that in R? Regards Alex [[alternative HTML version deleted]] [[alternative HTML version deleted]] __ R-help@r-project.org mailto: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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ __ 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] Simple use of dcast (reshape2 package)
you could try the following: DF - read.table(textConnection( Target Eaten ID 50 TPP 0 1 51 TPP 1 2 52 TPP 3 3 53 TPP 1 4 54 TPP 2 5 50.1GPA 9 1 51.1GPA11 2 52.1GPA 8 3 53.1GPA 8 4 54.1GPA10 5), header = TRUE) newDF - as.data.frame(with(DF, tapply(Eaten, list(ID, Target), c))) newDF$ID - unique(DF$ID) newDF I hope it helps. Best, Dimitris On 1/22/2013 10:23 AM, Patrick Connolly wrote: Suppose I have a small dataframe aa Target Eaten ID 50 TPP 0 1 51 TPP 1 2 52 TPP 3 3 53 TPP 1 4 54 TPP 2 5 50.1GPA 9 1 51.1GPA11 2 52.1GPA 8 3 53.1GPA 8 4 54.1GPA10 5 And I want to reshape it into ID TPP GPA 1 1 0 9 2 2 1 11 3 3 3 8 4 4 1 8 5 5 2 10 I realise that dcast function in the reshape2 package can handle much more complicated tasks than that, but I can't make it do a simple one. If I simply tried dcast(aa, ... ~ Target) Using ID as value column: use value.var to override. Aggregation function missing: defaulting to length Eaten GPA TPP 1 0 0 1 2 1 0 2 3 2 0 1 4 3 0 1 5 8 2 0 6 9 1 0 710 1 0 811 1 0 As per the help file, it's giving counts of the numbers in the Eaten column since that's the default fun.aggregate value. My questions are: what fun.aggregate would work? Alternatively, can value.var be set to something useful? TIA -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ __ 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] apply calculations to elements in a vector
Try this: x - c(10, 20, 30) head(x, -1) + tail(x, -1) I hope it helps. Best, Dimitris On 11/16/2012 3:50 PM, e-letter wrote: Readers, If a vector consists of: 10 20 30 how to create a new vector based upon the results of calculations to the elements, e.g. addition of successive elements, so that a new vector would be: 30 50 i.e. 10+20, then 20+30, etc.? __ 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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ __ 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] multiply each row in a matrix with the help of the for loop
Another alternative is:
aa - array(0, dim = c(3,3,3))
a - matrix(1, 3, )
for (i in 1:3) {
a[i, ] - -a[i, ]
aa[, , i] - a
}
aa
I hope it helps.
Best,
Dimitris
From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] on behalf of
arun [smartpink...@yahoo.com]
Sent: Tuesday, November 13, 2012 15:25
To: Haris Rhrlp
Cc: R help
Subject: Re: [R] multiply each row in a matrix with the help of the for loop
HI,
May be this helps:
list1-lapply(lapply(1:3,function(i) {aa[1:i,,i]-a[1:i,]*-1
return(aa[,,i])}),function(x) apply(x,2,function(i) ifelse(i==0,1,x)))
res-array(unlist(list1),dim=c(nrow(list1[[1]]),ncol(list1[[1]]),length(list1)))
res
#, , 1
#
#[,1] [,2] [,3]
#[1,] -1 -1 -1
#[2,]111
#[3,]111
#, , 2
#
# [,1] [,2] [,3]
#[1,] -1 -1 -1
#[2,] -1 -1 -1
#[3,]111
#
#, , 3
# [,1] [,2] [,3]
#[1,] -1 -1 -1
#[2,] -1 -1 -1
#[3,] -1 -1 -1
A.K.
- Original Message -
From: Haris Rhrlp haris_r_h...@yahoo.com
To: R-help@r-project.org R-help@r-project.org
Cc:
Sent: Tuesday, November 13, 2012 7:41 AM
Subject: [R] multiply each row in a matrix with the help of the for loop
Dear R users,
I have this program
aa-array(rep(0,27),dim=c(3,3,3))
a-matrix(rep(1,9),ncol=3)
n-0
for (i in 1:3) {
a[i,]-a[i,]*(-1)
n-n+1
aa[,,n]-a[i,]
}
but i real want to multiply each row with -1 according to for loop and after
that to put it in the array.
I will give an example for what excaclty want
-1 -1 -1
1 1 1
1 1 1
-1 -1 -1
-1 -1 -1
1 1 1
-1 -1 -1
-1 -1 -1
-1 -1 -1
[[alternative HTML version deleted]]
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Re: [R] Selected matrices of an array and put into a list
One approach is: BB - rnorm(6*5*27) dim(BB) - c(6, 5, 27) lapply(2:27, function (i) BB[, , i]) I hope it helps. Best, Dimitris On 11/12/2012 8:56 AM, Haris Rhrlp wrote: Dear R users, I have an array that has matrices that i want BB[16,5,2:27] i want to put each of the 26 matrices into a List thanks in advance [[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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ __ 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] simple coversion of matrix rows to matrix columns
try this: a - matrix(1:30, ncol= 3 ) t(a) I hope it helps. Best, Dimitris On 11/7/2012 12:50 PM, Andras Farkas wrote: Dear All I would like to convert matrix rows to columns. I am thinking the t() function should help, but am having a hard time converting the matrix into the dimensions I would like them to. Example: a -matrix(c(1:30),ncol=3) gives me:[,1] [,2] [,3] [1,]1 11 21 [2,]2 12 22 [3,]3 13 23 [4,]4 14 24 [5,]5 15 25 [6,]6 16 26 [7,]7 17 27 [8,]8 18 28 [9,]9 19 29 [10,] 10 20 30 I would like to convert the above into a matrix that looks like this with 3 rows and 10 columns: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 I have tried : b -t(matrix(a)) but I am getting a 1X30 double matrix. I also Tried to specify b -t(matrix(a),byrow=TRUE,ncol=10) but that does not help either... apreciate your help, 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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ __ 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] averaging a list of matrices element wise
If you don't have any NAs, then one way is:
n - 3
r - 5
s - 6
raw - lapply(seq_len(n), function(i){
matrix(rnorm(r * s), ncol = r)
})
Reduce(+, raw) / length(raw)
I hope it helps.
Best,
Dimitris
On 11/5/2012 11:32 AM, ONKELINX, Thierry wrote:
Dear all,
I have a list of n matrices which all have the same dimension (r x s). What
would be a fast/elegant way to calculate the element wise average? So
result[1, 1] - mean(c(raw[[1]][1, 1] , raw[[2]][1, 1], raw[[...]][1, 1],
raw[[n]][1, 1]))
Here is my attempt.
#create a dummy dataset
n - 3
r - 5
s - 6
raw - lapply(seq_len(n), function(i){
matrix(rnorm(r * s), ncol = r)
})
#do the calculation
result - array(dim = c(dim(raw[[1]]), length(raw)))
for(i in seq_along(raw)){
result[,,i] - raw[[i]]
}
result - apply(result, 1:2, mean)
Best regards,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie Kwaliteitszorg / team Biometrics Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
thierry.onkel...@inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more than
asking him to perform a post-mortem examination: he may be able to say what
the experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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--
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus University Medical Center
Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014
Web: http://www.erasmusmc.nl/biostatistiek/
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] convert list without same component length to matrix
try this: l - list(c(1,2,3,7), c(3,4,5,6,3), c(4,2,5,7), c(2,4,6,3,2), c(3,5,7,2)) sapply(l, head, 4) I hope it helps. Best, Dimitris On 11/1/2012 9:11 AM, Al Ehan wrote: Hi, I have this lame question. I want to convert a list (each with varies in length) to matrix with same row length by eliminating vectors outside the needed range. For example: l-list(NULL) l[[1]]=1,2,3.7 l[[2]]=3,4,5,6,3 l[[3]]=4,2,5,7 l[[4]]=2,4,6,3,2 l[[5]]=3,5,7,2 #so say I want to only have 4 rows and 5 column in my matrix (or data.frame) and eliminating the 5th index value in l[[2]] and l[[4]] #what is the simplest code would be? I actually have hundreds of the list components. thanks [[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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ __ 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-pkgs] New Package 'JMbayes' for the Joint Modeling of Longitudinal and Survival Data under a Bayesian approach
Dear R-users, I would like to announce the release of the new package JMbayes available from CRAN (http://CRAN.R-project.org/package=JMbayes). This package fits shared parameter models for the joint modeling of normal longitudinal responses and event times under a Bayesian approach using JAGS, WinBUGS or OpenBUGS. The package has a single model-fitting function called jointModelBayes(), which accepts as main arguments a linear mixed effects object fit returned by function lme() of package nlme, and a Cox model object fit returned by function coxph() of package survival. * jointModelBayes() allows for joint models with relative risk survival submodels with Weibull or B-spline approximated baseline hazard functions (controlled by argument 'survMod'). * In addition, argument 'param' of jointModelBayes() specifies the association structure between the longitudinal and survival processes; available options are: - td-value which is the classic joint model formulation used in Wulfsohn and Tsiatis (1997); - td-extra which is a user-defined, possibly time-dependent, term based on the specification of the 'extraForm' argument of jointModelBayes(). This could be used to include terms, such as the time-dependent slope (i.e., the derivative of the subject-specific linear predictor of the linear mixed model), and the time-dependent cumulative effect (i.e., the integral of the subject-specific linear predictor of the linear mixed model); - td-both which is the combination of the previous two parameterizations, i.e., the current value and the user-specified terms are included in the linear predictor of the relative risk model; and - shared-RE where only the random effects of the linear mixed model are included in the linear predictor of the survival submodel. The package also provides functionality for computing dynamic predictions for the longitudinal and time-to-event outcomes using functions predict() and survfitJM(), respectively. As always, any kind of feedback (questions, suggestions, bug-reports, etc.) is more than welcome. Best, Dimitris -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ 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.
