Re: [Rd] An interesting chat with ChatGPT

ChatGPT provided an R code with error when I asked a question related to prediction of a new data point for linear mixed effects model. So, it is not immune to coding mistakes! Ravi From: R-devel on behalf of Boris Steipe Sent: Monday, February 13, 2023

Re: [Rd] Use of MathJax (or something similar) in .Rd files

Thank you. This is a very useful idea! Best, Ravi From: R-devel on behalf of Viechtbauer, Wolfgang (SP) Sent: Thursday, April 30, 2020 6:59:02 AM To: r-devel Subject: Re: [Rd] Use of MathJax (or something similar) in .Rd files Thanks Gabor and Duncan! It

Re: [Rd] status of Java & rJava?

I, too, had encountered problems with Java on Windows 10 while I was trying to install the package "xlsx." I tried the fixes I found online, but to no avail. Thanks & Best regards, Ravi From: R-devel on behalf of Gregory Warnes Sent: Saturday, March 28,

Re: [Rd] unstable corner of parameter space for qbeta?

This is also strange: qbeta <- function (p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE) { if (missing(ncp)) .Call(C_qbeta, p, shape1, shape2, lower.tail, log.p) else .Call(C_qnbeta, p, shape1, shape2, ncp, lower.tail, log.p) } Since the default value is

Re: [Rd] diag(-1) produces weird result

It behaves as per documentation. " Using diag(x) can have unexpected effects if x is a vector that could be of length one. Use diag(x, nrow = length(x)) for consistent behavior." Ravi From: R-devel on behalf of Gábor Csárdi Sent: Monday, September 17,

Re: [Rd] Searching R Packages

Hi Spencer, Thank you for this wonderful service to the R community. A suggestion: it would be great to discuss how to search github and Bioconductor repositories. Thanks, Ravi From: R-devel on behalf of Spencer Graves

Re: [Rd] Wrongly converging glm()

: Friday, July 21, 2017 3:09 PM To: Ravi Varadhan <ravi.varad...@jhu.edu> Cc: Therneau, Terry M., Ph.D. <thern...@mayo.edu>; r-devel@r-project.org; jorism...@gmail.com; westra.harm...@outlook.com Subject: Re: [Rd] Wrongly converging glm() Hi Ravi: Well said. In John's Rvmmin package,

Re: [Rd] Wrongly converging glm()

Please allow me to add my 3 cents. Stopping an iterative optimization algorithm at an "appropriate" juncture is very tricky. All one can say is that the algorithm terminated because it triggered a particular stopping criterion. A good software will tell you why it stopped - i.e. the stopping

Re: [Rd] optim(…, method=‘L-BFGS-B’) stops with an error message while violating the lower bound

Spencer, Another option is to try the "lbfgs" package. Hans Werner Borchers has told me that this is a good implementation of L-BFGS. Best, Ravi From: R-devel on behalf of Spencer Graves Sent:

Re: [Rd] optim(…, method=‘L-BFGS-B’) stops with an error message while violating the lower bound

Have you tried "optimx" package that John Nash and I wrote? The main purpose is to be able to readily compare multiple optimizers on a particular class of problems and see which one seems to do the best. It doesn't include nloptr, but most other optimizers are there. Ravi

Re: [Rd] Milestone: 9000 packages on CRAN

Indeed! Ravi From: R-devel on behalf of Spencer Graves Sent: Monday, August 22, 2016 8:59 AM To: r-devel@r-project.org Subject: Re: [Rd] Milestone: 9000 packages on CRAN The entirety

Re: [Rd] Optimization bug when byte compiling with gcc 5.3.0 on windows

all.equal.eigen() should also accommodate complex vectors, right? Ravi From: R-devel on behalf of Martin Maechler Sent: Monday, April 11, 2016 3:08 AM To: William Dunlap Cc: r-devel; Jeroen Ooms

Re: [Rd] typo in R-exts.html section 6.9

You are correct that indefinite means an antiderivative. A definite integral has both limits specified. Technically correct terms are: proper and improper definite integrals (although improper integrals are not synonymous with, but include integrals with an infinite range). Your suggestion

Re: [Rd] Hyper-dual numbers in R

, if there is any interest. Thanks Best, Ravi From: Duncan Murdoch murdoch.dun...@gmail.com Sent: Friday, March 6, 2015 3:31 PM To: Ravi Varadhan; r-devel@r-project.org Subject: Re: [Rd] Hyper-dual numbers in R On 06/03/2015 11:18 AM, Ravi Varadhan wrote: Hi, Has

[Rd] Hyper-dual numbers in R

Hi, Has anyone in R core thought about providing hyper-dual numbers in R? Hyper-dual (HD) numbers, invented by Jeffrey Fike at Stanford, are useful for computing exact second-order derivatives (e.g., Hessian). HD numbers are extensions of complex numbers. They are like quaternions and have 4

Re: [Rd] Re R CMD check checking in development version of R

Hi, I second Bert's comment. I would like to go even farther and suggest that it would be really useful if one of the R gurus (like Simon) wrote a relatively non-technical article in the R journal on this topic of Depends/Imports/Suggested. Someone like myself would benefit immensely. Thank

Re: [Rd] A bug in princomp(), perhaps?

Thank you, Ben. Best, Ravi -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Ben Bolker Sent: Monday, June 02, 2014 8:07 PM To: r-de...@stat.math.ethz.ch Subject: Re: [Rd] A bug in princomp(), perhaps? Ben Bolker bbolker at

Re: [Rd] A bug in princomp(), perhaps?

Perhaps, adding Gavin's work around for a dataframe with missing values might also be useful to the documentation: princomp(na.omit(x)) Thanks, Ravi -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Ben Bolker Sent: Monday, June

Re: [Rd] A bug in princomp(), perhaps?

:15 AM To: Ravi Varadhan Cc: r-devel@r-project.org Subject: Re: [Rd] A bug in princomp(), perhaps? It's only documented to work for princomp.formula; other methods do not know about na.action. -pd On 29 May 2014, at 22:10 , Ravi Varadhan ravi.varad...@jhu.edu wrote: Hi, It may be my

Re: [Rd] A bug in princomp(), perhaps?

different than when a formula is provided, with regards to the NA action? It should be easy enough to remove the rows of `x’ with NAs. This is my main point. Ravi From: Gavin Simpson [mailto:ucfa...@gmail.com] Sent: Friday, May 30, 2014 10:46 AM To: Ravi Varadhan Cc: peter dalgaard; r-devel

[Rd] A bug in princomp(), perhaps?

Hi, It may be my misunderstanding, but it seems that the na.action in the princomp() function for principal components analysis does not work. Please see this simple example: u - matrix(rnorm(75), ncol=1) v - matrix(rnorm(20), ncol=1) x - u%*%t(v) + matrix(rnorm(20*75),ncol=20) x[1,1] - NA

Re: [Rd] What algorithm is R using to calculate mean?

This uses the idea of Kahan's summation, if I am not mistaken. http://en.wikipedia.org/wiki/Kahan_summation_algorithm Ravi From: r-devel-boun...@r-project.org [r-devel-boun...@r-project.org] on behalf of Joshua Ulrich [josh.m.ulr...@gmail.com] Sent:

Re: [Rd] eigen(symmetric=TRUE) for complex matrices

I am also able to reproduce this problem on Windows: library(eiginv) n - 33 # problem does not arise for n = 32 evals - sort(rnorm(n)) system.time(A - eiginv(evals, symmetric=TRUE)) all.equal(evals, sort(eigen(A+0i,,TRUE)$val)) cbind(evals, sort(eigen(A+0i,,TRUE)$val)) Best, Ravi

Re: [Rd] RFC: a safe uniroot() function for future R

Dear Martin, I am not sure I like this idea of expanding the interval. It can have bad consequences. The best feature of uniroot is that it makes the user think about the behavior of the function. Your suggestion is in the spirit of making him unthink (if there is such a word!). Here is a

Re: [Rd] nobs() with glm(family=poisson)

This is getting further away from typical R-devel issues, but let me add another perspective: the `n' in BIC reflects the rate at which the information in the log-likelihood grows. Ravi -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On

Re: [Rd] Regression stars

I think that we should use P .03 (which approximates the probability of 5 consecutive heads) for assigning significance! Ravi -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Frank Harrell Sent: Tuesday, February 12, 2013 9:43

Re: [Rd] Regression stars

They are reaching for the stars. Pardon my jest, but I couldn't resist. Ravi -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Uwe Ligges Sent: Tuesday, February 12, 2013 10:01 AM To: Frank Harrell Cc: r-devel@r-project.org

Re: [Rd] Catching errors from solve() with near-singular matrices

I am not sure that this query is appropriate for r-devel, it seems to be more appropriate for r-help. In any case, you might want to try MASS::ginv instead of solve(), if you expect ill-conditioning. Here is one possible solution: f - function(X) { invX - tryCatch(ginv(X,

Re: [Rd] non-differentiable evaluation points in nlminb(), follow-up of PR#15052

Can you provide a correct/sensible example that illustrates the problem? Your gradient function is wrong. So, how do you expect the algorithms to work? Why is the gradient Inf when |x| 1.e-5? It should be 0. Here the following works fine: require(optimx) f - function (x) { if(is.na(x))

Re: [Rd] The constant part of the log-likelihood in StructTS

Thanks, Tom, for the reply as well as to the reference to Claeskens Hjort. Ravi From: Thomas Lumley [tlum...@uw.edu] Sent: Thursday, May 03, 2012 4:41 PM To: Mark Leeds Cc: Ravi Varadhan; r-devel@r-project.org Subject: Re: [Rd] The constant part

Re: [Rd] The constant part of the log-likelihood in StructTS

model gives lower BIC value. Hadn't though about it before, have to be more careful in future when checking results from different packages etc. Jouni On Tue, May 1, 2012 at 4:51 PM, Ravi Varadhan rvarad...@jhmi.edu wrote: This is not a problem at all. The log likelihood function

Re: [Rd] The constant part of the log-likelihood in StructTS

This is not a problem at all. The log likelihood function is a function of the model parameters and the data, but it is defined up to an additive arbitrary constant, i.e. L(\theta) and L(\theta) + k are completely equivalent, for any k. This does not affect model comparisons or hypothesis

Re: [Rd] Column(row)wise minimum and maximum

hoping that such basic operations would be part of base distribution. Ravi -Original Message- From: oliver [mailto:oli...@first.in-berlin.de] Sent: Thursday, April 19, 2012 2:34 PM To: Ravi Varadhan Cc: r-devel@r-project.org Subject: Re: [Rd] Column(row)wise minimum and maximum On Thu

Re: [Rd] Column(row)wise minimum and maximum

, 2012 3:57 PM To: Ravi Varadhan Cc: oliver; r-devel@r-project.org Subject: Re: [Rd] Column(row)wise minimum and maximum This is why the matrixStats package was created, cf. http://cran.r-project.org/web/packages/matrixStats/ 1. Yes, it would be nice to have them in one of the default packages. 2

[Rd] Conditional means and variances of a multivariate normal distribution

Hi, Let X = (x_1, x_2, ... , x_p) be multivariate normal with mean, mu = (mu_1, ... , mu_p) and covariance = Sigma. I was looking for an R function to compute conditional mean and conditional variance of a given subset of X given another subset of X. While this is trivially easy to do,

Re: [Rd] Conditional means and variances of a multivariate normal distribution

-boun...@r-project.org [r-devel-boun...@r-project.org] on behalf of Ravi Varadhan [rvarad...@jhmi.edu] Sent: Sunday, March 04, 2012 10:32 AM To: r-devel@r-project.org Subject: [Rd] Conditional means and variances of a multivariate normal distribution Hi, Let X = (x_1, x_2, ... , x_p

Re: [Rd] Task views

A couple of (lengthier!) suggestions: topic-area resources or task-oriented resources Ravi From: r-devel-boun...@r-project.org [r-devel-boun...@r-project.org] on behalf of Patrick Burns [pbu...@pburns.seanet.com] Sent: Monday, February 13, 2012 4:32 AM

Re: [Rd] An example of very slow computation

Varadhan Cc: 'cbe...@tajo.ucsd.edu'; r-de...@stat.math.ethz.ch; 'nas...@uottawa.ca' Subject: Re: [Rd] An example of very slow computation On Aug 17, 2011, at 23:24 , Ravi Varadhan wrote: A principled way to solve this system of ODEs is to use the idea of fundamental matrix, which is the same

Re: [Rd] An example of very slow computation

than that in Matrix package. Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu -Original Message

Re: [Rd] An example of very slow computation

(and negative). Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu -Original Message- From: r

Re: [Rd] Improved Nelder-Mead algorithm - a potential replacement for optim's Nelder-Mead

Take a look at the `nmk' function indfoptim package. Ravi. From: r-devel-boun...@r-project.org [r-devel-boun...@r-project.org] on behalf of Kellner [ralf.kell...@wiso.uni-erlangen.de] Sent: Tuesday, July 19, 2011 1:33 PM To: r-devel@r-project.org Subject:

Re: [Rd] Time-machine typo

Indeed, Dirk, but realistic, I might add! BTW, I enjoyed some of the Gaussian Facts. My favorite: It only takes Gauss 4 minutes to sing Aleph-Null Bottles of Beer on the Wall. Best, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor

Re: [Rd] Curry: proposed new functional programming, er, function.

) # but this doesn't work rm(a) adaptIntegrate(function(x, argA=a) f(x, a=argA), lower=0, upper=2, a=0.2) # Use of Curry adaptIntegrate(Curry(f, a=0.2), lower=0, upper=2) Best, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, Division

Re: [Rd] Curry: proposed new functional programming, er, function.

Thanks, Hadley. This (i.e., different ways to prepare curry) is quite instructive to me. Best, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph

Re: [Rd] Suggested change to integrate.Rd (was: Re: 0.5 != integrate(dnorm, 0, 20000) = 0)

is any good? The simple and best solution is to understand your integrand as best as you can. I realize that this may be viewed as being too pedantic, but unfortunately, it is also the best advice. Best, Ravi. --- Ravi Varadhan, Ph.D. Assistant

Re: [Rd] Competing with one's own work

that can handle linear/nonlinear and equality/inequality constraints. John, thanks for raising an important issue. Thanks Best, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School

Re: [Rd] Competing with one's own work

. --- Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu -Original Message- From: dmba...@gmail.com [mailto:dmba...@gmail.com

Re: [Rd] Competing with one's own work

The decision about whether it belongs in a package or in base R is about who should maintain the code. Ok. I understand it now. Thanks, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology

Re: [Rd] GPL and R Community Policies (Rcpp)

. --- Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org

Re: [Rd] Wierd nlm behaviour in 2.10.1 and 2.12.0 [Sec=Unclassified]

Hi Troy, I think that your problem is poorly scaled. You have variables that vary over several orders of magnitude. This means that any small changes (due to subtle differences between R versions) could cause a big difference in the convergence behavior of the algorithms. So, you are asking for

Re: [Rd] Wierd nlm behaviour in 2.10.1 and 2.12.0 [Sec=Unclassified]

=Rates)$estimate This should work quite robustly under various R versions on different platforms. Ravi. -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Ravi Varadhan Sent: Wednesday, October 13, 2010 9:27 AM To: 'Troy Robertson

Re: [Rd] Wierd nlm behaviour in 2.10.1 and 2.12.0 [Sec=Unclassified]

. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu - Original Message - From: Troy Robertson troy.robert...@aad.gov.au Date: Wednesday

Re: [Rd] No RTFM?

I completely agree with you, John. In my view, there is no need for explicit RTFM or GLOG statements. Best, Ravi. -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of P J JAYNES Sent: Friday, August 20, 2010 4:40 PM To:

Re: [Rd] constrained optimization

Hi Christophe, I have an algorithm for solving nonlinearly constrained optimization. It is a combination of an interior point (for inequalities) algorithm with an augmented Lagrangian (for equalities). It is coded entirely in R, and hence is a bit slow, but it seems to do the job quite robustly

Re: [Rd] constrOptim( ): conflict between help page and code

the old and new versions of `constrOptim'. Best, Ravi. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad

Re: [Rd] constrOptim( ): conflict between help page and code

Nolan, You are correct that there is inconsistency. The feasible region should be ui %*% theta - ci 0, so that log(ui %*% theta - ci) is defined. There is a more serious problem in termination criterion for iterations: if (is.finite(r) is.finite(r.old) abs(r - r.old)/(outer.eps +

Re: [Rd] constrOptim( ): conflict between help page and code

be desirable if Tom Lumley can commit these changes to constrOptim. In the meanwhile, I can send the function with these upgrades to anyone who is interested. Best, Ravi. -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Ravi Varadhan

Re: [Rd] constrOptim( ): conflict between help page and code

: if (obj obj.old * sign(mu)) break Ravi. -Original Message- From: Ravi Varadhan [mailto:rvarad...@jhmi.edu] Sent: Thursday, June 17, 2010 10:55 AM To: 'Ravi Varadhan'; 'Duncan Murdoch'; 'John Nolan' Cc: 'r-devel@r-project.org' Subject: RE: [Rd] constrOptim( ): conflict between help page

[Rd] Documentation of biplot for princomp

. -- Ravi Varadhan, Ph.D. Assistant Professor, Center on Aging and Health, Johns Hopkins University School of Medicine (410)502-2619 rvarad...@jhmi.edu http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.h tml [[alternative

Re: [Rd] Improved Nelder-Mead algorithm - a potential replacement for optim's Nelder-Mead

will get lost in a sea of 2200+ packages. Best regards, Ravi. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad

[Rd] Improved Nelder-Mead algorithm - a potential replacement for optim's Nelder-Mead

). Best, Ravi. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu ---BeginMessage--- Dear Ravi

Re: [Rd] lower.tail option in pnorm

- pnorm(Xb))) ans2 - apply(cbind(Xb, Resp), 1, function(x) pnorm(x[1], lower.tail=x[2], log.p=TRUE)) all.equal(ans1, as.numeric(ans2)) Ravi. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine

Re: [Rd] bug in '...' of constrOptim (PR#14071)

' argument. So, apart from `control' and `hessian' you cannot pass any other argument to optim. Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine

Re: [Rd] bug in '...' of constrOptim (PR#14071)

an extension of constrOptim that can use numerical gradients, and can also handle nonlinear constraints. Hope this helps, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division

Re: [Rd] Buglet in optim() SANN

. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: rvarad...@jhmi.edu Webpage: http://www.jhsph.edu

Re: [Rd] Inaccurate complex arithmetic of R (Matlab is accurate)

. Thanks very much to all, especially to, Martin Maechler. Best, Ravi. -Original Message- From: Martin Maechler [mailto:maech...@stat.math.ethz.ch] Sent: Wednesday, August 05, 2009 3:35 AM To: John Nolan Cc: Ravi Varadhan; hwborch...@googlemail.com; r-de...@stat.math.ethz.ch Subject: Re

Re: [Rd] Inaccurate complex arithmetic of R (Matlab is accurate)

. Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu - Original Message - From: John Nolan jpno...@american.edu Date

Re: [Rd] Inaccurate complex arithmetic of R (Matlab is accurate)

. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: rvarad...@jhmi.edu Webpage: http://www.jhsph.edu/agingandhealth

Re: [Rd] Inaccurate complex arithmetic of R (Matlab is accurate)

-step derivative could not be implemented in R. Thanks, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University

[Rd] Inaccurate complex arithmetic of R (Matlab is accurate)

if there is a way to obtain accurate small imaginary part for complex arithmetic. I am using Windows XP operating system. Thanks for taking a look at this. Best regards, Ravi. Ravi Varadhan, Ph.D. Assistant Professor, Division

Re: [Rd] Adding a Matrix Exponentiation Operator

this be of interest to the R group? Best, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619