Re: [R] comparing random forests and classification trees

E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] Design Package - Penalized Logistic Reg. - Query

-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 E Harrell Jr Professor and Chair School of Medicine

Re: [R] Slightly OT: Does anyone use latex2rtf with sweave output ?

remarkably well. Our web page has the pdf and resulting .doc file for an advanced example containing complex tables containing micrographics in some of the table cells. Simpler html conversions are also worth trying. Frank -- Frank E Harrell Jr Professor and ChairmanSchool

Re: [R] Type-I v/s Type-III Sum-Of-Squares in ANOVA

reason for using Type-I as default rather than Type-III. (Given a choice, believe R!) A reference (stats book, URL...) would be helpful... Ravi -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University

Re: [R] ANOVA Types and Regression models: the same?

, there should be at least one value of # x1 between any two knots and beyond the outer knots. -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ R-help@r

Re: [R] ANOVA Types and Regression models: the same?

Sorry there were 2 typos in my note: John Fox's posting provided a lot of information. Briefly, the Types refer to whether effects are adjusted for all other effects in the model (Types II, III, IV) or no (Type I or sequential tests only adjust for no - not EARLIER terms in the model).

Re: [R] Nonparametric generalization of ANOVA

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 E Harrell Jr Professor and ChairmanSchool of Medicine

Re: [R] About the interaction A:B

-1.69261273 10.68151168 -4.25819000 -2.60424217 -4.67668454 -0.03586951 AAc:BBd NA -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ R-help@r

Re: [R] Nonparametric generalization of ANOVA

as BlueSky. David W has got it right when he replied to ManInMoon. Shall we stop this thread now, and follow his lead ? I would have picked ManOnMoon myself but maybe that one was taken. Its rather difficult to be on a moon, let alone inside it. Matthew -- Frank E Harrell Jr Professor

Re: [R] Robust SE for lrm object

is obtain in the rms and Design packages by using the robcov function on a fit object. You can also use the bootstrap with bootcov. Frank -- David Winsemius, MD West Hartford, CT __ -- Frank E Harrell Jr Professor and ChairmanSchool

Re: [R] Cox Calibration regression test double graphs

questions. B) Calibration plots are very easy for either logistic regression or Cox models when using the calibrate function in either Harrell's rms or Design packages. (Not sure about how well they play with survfit objects, but you ought to be able to apply the same methods.) -- Frank E Harrell

Re: [R] logistic model diagnostics residuals.lrm {design}, residuals()

-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 E Harrell Jr Professor and ChairmanSchool of Medicine

Re: [R] How good is R at making publication quality tables?

for the perfect gift? Give the gift of Flickr! [[alternative HTML version deleted]] -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ R-help@r

Re: [R] summary.formula and continuous variables

on the code should get the master code from our subversion repository. Frank -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing

Re: [R] Find a rectangle of maximal area

-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University

Re: [R] ordinal regression

E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] I have a question on nomograms.

modeling used to produce a reliable model that is then displayed in a nomogram. The nomogram is the easy part; it is just a graphical display of a model. It is not the model itself. Frank -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department

Re: [R] I have a question on nomograms.

software (and I doubt it would work well in many cases). Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 25-Mar-10 -- Frank E Harrell Jr Professor and ChairmanSchool

Re: [R] I have a question on nomograms.

Gabor Grothendieck wrote: On Thu, Mar 25, 2010 at 10:43 PM, Frank E Harrell Jr f.harr...@vanderbilt.edu wrote: (Ted Harding) wrote: http://www.nomogram.org They call this sort of interface nomogram too, and you can have a go at the one they offer for bladder cancer. This is not a graphical

Re: [R] how to measure accuracy of regression tree?

commented, minimal, self-contained, reproducible code. -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https

Re: [R] Paik, et al., NEJM, 2004, Fig. 4, rate of event at 10 years as a function of covariate

(covariate,4) + sex + ..., x=TRUE, y=TRUE) # restricted cubic spline with 4 knots plot(Predict(f, covariate, sex, time=10)) # separate curves for male and female; omit sex to make one curve; add age=50 to predict for a 50 year old -- Frank E Harrell Jr Professor and ChairmanSchool

Re: [R] Problem comparing hazard ratios

of the likelihood ratio chi-square statistics of the competing biomarkers. Frank -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list

Re: [R] Problem comparing hazard ratios

-boun...@r-project.org] On Behalf Of Frank E Harrell Jr Sent: Tuesday, March 30, 2010 3:57 PM To: Michal Figurski Cc: r-help@r-project.org Subject: Re: [R] Problem comparing hazard ratios Michal Figurski wrote: Dear R-Helpers, I am a novice in survival analysis. I have the following code: for (i in 3

Re: [R] Problem comparing hazard ratios

, TRUE) adjust - model.matrix(~ rcs(age,3)*sex) candidates - matrix(rnorm(n*50), ncol=50, dimnames=list(NULL, c(letters,LETTERS)[1:50])) S - Surv(runif(n)) w - bootrankcph(adjust, candidates, S, B=100) w$stats plot(w) Frank E Harrell Jr wrote: Ravi Varadhan wrote: Frank

Re: [R] fitness of regression tree: how to measure???

and that the form of the tree will not replicate in future datasets. Frank -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org

Re: [R] sample size 20K? Was: fitness of regression tree: how to measure???

-project.org] On Behalf Of Frank E Harrell Jr Sent: Thursday, April 01, 2010 5:02 AM To: vibha patel Cc: r-help@r-project.org Subject: Re: [R] fitness of regression tree: how to measure??? vibha patel wrote: Hello, I'm using rpart function for creating regression trees. now how to measure the fitness

Re: [R] SAS and R on multiple operating systems

) dev.off() Also I have seen 5,000 page listings in SAS. -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics

Re: [R] glmpath in R

-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ R

Re: [R] C-index and Cox model

C-index statistic to measure the predictive power, is it a time-dependent value (i.e. do I need to calculate it for each time period?) or we can calculate it as a single value for the whole model ignoring the time? Thank you so much. Bessy install.packages('Hmisc') ?rcorr.cens -- Frank E

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

__ 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. -- Frank E Harrell Jr Professor and ChairmanSchool

Re: [R] How to get the penalty matrix for natural cubic spline?

! Lee In usual practice the natural cubic spline does not use penalization. Frank -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org

Re: [R] Brier's score for bootstrap sample (coxph)

but will be noisy. You did not point to a function or package that claims to be able to compute a Brier score with censored data. Frank -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University

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