Re: [R] How to plot linear, cubic and quadratic fitting curve in a figure?

-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/How-to-plot-linear-cubic-and-quadratic-fitting-curve

Re: [R] Odds Ratios in rms package

-help@ 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. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View

Re: [R] Odds Ratios in rms package

://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. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r

Re: [R] rms package-superposition prediction curve of ols and data points

. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/rms-package-superposition-prediction-curve-of-ols-and-data-points-tp4634503p4634566.html Sent from the R help mailing list archive at Nabble.com

Re: [R] Simple mean trajectory (ordinal variable)

guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Simple-mean-trajectory-ordinal-variable

Re: [R] Hosmer-Lemeshow test for Cox model

, probs=seq(0, 1, 1/g)), include.lowest=TRUE) obs = xtabs(cbind(1 - y, y) ~ cutyhat) expect = xtabs(cbind(1 - yhat, yhat) ~ cutyhat) chisq = sum((obs - expect)^2/expect) P = 1 - pchisq(chisq, g - 2) return(list(chisq=chisq,p.value=P)) } - Frank Harrell Department

Re: [R] Plotting the probability curve from a logit model with 10 predictors

guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Plotting-the-probability-curve-from-a-logit

Re: [R] validate.lrm - confidence interval for boostrap-corrected AUC ?

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. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context

Re: [R] LaTeX consistent publication graphics from R and Comparison of GLE and R

/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/LaTeX-consistent-publication-graphics-from-R-and-Comparison-of-GLE-and-R

[R] R Package for Longitudinal Binary Response Data?

Markov version of this. I believe this is called alternating logistic regression. Does anyone know of an R package that handles continuous time, i.e., measurement times can be at any follow-up time? I don't need random effects in the model. Thanks Frank - Frank Harrell Department

Re: [R] R Package for Longitudinal Binary Response Data?

I didn't get any responses to this question so just trying one more time ... -Frank Frank Harrell wrote The bild package appears to be an excellent package for serial binary responses. But it is for discrete time. I would like to specify a smooth function of time for the odds ratio

Re: [R] rms plot.Predict question: swapping x- and y- axis for categorical predictors

of the effects at once. Thank you so much in advance for your replies! My apologies if this question has been answered already; I've tried searching to no avail. Best, Stephanie (Stanford University, Department of Linguistics) - Frank Harrell Department of Biostatistics, Vanderbilt

Re: [R] Package Design

://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Package-Design-tp4646994p4647052.html Sent from the R

Re: [R] rms plot.Predict question: swapping x- and y- axis for categorical predictors

Stephanie, I just realized this is already implemented. For your problem use p - Predict(f,x2); plot(p, ~ x2, nlines=TRUE) Frank Frank Harrell wrote Stephanie, I'm working on an option for the plot method for Predict that will allow you to do this. Note that this approach will not result

Re: [R] Longitudinal categorical response data

-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Longitudinal-categorical-response-data-tp3403619p4647190.html Sent

Re: [R] Is there any way of weighting individual data points in a logistic regression

-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Is-there-any-way-of-weighting-individual-data-points

Re: [R] rms plot.Predict question: swapping x- and y- axis for categorical predictors

, Frank Harrell [via R] ml-node+s789695n4647187h22@.nabble wrote: Stephanie, I just realized this is already implemented. For your problem use p - Predict(f,x2); plot(p, ~ x2, nlines=TRUE) Frank Frank Harrell wrote Stephanie, I'm working on an option for the plot method for Predict

Re: [R] bootstrapping quantile regression

read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/bootstrapping-quantile

Re: [R] How to nicely display R code with the LaTeX package 'listings'?

commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/How-to-nicely-display-R-code-with-the-LaTeX-package-listings-tp4648110p4648149.html Sent from the R help

Re: [R] Survplot, Y-axis in percent

/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Survplot-Y-axis-in-percent-tp4648572p4648697.html Sent from the R help

Re: [R] how to do an external validation with R

with this or suggest an R package ? I would be very very grateful for help with this task ! - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/how-to-do-an-external-validation-with-R-tp4667404p4667426.html Sent from the R help

Re: [R] Weighted regression in rms/Hmisc

-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Weighted-regression-in-rms-Hmisc-tp4667437p4667446.html Sent

Re: [R] rmean in survfit

). Is there an easy way to do this? - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/rmean-in-survfit-tp4667668p4667708.html Sent from the R help mailing list archive at Nabble.com

Re: [R] stepwise discriminant analysis using wilks lambda

Unless you have detailed simulations to back up the performance of this method I would avoid it. It violates several statistical principles. Frank Hari wrote Hello R geeks, Waiting for an reply. Thanks, Hari - Frank Harrell Department of Biostatistics, Vanderbilt University

Re: [R] Nomogram (rms) for model with shrunk coefficients

You are using an informal shrinkage method. It is much better to use penalized maximum likelihood estimation, built in to lrm. If you really want to go the informal route, compute the linear predictor from your final estimates and use ols( ) to predict that from the component variables

Re: [R] Quantile Regression/(package (quantreg))

Mike, Do something like: require(rms) dd - datadist(mydatarame); options(datadist='dd') f - Rq(y ~ rcs(age,4)*sex, tau=.5) # use rq function in quantreg summary(f) # inter-quartile-range differences in medians of y (b/c tau=.5) plot(Predict(f, age, sex)) # show age effect on median as a

[R] Appropriate forum for announcing R package updates

I have been confused about the appropriate e-mail address to use to make announcements to r-help for major package update. In the past I've submitted to r-packa...@lists.r-project.org without seeing the announcement appear on r-help. Thanks for any guidance. Frank -- Frank E Harrell Jr

Re: [R] Appropriate forum for announcing R package updates

Thank you Marc Frank Marc Schwartz-3 wrote On Jul 10, 2013, at 1:29 PM, Frank Harrell lt; f.harrell@ gt; wrote: I have been confused about the appropriate e-mail address to use to make announcements to r-help for major package update. In the past I've submitted to R-packages@.r

[R] [R-pkgs] Major Update to rms package

The rms (Regression Modeling Strategies) package has undergone a massive update. The entire list of updates is at the bottom of this note. CRAN has the update for linux and will soon have it for Windows and Mac - check http://cran.r-project.org/web/packages/rms/ for availability. This rms

[R] Can't figure out why short figure won't work

I can't get the points and a and b to render correctly (they are squeezed into the axis) unless I make the height of the figure waste a lot of space. I'd appreciate any ideas. The code is below. Thanks! png('/tmp/z.png', width=480, height=100) par(mar=c(3,.5,1,.5)) plot.new() par(usr=c(-10,

[R] Jul 26, 2013; 12:34am

Thanks Rich and Jim and apologies for omitting the line x - c(285, 43.75, 94, 150, 214, 375, 270, 350, 41.5, 210, 30, 37.6, 281, 101, 210) But the fundamental problem remains that vertical spacing is not correct unless I waste a lot of image space at the top. Frank -- Frank E Harrell Jr

Re: [R] Can't figure out why short figure won't work

[Sorry I can't quote past messages as I get mail on Nabble and have been told I can't reply through Nabble]. Thanks Kennel for recommended a narrowing range for usr y-limits. That does help quite a bit. But I found a disappointing aspect of the graphics system: When you change height= on

[R] Does a general latex table-making function exist?

Our Hmisc package summary.formula function and its latex methods can make some fairly advanced tables. But the tables have to be regular. For example, all rows of the tables are based on the same data frame. I'm thinking that what is needed is a ggplot2-like set of functions for building a

Re: [R] Does a general latex table-making function exist?

Duncan, I had read your excellent tables package vignette at http://cran.r-project.org/web/packages/tables/vignettes/tables.pdf when it first came out. It is extremely impressive. I'm glad to be reminded to give it another look. Is there a way to make the special symbols n and 1 refer to

Re: [R] rms plot.Predict when type=p

(here on the x-axis) where the labels tell all. The last 2 lines in the code uses superpositioning for group but the col argument affects the color of confidence bands; I didn't look into that further. Frank Harrell -- require(rms) n = 30 group = factor(sample(c('a','b','c'), n, TRUE

Re: [R] Hire person to convert R code to SAS

at this, or could point me to someone who would, it would be very much appreciated. Thanks in advance! -will - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Hire-person-to-convert-R-code-to-SAS

Re: [R] stepwise in svyglm???

]] __ R-help@ 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. - Frank Harrell Department

Re: [R] stepwise in svyglm???

On Tue, Jul 24, 2012 at 3:00 PM, Frank Harrell lt;f.harrell@gt; wrote: Stepwise variable selection is invalid in this context. Frank Diana Marcela Martinez Ruiz wrote Hello, I want to know how to perform stepwise elimination of variables to svyglm thanks [[alternative HTML

Re: [R] optimal cut off with Epi package

, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/optimal-cut-off-with-Epi-package-tp4637904p4637932.html Sent from the R help mailing list archive at Nabble.com

Re: [R] Hmisc improveProb() and PredictABEL reclassification () function and continuous NRI

-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Hmisc-improveProb-and-PredictABEL-reclassification-function-and-continuous-NRI

Re: [R] sensitivity and specificity in svyglm??

http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/sensitivity-and-specificity-in-svyglm

Re: [R] error: in catg (xi, name=nam, label=lab): LO2 has 2 category levels

. Does anyone know what the problem is and how I can correct it? Kind regards, Tobias - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/error-in-catg-xi-name-nam-label-lab-LO2-has-2-category-levels

Re: [R] Package for comparing sensitivity, specificity, PPV, NPV, and accuracy?

commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Package-for-comparing-sensitivity-specificity-PPV-NPV-and-accuracy-tp4643024p4643046.html Sent from the R

[R] [R-pkgs] New version of Hmisc package on CRAN

Recent changes include the following. Changes in version 3.14-2 (2014-02-26) * latex.default: improved logic using new function in Misc: latexBuild * latex.default: fixed bug with ctable=TRUE with no caption by removing default label * latex.default: improved formatting for insert.top

[R] [R-pkgs] rms package updated

Changes are listed below. NOTE: The next release of rms will replace the survfit.formula function with a new function named npsurv (nonparametric survival estimates) so as to not conflict with the survival package. This is a NON-DOWNWARD-COMPATIBLE change. To get Kaplan-Meier estimates in

[R] [R-pkgs] New package on CRAN: greport

The first submission of the new greport package is now on CTAN. This package facilitates graphical reporting of clinical trials an is highly tied to LaTeX, Hmisc, and lattice. It creates hyperlinks and pop-up tooltips in the resulting pdf report. Tables are greatly de-emphasized, but

[R] [R-pkgs] Updates to Hmisc, rms, and greport packages

The Hmisc package has had a number of updates/fixes: Changes in version 3.14-4 (2014-04-13) * rcspline.eval: stop new logic for ignoring outer values when there are many ties when there are also many ties on interior values. Added new logic to use interior unique values of x when the

Re: [R] SAS VS R - What type of analysis is better?

I can't think of an example where R does not work better than SAS except for a few cases of mixed effects regression models and for processing enormous datasets when the R user does not want to learn about the latest R tools for large datasets. I quit using SAS in 1991 (in favor of S-Plus and

[R] regex challenge

I would like to be able to use gsub or gsubfn to process a formula and to translate the variables but to ignore expressions in the formula. Supposing that the R formula has already been transformed into a character string and that the transformation is to convert variable names to upper case

Re: [R] regex challenge

I really appreciate the excellent ideas from Bill Dunlap and Greg Snow. Both suggestions almost work perfectly. Greg's recognizes expressions such as sex=='female' but not ones such as age 21, age 21, a - b 0, and possibly other legal R expressions. Bill's idea is similar to what Duncan

Re: [R] regex challenge

-Original Message- From: [hidden email] [mailto:[hidden email]] On Behalf Of William Dunlap Sent: Thursday, August 15, 2013 6:03 PM To: Frank Harrell; RHELP Subject: Re: [R] regex challenge Try this one ff - function (expr) { if (is.call(expr) is.name(expr[[1

Re: [R] regex challenge

) } } else if (is.name(expr)) { expr - as.name(convertName(expr)) } expr } Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: [hidden email] [mailto:[hidden email]] On Behalf Of Frank Harrell Sent: Thursday, August 15, 2013 7:47

Re: [R] regex challenge

Bill I found a workaround: f - ff(formula, lab) f - as.formula(gsub(`, , as.character(deparse(f Thanks for your elegant solution. Frank -- Thanks Bill. The problem is one of the results of convertName might be 'Heading(Age in Years)*age' (this is for the

Re: [R] Regression model for predicting ranks of the dependent variable

require(rms) ?orm# ordinal regression model For a case study see Handouts in http://biostat.mc.vanderbilt.edu/CourseBios330 Since you have lost the original values, one part of the case study will not apply: the use of Mean(). Frank - I have a dataset which has

Re: [R] Interperting results of glmnet and coxph plot, Brier score and Harrel's C-Index - am I doing something wrong ???

__ R-help@ 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. - Frank Harrell Department

Re: [R] missclassification in estimating proportions

This is dichotomania and is an inappropriate use of continuous variables. Use an information-preserving approach such as rank correlation. Also, this is not an R question. Frank --- Assume that I want to compare two methods, say skinfold measurement and BMI, in how they classify

Re: [R] Code Book from SPSS Data

Not certain about .por but this works with ordinary SPSS files: require(Hmisc) dat - spss.get(...) # gets variable labels, etc. contents(dat) html(contents(dat), ...) The last command produces a hyperlinked data dictionary, e.g., for each variable the number of levels is given and you click

Re: [R] R: net reclassification index after Cox survival analysis

, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/R-net-reclassification-index-after-Cox-survival-analysis-tp4648710p4648895.html Sent from the R help mailing list

Re: [R] Jackknife in Logistic Regression

deleted]] __ R-help@ 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. - Frank Harrell

Re: [R] additive interaction for a dichotomous dependent variable (i.e. risk difference)

for additive interaction in R? In the glm package the binomial family and identity link do not seem to go together. Thanks in advance. Best regards, Wouter Johannes - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695

Re: [R] bootstrapped cox regression (rms package)

guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/bootstrapped-cox-regression-rms-package

Re: [R] bootstrapped cox regression (rms package)

the original estimate of Cox beta coefficients in the test (i.e. a new point estimate is not generated for the statistical test) Thanks again, Eric - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com

Re: [R] bootstrapped cox regression (rms package)

that is not clear is the generation of p-values from the distribution of parameter estimates; spss appears to be testing the parameter estimate from the original cox regression, but the method of testing that parameter is not clear. Eric - Frank Harrell Department of Biostatistics

Re: [R] e1071 SVM: Cross-validation error confusion matrix

wrong? Thanks for you help, - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/e1071-SVM-Cross-validation-error-confusion-matrix-tp4651652p4651692.html Sent from the R help mailing list archive

Re: [R] Design library

/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. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com

[R] Score residuals with glm()

the cluster sandwich estimator to account for intra-cluster correlation. Thanks Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Score-residuals-with-glm-tp4652534.html Sent from the R help mailing list archive

Re: [R] rms R code

, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/rms-R-code-tp4653376p4653400.html Sent from the R help mailing list archive at Nabble.com

Re: [R] rms R code

Hi David, I'm always working on a second edition :-) Making more progress now and hope to submit to publisher in April. Frank David Winsemius wrote On Dec 17, 2012, at 7:30 PM, Frank Harrell wrote: In http://biostat.mc.vanderbilt.edu/RmS see the section marked R Code. The zip file

Re: [R] NRI reclassification table improveProb Cox

someone mentioning the possibility, but I can't find the syntax in the R help. Thanks, Peter Godsk - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/NRI-reclassification-table-improveProb-Cox

[R] Regression Modeling Strategies 3-Day Short Course March 2013

*RMS Short Course 2013* Frank E. Harrell, Jr., Ph.D., Professor and Chair Department of Biostatistics, Vanderbilt University School of Medicine *March 4, 5 6, 2013* 8:00am - 4:30pm Student Life Center Board of Trust Room Vanderbilt University Nashville Tennessee USA See

Re: [R] NRI reclassification table improveProb Cox

- not by the reclassification function in the PredictABEL package. Does anyone have a solution? Thanks, Peter Godsk - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/NRI-reclassification-table-improveProb-Cox

Re: [R] Ridge Regression variable selection

I have no idea what that is telling me and where I am supposed to work out which variables have been selected. Someone help me out please! - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Ridge

Re: [R] suggestions about import SAS results to R.

the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/suggestions-about-import-SAS

Re: [R] suggestions about import SAS results to R.

on individual variables. Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/suggestions-about-import-SAS-results-to-R-tp465p4654554.html Sent from the R help mailing list archive at Nabble.com

Re: [R] Preparing dataset for glmnet: factors to dummies

I believe that glmnet scales variables by their standard deviations. This would not be appropriate for categorical predictors. Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Preparing-dataset

Re: [R] Optimal Y=q cutoff after logistic regression

are two good ones. There is a reason that the speedometer in your car doesn't just read slow and fast. Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Optimal-Y-q-cutoff-after-logistic-regression

[R] [R-pkgs] New version of rms package on CRAN

A new version of rms is now available on CRAN for Linux/UNIX. I expect Mac and Windows versions to be available in a day or so. This version works with and requires the newest version of Therneau's survival package. More information is at http://biostat.mc.vanderbilt.edu/Rrms Changes in

Re: [R] Interpreting the example given by Prof Frank Harrell in {Design} validate.cph

. Please following the posting guide, i.e., include a simple self-reproducing script that I can run - one that simulates its own dataset. Please switch to the rms package is this is the one that is being fully supported. See http://biostat.mc.vanderbilt.edu/Rrms. Frank - Frank Harrell Department

Re: [R] Interpreting the example given by Prof Frank Harrell in {Design} validate.cph

as for the first model, before bringing strat into the picture. rms and Design prefer for you to store the predictors as factor()s in the dataset instead of specifying this in the model formula. Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message

Re: [R] Interpreting the example given by Prof Frank Harrell in {Design} validate.cph

to have only two covariates. Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Interpreting-the-example-given-by-Prof-Frank-Harrell-in-Design-validate-cph-tp3316820p3319138.html Sent from the R help mailing

Re: [R] Interpreting the example given by Prof Frank Harrell in {Design} validate.cph

information; large in abs. value ## than model ignoring rx (0.3842 vs. 0.3177) - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Interpreting-the-example-given-by-Prof-Frank-Harrell-in-Design-validate-cph

Re: [R] Interpreting the example given by Prof Frank Harrell in {Design} validate.cph

P.S. I used the latest version of the rms package to run this. The Design package is no longer supported. Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Interpreting-the-example-given-by-Prof-Frank

Re: [R] tansformation of variables in cph from rms package

). It is often the case the the proper origin is not zero. This also impacts the problem you encountered. Besides all that, you can specify limits to predictors to nomogram() in a variety of ways as listed in the help file. Try that. Frank - Frank Harrell Department of Biostatistics, Vanderbilt

Re: [R] Forced inclusion of varaibles in validate command as well as step

health. If you are using Linux I can send the new version by e-mail. Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Forced-inclusion-of-varaibles-in-validate-command-as-well-as-step-tp3324901p3325922.html

Re: [R] what does the S.D. returned by {Hmisc} rcorr.cens measure?

of 0.0462.. Any advice is appreciated. Vikki - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/what-does-the-S-D-returned-by-Hmisc-rcorr-cens-measure-tp3329609p3329899.html Sent from the R help mailing

[R] [R-pkgs] Major update to rms package

A new version of rms is now available on CRAN for Linux and Windows (Mac will probably be available very soon). Largest changes include latex methods for validate.* and adding the capability to force a subset of variables to be included in all backwards stepdown models (single model or

Re: [R] what does the S.D. returned by {Hmisc} rcorr.cens measure?

the algorithm. Frank vikkiyft wrote: Thanks for your reply Prof Harrell!! Could you kindly list some references of the fomula for calculating the SD of Somer's D in this kind of application? Because I couldnt find any.. - Frank Harrell Department of Biostatistics, Vanderbilt University

Re: [R] Multivariate Granger Causality Tests

Beware that causality can only be inferred using information that extends far beyond the data at hand. Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Multivariate-Granger-Causality-Tests

[R] How to enforce location of installation of downloaded packages

/site-library') But sometimes install.packages (with R run as superuser using sudo) will create a directory called x86... under ~/R and put installed packages there. How do I force the system to always use /usr/local/lib/...? Thanks Frank - Frank Harrell Department of Biostatistics

Re: [R] How to enforce location of installation of downloaded packages

that it is not changed by any of the many mechanisms that allow for adding libraries to the search path. Uwe On 09.03.2011 00:53, Frank Harrell wrote: Using R on Linux I want to force downloaded packages to go into /usr/local/lib/R/site-library. I have an .Rprofile file in my home directory

Re: [R] fitting a distribution to a ecdf plot

-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. - Frank Harrell Department of Biostatistics, Vanderbilt University

[R] Bootstrap BCa confidence limits with your own resamples

m - length(bca) bca - bca[c(m-1, m)] } list(np=np, bca=bca) } - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Bootstrap-BCa-confidence-limits-with-your-own-resamples-tp4661045.html Sent from the R

Re: [R] Bootstrap BCa confidence limits with your own resamples

) -- snip -- I hope this helps, John -Original Message- From: r-help-bounces@ [mailto:r-help-bounces@r- project.org] On Behalf Of Frank Harrell Sent: Tuesday, March 12, 2013 11:27 AM To: r-help@ Subject: [R] Bootstrap BCa confidence limits with your own

Re: [R] Export R generated tables and figures to MS Word

deleted]] __ R-help@ 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. - Frank

Re: [R] Accuracy some classifiers

the accuracy, for example, for KNN,neural networks and J48, for each one of 5-fold because when I apply CV to my classifier, I obtain the mean accuracy of 5-fold but each accuracy/error of each fold is not returned. Any help is welcome and grateful. Thanks in advance! Regards!! - Frank

Re: [R] Re-order variables listed in nomogram?

__ R-help@ 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. - Frank Harrell Department of Biostatistics, Vanderbilt

Re: [R] Model Selection based on individual t-values with the largest possible number of variables in regression

, there are thousands of such combinations and R simply refuses to calculate them! (computer crashes) I wonder if you can help me to write the code in R in order to find the model wich include as many variables as it possible with significant t-values? cheers, Oleg - Frank Harrell

[R] Composite Quantile Regression

Does anyone know of R functions for doing composite quantile regression (Hou and Yuan Ann Stat 36:1108, 2008)? The paper's authors do not talk about software in their paper or on their web sites. Thanks Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View

Re: [R] the joy of spreadsheets (off-topic)

What a terrific article. Thanks for sharing! The more we critically examine how research is actually done the more frightened we become. Frank -- Frank E Harrell Jr Professor and Chairman School of Medicine Department of Biostatistics Vanderbilt University

[R] NAMESPACE and imports

, summary.rms, validate)) ERROR: lazy loading failed for package ‘rms’ Any advice appreciated. Frank - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/NAMESPACE-and-imports-tp4664718.html Sent from the R help mailing

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