Re: [ESS] Have M-x R point at the most recent version of R

Hi Johannes, I set the R version using something like this in my init file: (setq inferior-ess-r-program "C:/Program Files/R/R-4.3.1/bin/x64/Rterm.exe") But I'm still using ESS 18.10.2 (in Vincent Goulet's Emacs distribution) so that line might not be the right way to do it in the version you're

Re: [ESS] Difficulty installing ESS from MELPA

> From: Woody Setzer > > Try changing your repository from Melpa to Melpa-stable: > > (add-to-list 'package-archives > '("melpa-stable" . "https://stable.melpa.org/packages/;) t) > > I had a similar problem after a recent update of ESS in MELPA, but > after I deleted ESS and

Re: [ESS] spurious (list ....)

> From: "Richard M. Heiberger" > > ess sends spurious commands to the *R* buffer, for example > > > (list "base" '(("..." . "") ("deparse.level" . "1")) '("..." > > "deparse.level" "recursive" "make.row.names" "stringsAsFactors" > > "factor.exclude" "use.names" "fill" "idcol" "size" "z"

[ESS] Difficulty installing ESS from MELPA

ng the error messages "Symbol’s function definition is void: ess-local-process-name" and "Error running timer ‘ess--idle-timer-function’: (void-function ess-local-process-name)"? Thanks, Mark Seeto - __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help

[ESS] Latest Emacs distributions out!

> Date: Thu, 17 Sep 2020 16:34:54 -0400 > From: Vincent Goulet > To: ess-help@r-project.org > Subject: [ESS] Latest Emacs distributions out! > Message-ID: <0281e8bb-019e-413d-9d10-43ad71cb4...@me.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > With some delay, I'm glad to

[R] rms package: residual df for penalised ols

Dear R-help, In the rms package, when using the ols function with a penalty, the df.residual appears to always be n-1 (with n being the sample size). That seems strange to me, but I don't have much knowledge in this area. Here's an example: library(rms) set.seed(1) n <- 50 d <- data.frame(x1

Re: [R] glmnet: converting coefficients back to original scale

Thanks for your reply Mehmet. I've found that the problem was that I didn't scale the lambda value. My original example did not follow the instruction not to give a single lambda value, but that in itself wasn't the problem. Example shown below. library(glmnet) library(MASS) set.seed(1) n - 20

[R] glmnet: converting coefficients back to original scale

Dear R-help, I'm having trouble understanding how glmnet converts its coefficient estimates back to the original scale. Here's an example with ridge regression: library(glmnet) set.seed(1) n - 20 # sample size d -

[R] rms package: error with Glm

can give. Mark Seeto # library(rms) set.seed(1) n - 100 # sample size beta0 - 3.7 beta1 - 1.5 beta2 - 0.9 beta3 - 0.5 rate.x1 - 2 mean.x2 - 1 sd.x2 - 2 nu - 1.3 d - data.frame(x1 = rexp(n, rate = rate.x1

[R] oblique.scores argument for fa function in psych package

, ] ### Have I misunderstood something? Thanks, Mark Seeto __ 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

Re: [R] Gls function in rms package

(gls.intercept, gls.rcs4) Thanks, Mark Seeto National Acoustic Laboratories, Australia Appears to be a definite bug, probably caused by having more than one correlation parameter. I hope to have this fixed within 3 days. Frank Mark Seeto wrote Dear R-help, I don't understand why Gls gives

[R] Gls function in rms package

with a spline using rcs. I'm using version 3-5.0 of rms in R 2.15.0. Thanks for any help you can give. Mark Seeto __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R

[R] Warnings when plotting after x11() in R 2.14.2

plots. I'm using RGui on Windows 7. It did not happen with R 2.13.1. It's not a major problem, because the plots still appear to be produced correctly, but if anyone can tell me how to fix it, I'd appreciate it. Thanks, Mark Seeto __ R-help@r-project.org

[R] Column name containing -

x a.-5 y 1 00 0 2 11 1 Why does the a.-5 column name change to a..5 when another column is added? Thanks, Mark Seeto __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

Re: [R] a question on plotting nonlinear regression

garciap wrote: Hi to all the people, I'm having a trouble when trying to plot a quadratic function. I have the code: regression-nls(Survival~beta1+beta2*PI+beta3*PI^2, data=cubs, start=list(beta1 = 1, beta2 = 1, beta3 = 1)) plot(Survival~PI,data=cubs, ylab=Survival, xlab=PI)

Re: [R] a question on plotting nonlinear regression

Mark Seeto wrote: garciap wrote: Hi to all the people, I'm having a trouble when trying to plot a quadratic function. I have the code: regression-nls(Survival~beta1+beta2*PI+beta3*PI^2, data=cubs, start=list(beta1 = 1, beta2 = 1, beta3 = 1)) plot(Survival~PI,data=cubs, ylab

[R] Replying on Nabble

list. If I reply to the list, there's an option to email the post to someone, but I don't know the person's email address. Thanks, Mark Seeto -- View this message in context: http://r.789695.n4.nabble.com/Replying-on-Nabble-tp3691214p3691214.html Sent from the R help mailing list archive

Re: [R] R graphs differ from exported one

you forget to run dev.off(), as in that example. But we don't have the   commented, minimal, self-contained, reproducible code. the posting guide and the footer of every R message asks for. On Sun, 12 Jun 2011, Mark Seeto wrote: Raptorista wrote: Now, the graph that appears is very

Re: [R] R graphs differ from exported one

Raptorista wrote: Now, the graph that appears is very nice: indeed it has a title, two axes with their labels and all the rest; but when I give commands postscript(file=plot.eps, onefile=FALSE) qqnorm (col) to save the graph to a file plot.eps to include it in a TeX, the file created

Re: [R] predict with model (rms package)

Thanks for your reply, Frank. I've noticed that the x.knots object doesn't actually have to be the vector of knots. Just having x.knots - 0 or even x.knots - a will allow predict to work. Mark Seeto Frank Harrell wrote: This is a consequence of predict.ols calling predictrms which relies

[R] predict with model (rms package)

as a vector like c(-1, 0, 1) (i.e. not using quantile). Is this the intended behaviour? The requirement that x.knots be in the workspace seems strange, given that the knot locations are stored in ols1$Design$parms. Thanks for any help you can give. Mark Seeto National Acoustic Laboratories, Australia

[R] Model formula for ols function (rms package)

Is there a way to do these things without first creating new variables in the data frame? Thanks, Mark Seeto National Acoustic Laboratories __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] Model formula for ols function (rms package)

. Frank Mark Seeto wrote: Dear R help, I'm having some trouble with model formulas for the ols function in the rms package. I want to have two variables represented as restricted cubic splines, and also include an interaction as a product of linear terms, but I get an error message. library(rms) d

[R] rms: getting adjusted R^2 from ols object

there. Thanks, Mark Seeto __ 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] Help with Amelia

Amit Patel-7 wrote: Hi I have used the amelia command from the Amelia R package. this gives me a number of imputed datasets. This may be a silly question, but i am not a statistician, but I am not sure how to combine these results to obtain the imputed dataset to usse for further

Re: [R] Urgent Help with R calculation correlation coefficient

Try excluding the first column. cor(gse20437[, 2:4]) chintan85 wrote: Tab delimited file looks like this Id v1 v2v3 df 56 9045 gh 87 9878 ty 897867 I used this code [code] gse20437 - read.csv(C:/Users//Desktop/data/GSE20437_matrix.txt,header =

[R] When to use bootstrap confidence intervals?

, the ordinary t interval appears to be better than the bootstrap BCA interval. I would really appreciate any recommendations anyone can give on when bootstrap confidence intervals should be used. Thanks, Mark -- Mark Seeto National Acoustic Laboratories, Australian Hearing

Re: [R] Multiple imputation, especially in rms/Hmisc packages

(ols.imp2) anova(fmi) unexpectedly give the same result in the ERROR line. I would be most grateful if anyone could explain this to me. I need to add some more warnings. For many of the calculations, the last imputation is used. Frank Thanks, Mark -- Mark Seeto Statistician National Acoustic

[R] Multiple imputation, especially in rms/Hmisc packages

. Thanks, Mark -- Mark Seeto Statistician National Acoustic Laboratories http://www.nal.gov.au/ A Division of Australian Hearing __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R

Re: [R] Multiple imputation, especially in rms/Hmisc packages

Thank you for your reply Frank. I am not familiar with the contrast test, but I'll see what I can find out about it. Mark Frank Harrell wrote: On Mon, 9 Aug 2010, Mark Seeto wrote: Hello, I have a general question about combining imputations as well as a question specific to the rms

[R] Model validation and penalization with rms package

of 9 gives a corrected slope of about 1.17 (corrected slope of 1 is achieved with a penalty of about 1 or 2). Thanks for any help/advice you can give. Mark -- Mark Seeto Statistician National Acoustic Laboratories A Division of Australian Hearing __ R

[R] Specifying formula inside a function

can give. Regards, Mark -- Mark Seeto Statistician National Acoustic Laboratories A Division of Australian Hearing __ 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

Re: [R] Specifying formula inside a function

Bill and Erik, thank you very much for your help. In addition to solving my problem, both solutions contain other good things I didn't know about. Regards, Mark Seeto On Thu, Jun 10, 2010 at 2:44 PM, Erik Iverson er...@ccbr.umn.edu wrote: Hello, How does one specify a formula to lm inside

Re: [R] ols function in rms package

On 06/06/2010 10:49 PM, Mark Seeto wrote: Hello, I have a couple of questions about the ols function in Frank Harrell's rms package. Is there any way to specify variables by their column number in the data frame rather than by the variable name? For example, library(rms) x1- rnorm

Re: [R] ols function in rms package

On 06/08/2010 05:29 AM, Mark Seeto wrote: On 06/06/2010 10:49 PM, Mark Seeto wrote: Hello, I have a couple of questions about the ols function in Frank Harrell's rms package. Is there any way to specify variables by their column number in the data frame rather than by the variable

[R] ols function in rms package

) : '.' in formula and no 'data' argument Thanks for any help you can give. Regards, Mark -- Mark Seeto Statistician National Acoustic Laboratories http://www.nal.gov.au/ A Division of Australian Hearing 126 Greville Street Chatswood NSW 2067 Australia P +61 2 9412 6800 F +61 2 9411 8273

[R] Overfitting/Calibration plots (Statistics question)

Harrell says should happen. I am either misunderstanding something or making a mistake in the code (I'm almost 100% certain I'm not mixing up the axes). I would be most appreciative if anyone could explain where I'm going wrong. Thanks for any help you can provide. Mark Seeto

Re: [R] Overfitting/Calibration plots (Statistics question)

Thank you very much for your help, Prof. Harrell. I was making the bad mistake of judging the appearance of the calibration plots without actually calculating the regression line. I was misjudging slopes of 0.8 or 0.9 as being slopes greater than 1. Kind regards, Mark Seeto Mark, Try

[R] Double inequality with plotmath

Hello, I'm fairly new to R and I can't work out how to produce a double inequality like (LaTeX) $0 \leq x \leq 1$ in the legend of a graph. If I try legend(50, 0.1, legend = c(expression(0 = x = 1), c(2 = x = 3)), pch = c(1,1), col = c(2, 3)) then I get an error message unexpected '=' in

Re: [R] Double inequality with plotmath

Thank you very much Duncan. I see I also had the mistake of a c instead of expression in my question. Mark On Fri, Jan 22, 2010 at 7:59 AM, Duncan Murdoch murd...@stats.uwo.ca wrote: On 21/01/2010 3:50 PM, Mark Seeto wrote: Hello, I'm fairly new to R and I can't work out how to produce