[R] Mantel-Haenszel relative risk with Greenland-Robins variance estimate

2007-05-08 Thread Frank E Harrell Jr
Does anyone know of an R function for computing the Greenland-Robins variance for Mantel-Haenszel relative risks? Thanks Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] Mantel-Haenszel relative risk with Greenland-Robins variance estimate

2007-05-08 Thread Frank E Harrell Jr
ratification factor other than occupational group. Thanks again Frank > > > > > Frank E Harrell

Re: [R] Follow-up about ordinal logit with mixtures: how about 'continuation ratio' strategy?

2007-05-10 Thread Frank E Harrell Jr
Paul Johnson wrote: > This is a follow up to the message I posted 3 days ago about how to > estimate mixed ordinal logit models. I hope you don't mind that I am > just pasting in the code and comments from an R file for your > feedback. Actual estimates are at the end of the post. . . . Paul,

Re: [R] Read SAS data into R

2007-05-10 Thread Frank E Harrell Jr
ml >> and provide commented, minimal, self-contained, >> reproducible code. >> > > ______________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE d

Re: [R] Read SAS data into R

2007-05-11 Thread Frank E Harrell Jr
at an upcoming release of the Hmisc package has a new Access import function for users who have access to the mdbtools package on their operating system (e.g., linux). -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biost

Re: [R] Follow-up about ordinal logit with mixtures: how about 'continuation ratio' strategy?

2007-05-11 Thread Frank E Harrell Jr
Paul Johnson wrote: > On 5/10/07, Frank E Harrell Jr <[EMAIL PROTECTED]> wrote: >> Paul Johnson wrote: >>> This is a follow up to the message I posted 3 days ago about how to >>> estimate mixed ordinal logit models. I hope you don't mind that I am >>>

Re: [R] OT: Predicted probabilities from ordinal regressions

2007-05-11 Thread Frank E Harrell Jr
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 Department of

Re: [R] Predicted values from a logistic model

2007-05-13 Thread Frank E Harrell Jr
mymodel, list of covariates you care to specify)) Frank Harrell > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > a

Re: [R] Nicely formatted summary table with mean, standard deviation or number and proportion

2007-05-13 Thread Frank E Harrell Jr
acebo | > | |(N=263) |(N=237) | > +---+------+------+ > |age|46.5/49.9/53.2|46.7/50.0/53.4| > +---+--+--+ > |sex : m| 47% (123) | 44% (104) | > +---+--+--+ > > > >

Re: [R] Re : Bootstrap sampling for repeated measures

2007-05-15 Thread Frank E Harrell Jr
sion deleted]] > > > > ------------ > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide

Re: [R] How to analyse simple study: Placebo-controlled (2 groups) repeated measurements (ANOVA, ANCOA???)

2007-05-17 Thread Frank E Harrell Jr
s on t4 it is easy to specify a contrast (after fitting is completed) that tests t4. If time is continuous this contrast would involve predicted values at the 4th time, otherwise testing single parameters. Frank Harrell > > Perhaps somebody can recommend a book or weblink where

Re: [R] clustered standarderrors using design package

2007-05-19 Thread Frank E Harrell Jr
> R-help@stat.math.ethz.ch 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

Re: [R] normality tests

2007-05-25 Thread Frank E Harrell Jr
proach that it's hard to know where to begin. But first of all, why care about normality? Why not use distribution-free methods? You should examine the power of the tests for n=20. You'll probably find it's not good enough to reach a reliable concl

Re: [R] normality tests [Broadcast]

2007-05-25 Thread Frank E Harrell Jr
gt; [mailto:[EMAIL PROTECTED] On Behalf Of Liaw, Andy > Sent: Friday, May 25, 2007 12:04 PM > To: [EMAIL PROTECTED]; Frank E Harrell Jr > Cc: r-help > Subject: Re: [R] normality tests [Broadcast] > > From: [EMAIL PROTECTED] >> On 25/05/07, Frank E Harrell Jr <[EMAIL

Re: [R] normality tests [Broadcast]

2007-05-25 Thread Frank E Harrell Jr
>> [mailto:[EMAIL PROTECTED] On Behalf Of Liaw, Andy >> Sent: Friday, May 25, 2007 12:04 PM >> To: [EMAIL PROTECTED]; Frank E Harrell Jr >> Cc: r-help >> Subject: Re: [R] normality tests [Broadcast] >> >> From: [EMAIL PROTECTED] >> > >> > On 25/05

Re: [R] normality tests [Broadcast]

2007-05-25 Thread Frank E Harrell Jr
in testing for stochastic ordering and not just for a mean. Frank > > > > > Frank E Harrell > Jr

Re: [R] AIC for lrm(Hmisc/Design) model.

2007-05-29 Thread Frank E Harrell Jr
ange AIC to have it on the chi-square scale. For that you can do aic <- function(fit) round(unname(fit$stats['Model L.R.'] - 2*fit$stats['d.f.']),2) f <- lrm( ) aic(f) If unname doesn't exist in S-Plus as it does in R, you can remove that part. -- Frank E

Re: [R] segmentation fault with Hmisc areg.boot()

2006-02-16 Thread Frank E Harrell Jr
Martin Henry H. Stevens wrote: > Hi Folks, > Mac OS 10.4.4 > R 2.2.1(2005-12-20 r36812) > Hmisc 3.0-10 > acepack 1.3-2.2 > > I keep getting a "segmentation fault" when trying to run areg.boot in > the Hmisc package. I include below output from two different attempts. > Thank you in advance for a

Re: [R] Help to find correlation. Oops

2006-02-16 Thread Frank E Harrell Jr
(513) 529-4243 > http://www.cas.muohio.edu/~stevenmh/ > http://www.muohio.edu/ecology/ > http://www.muohio.edu/botany/ > "E Pluribus Unum" > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo

Re: [R] Matrix with p-values with reference to a correlation matrix

2006-02-20 Thread Frank E Harrell Jr
t; > > > Kind regards, > Robin Smit This was answered just a few days ago in r-help. One way is library(Hmisc) rcorr(data matrix) -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University _

Re: [R] How to do a "proc summary" in R?

2006-03-01 Thread Frank E Harrell Jr
ology Department > Sherbooke University > Sherbrooke, Québec > CANADA > > [EMAIL PROTECTED] > [[alternative HTML version deleted]] > > > > > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do

Re: [R] "proc summary" in R?: follow up

2006-03-02 Thread Frank E Harrell Jr
for your help, > > Emilie See the example I posted 2 hours ago, especially how you need to specify FUN. FH > > - Original Message - From: "Frank E Harrell Jr" > <[EMAIL PROTECTED]> > To: "Emilie Berthiaume" <[EMAIL PROTECTED]> &

Re: [R] Compute quantiles with values and correspondent frequencies

2006-03-03 Thread Frank E Harrell Jr
gt;R-help@stat.math.ethz.ch mailing list >>https://stat.ethz.ch/mailman/listinfo/r-help >>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html >> > > Look at wtd.quantile in the Hmisc package. Frank -- Frank E Harrell Jr Professor and Chair

Re: [R] Multiple logistic regression

2006-03-08 Thread Frank E Harrell Jr
> R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > -- Frank E Harrell Jr Professor and Chair School of Med

Re: [R] how to calculate the quantile of the weighted data

2006-03-10 Thread Frank E Harrell Jr
Jing Yang wrote: > Dear R-users, > > Does anyone have an idea of how to calculate the quantile of the weighted > data? > Any suggestion will be appreciated! > > Best,Jing library(Hmisc) ?wtd.quantile -- Frank E Harrell Jr Professor and Chair

Re: [R] Ordered logistic regression in R vs in SAS

2006-03-14 Thread Frank E Harrell Jr
> graduate student > Biology Department > Sherbrooke University > Sherbrooke, Quebec > CANADA > > [EMAIL PROTECTED] > [[alternative HTML version deleted]] > > __ > R-help@stat.math.ethz.ch mailing list >

Re: [R] errorbars with xyplot

2006-03-15 Thread Frank E Harrell Jr
or helping me, maybe others out there will find it usefull too. > > Best > Ronny library(Hmisc) ?xYplot Frank Harrell -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University _

Re: [R] legend in bubble plots made with symbols()

2006-03-18 Thread Frank E Harrell Jr
rgument and the use of the skey function that is generated by xYplot. Frank > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide

Re: [R] How to compare areas under ROC curves calculated with ROC R package

2006-03-20 Thread Frank E Harrell Jr
info/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://w

Re: [R] Simulating survival data

2006-03-20 Thread Frank E Harrell Jr
sured up to 30 days from randomization. > > Thanks for the help. > Peter library(Hmisc) ?spower -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __

Re: [R] ROC optimal threshold

2006-03-31 Thread Frank E Harrell Jr
(signal)} > \] > > I believe that your attempt to minimize false positives while > maximizing true positives amounts to maximizing the proportion of > correct answers. For that you just set $\beta = 0$. Otherwise it > might be best to explicitly state your costs and benefits b

Re: [R] ROC optimal threshold

2006-03-31 Thread Frank E Harrell Jr
mometer plots which give some of the most accurate human perception of a continuous variable. For the first 2 ideas you may have to round probabilities to give just 10 intervals (or use deciles). If you choose cutpoints from the data, there is uncertainty from the cutpoint that may have to be

[R] (no answer)

2006-04-01 Thread Frank E Harrell Jr
I have never taken a statistics class nor read a statistics text, but I am in dire need of help with a trivial data analysis problem for which I need to write a report in two hours. I have spent 10,000 hours of study in my field of expertise (high frequency noise-making plant biology) but I've alw

Re: [R] Boxplot

2006-04-02 Thread Frank E Harrell Jr
y example : > boxplot(serie,range=91) for french boxplot ? > > jean-pierre gerbal > > http://mathazay.free.fr/spip/ library(Hmisc) ?panel.bpplot With library(lattice), bwplot, and panel.bpplot you can show all deciles or any vector of quantiles. -- Frank E Har

Re: [R] F test for clustered data regression ?

2006-04-04 Thread Frank E Harrell Jr
> Benn Once you adjust for clustering using robcov or bootcov, only Wald chi-square tests are available. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University ___

Re: [R] using latex() in R for Unix

2006-04-05 Thread Frank E Harrell Jr
on the file produced by latex() > > > The last bit is easy. It's the print method that does that, so just > don't print. E.g. > > invisible(latex(....)) Or do w <- latex(.., file='...') Frank > -- Frank E Harrell Jr Professor and Chair

Re: [R] long caption titles for tables

2006-04-11 Thread Frank E Harrell Jr
h mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt Unive

Re: [R] variable selection when categorical variables are available

2006-04-11 Thread Frank E Harrell Jr
ates to the mean of all 4 groups (see for example the ols function in the Design package). -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-

Re: [R] dcolumn

2006-04-16 Thread Frank E Harrell Jr
Brian Quinif wrote: > Does anyone out there use dcolumn=TRUE in the latex() function in the > Hmisc library? > > I would like to line up the data in a latex table I'm making using > latex(), but I'm having some issues with this feature. Since there is > no description of it in the help, I thought

Re: [R] logistic regression model with non-integer weights

2006-04-16 Thread Frank E Harrell Jr
e odds ratio depends only > on beta1. > > Cheers, > This makes me think you are trying to go against maximum likelihood to optimize an improper criterion. Forcing a single cutpoint to be chosen seems to be at the heart of your problem. There's nothing wrong

Re: [R] logistic regression model with non-integer weights

2006-04-16 Thread Frank E Harrell Jr
Ramón Casero Cañas wrote: > Frank E Harrell Jr wrote: > >>This makes me think you are trying to go against maximum likelihood to >>optimize an improper criterion. Forcing a single cutpoint to be chosen >>seems to be at the heart of your problem. There's nothing wro

Re: [R] lambda, uncertainty coefficient (& Somers D)

2006-04-18 Thread Frank E Harrell Jr
X may have any number of categories as long as they are ordered. Frank Harrell > > Thanks and regards, > > -Antti Arppe -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University ___

Re: [R] Hmisc + summarize + quantile: Why only quantiles for first variable in data frame?

2006-04-19 Thread Frank E Harrell Jr
s. FH > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > -- Frank E Harrell Jr Profe

Re: [R] 3D pie

2006-04-19 Thread Frank E Harrell Jr
second that. Helping people do things known to have major problems with the approaches can actually hurt others in the long run. 2-D pie charts are terrible. That makes 3-D pie charts terrible to the 3/2 power. Excel has serious errors and is not a good model for reproducible research. -- F

Re: [R] smooth the ecdf plots

2006-04-20 Thread Frank E Harrell Jr
se e.g. library(Hmisc) ?ecdf (look at groups argument) Someday I may rename ecdf in Hmisc to avoid confusion with the builtin ecdf function. Frank > > > [[alternative HTML version deleted]] > > ______________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz

Re: [R] rcorrp.cens

2006-04-21 Thread Frank E Harrell Jr
ind many cases where one model increases C by only 0.02 but it has many more useful (more extreme) predictions. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University ___

Re: [R] Hmisc + summarize + quantile: Why only quantiles for first variable in data frame?

2006-04-21 Thread Frank E Harrell Jr
27;fun'). Frank > >>> Please read the documentation and see the examples. The first >>> argument to summarize is a matrix or vector and if a matrix, FUN must >>> use matrix operations if you want column-by-column results. >>> >

Re: [R] Creat new column based on condition

2006-04-21 Thread Frank E Harrell Jr
== 20, 6, 10 )) > > Duncan Murdoch > >> >> So the O/P looks like this >> >>V1 V2 >>10 4 >>20 6 >>30 10 >>10 4 >>10 4 >>20 6 >> >> Thanks in advance. >> &

Re: [R] regression modeling

2006-04-25 Thread Frank E Harrell Jr
true that the larger the sample size the greater the complexity of the model we can afford to fit, and the better the fit of the model. This is the "AIC" school. The "BIC" school assumes there is an actual model out there waiting for us, of finite dimension, and the co

Re: [R] stepwise regression

2006-04-28 Thread Frank E Harrell Jr
2 X13 X23/SELECTION=STEPWISE; > RUN; > > Any help will be really appreciated. > > Wishes, > > Jinsong Zhao -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University ___

Re: [R] function for linear regression with White std. errors

2006-04-28 Thread Frank E Harrell Jr
> > -thomas > > Thomas Lumley Assoc. Professor, Biostatistics > [EMAIL PROTECTED] University of Washington, Seattle > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/

Re: [R] New-user support package - suggestions?

2006-05-04 Thread Frank E Harrell Jr
for some > more promising projects... > > Just my first thoughts, just go on with your project if you are convinced. > > Best, > Uwe Ligges > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mai

Re: [R] data manipulation docs

2006-05-05 Thread Frank E Harrell Jr
ulation section on the Alzola Harrell document available on CRAN under contributed docs, or a slightly more up to date version at biostat.mc.vanderbilt.edu -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt

Re: [R] R vs SPSS

2004-11-25 Thread Frank E Harrell Jr
d like SAS, SPSS tends to lead users to make to many assumptions (linearity in regression being one of the key ones). -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt

Re: [R] problem with using transace

2004-11-29 Thread Frank E Harrell Jr
quot;) print(rsq) attr(xt, "rsq") <- rsq attr(xt, "omitted") <- omitted invisible(xt) } ______ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.

Re: [R] impute missing values in correlated variables: transcan?

2004-11-30 Thread Frank E Harrell Jr
t that missing data at the high or low end of each variable (each member's ratings) would change its mean. Jon -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __

[R] [R-pkgs] New Hmisc Package Available

2004-12-01 Thread Frank E Harrell Jr
datasets are being imported. Other changes include bug and documentation fixes. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University ___ R-packages mailing list

Re: [R] What is the most useful way to detect nonlinearity in lo

2004-12-05 Thread Frank E Harrell Jr
icant results cause you to reduce an effect to linear, confidence levels and type I errors are no longer preserved. I use tests of linearity mainly to demonstrate that effects are more often nonlinear than linear, given sufficient sample size. I.e., good analysts are needed. I usually leave

Re: [R] Gam() function in R

2004-12-06 Thread Frank E Harrell Jr
g that you use P-values but do not care that the strategy you use (variable selection as opposed to pre-specifying models or just using shrinkage) does not preserve type I error or confidence interval coverage probabilities in subsequent analyses with mgcv. -- Frank E Harrell Jr Professor

Re: [R] cbind() and factors.

2004-12-11 Thread Frank E Harrell Jr
dian(x[,'y1']-x[,'y2']), med.sum =median(x[,'y1']+x[,'y2'])) names(y) <- c('med.diff','med.sum') y } system.time(by(d, llist(sex=d$sex,country=d$country), g)) system.time({ x <- asNumericMatrix(d) a &

Re: [R] how to fit a weighted logistic regression?

2004-12-15 Thread Frank E Harrell Jr
__ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt

Re: [R] MIME decoding in Mozilla Thunderbird

2004-12-15 Thread Frank E Harrell Jr
messages in a day, Thunderbird inefficiently handles all the mime 'attachments', and navigating them all is incredibly slow. I didn't have the decoding problem you mentioned though. -- Frank E Harrell Jr Professor and Chair School of Medicine

Re: [R] AUC for logistic regression [was: (no subject)]

2004-12-15 Thread Frank E Harrell Jr
ndard output in the lrm function in the Design package (the "C Index"). validate.lrm computes the overfitting-corrected C index. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] Advice on parsing formulae

2004-12-16 Thread Frank E Harrell Jr
c!=9], from, to),")",sep="") #change wrapping function to h() h <- function(x,...) deparse(substitute(x)) for(i in (1:pm)) trans[i] <- eval(parse(text=trans[i])) This may indirectly give you an idea, or you might see if the Design package does what you need in ge

Re: [R] SAS or R software

2004-12-17 Thread Frank E Harrell Jr
mation Sciences University of Louisville -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r

Re: [R] SAS or R software

2004-12-18 Thread Frank E Harrell Jr
rding CDISC, the SAS transport format that is now accepted by FDA is deficient because there is no place for certain metadata (e.g., units of measurement, value labels are remote from the datasets, variable names are truncated to 8 characters). The preferred format for CDISC will become

Re: [R] SAS or R software

2004-12-18 Thread Frank E Harrell Jr
fairly certain that it is not applicable or at the least is not enforced in any meaningful way. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University ___

Re: [R] SAS or R software

2004-12-18 Thread Frank E Harrell Jr
Henric Nilsson wrote: Frank E Harrell Jr said the following on 2004-12-18 15:03: That is not clear. Perhaps. And I think this is the issue. From the clients' perspective, not a single FDA document states that you can use other software than SAS. They haven't really thought about the

Re: [R] SAS or R software

2004-12-19 Thread Frank E Harrell Jr
mple http://www.nwpho.org.uk/sadb/Poisson%20CI%20in%20spreadsheets.pdf . . . Also see http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/ExcelProblems -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt

Re: [R] Producing "Editable" Graphs for PowerPoint

2004-12-20 Thread Frank E Harrell Jr
ake Circus Plymouth PL4 8AA tel (01752) 232778 fax (01752) 232780 email [EMAIL PROTECTED] www.plymouth.ac.uk I had hoped that journals engaged in reproducible research by now. -- Frank E Harrell Jr Professor and Chair School of Medicine D

Re: [R] How to display each symbol in a different color using plot with summary.formula.reverse

2004-12-21 Thread Frank E Harrell Jr
the dotchart2 function used by plot.summary.formula.reverse, and the addition of a new argument to it from plot I have found symbols (esp. circle vs. triangle) to be more effective for this purpose so I am not motivated to work on this very soon but would consider it. -Frank -- Frank E Har

Re: [R] GAM: Overfitting

2004-12-21 Thread Frank E Harrell Jr
ck of fit) from 'overfitting'. Overfitting can cause the model fit to appear to be excellent, but there is still a huge problem. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistic

Re: [R] Developing R classes

2004-12-28 Thread Frank E Harrell Jr
xplanation using S and not R. Am I right or I´m looking in the wrong place ? Thanks a lot! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.

[R] Black and white graphics and transparent strip panels with lattice under Sweave

2005-01-02 Thread Frank E Harrell Jr
guage R Thanks, Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help P

Re: [R] Black and white graphics and transparent strip panels with lattice under Sweave

2005-01-02 Thread Frank E Harrell Jr
Deepayan Sarkar wrote: On Sunday 02 January 2005 19:40, Frank E Harrell Jr wrote: What is the most elegant way to specify that strip panels are to have transparent backgrounds and graphs are to be in black and white when lattice is being used with Sweave? I would prefer a global option that stays

Re: [R] different DF in package nlme and lme4

2005-01-03 Thread Frank E Harrell Jr
Douglas Bates wrote: Christoph Buser wrote: Hi all I tried to reproduce an example with lme and used the Orthodont dataset. library(nlme) fm2a.1 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1 | Subject) anova(fm2a.1) ... Regards, Christoph Buser No. The calculation of denominator deg

[R] JOBS: Vanderbilt University Department of Biostatistics

2005-01-05 Thread Frank E Harrell Jr
/affirmative action employer; all qualified persons are encouraged to apply. CVs may be sent electronically to both [EMAIL PROTECTED] and [EMAIL PROTECTED] Please state in the subject of the E-mail the position for which you are applying or inquiring. -- Frank E Harrell Jr Professor and Chair

Re: [R] "labels" attached to variable names

2005-01-06 Thread Frank E Harrell Jr
o units(x) <- 'whatever units of measurement' then xYplot, describe, and other Hmisc functions will include the units (in a different font on graphs or when using latex()). Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of B

Re: [R] R-etiquette

2005-01-09 Thread Frank E Harrell Jr
iling list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt

Re: [R] R-etiquette

2005-01-09 Thread Frank E Harrell Jr
Prof Brian Ripley wrote: On Sun, 9 Jan 2005, Anne wrote: I'm about to present a report (for internal use of governmental agency). I used extensively R , contibuted packages, as well as communications on the R-list As well as citing R, I would like to know how to cite the contributed packages (i

Re: [R] how to do by-processing using weighted.mean

2005-01-09 Thread Frank E Harrell Jr
#x27;s in one of the summarize examples! -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/li

Re: [R] R-etiquette

2005-01-10 Thread Frank E Harrell Jr
le to include their names in an Ack. section, usually. Referencing as a personal communication is perhaps better. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt Unive

Re: [R] Standard error for the area under a smoothed ROC curve?

2005-01-12 Thread Frank E Harrell Jr
U statistic methods to get the standard error of Dxy. You can easily translate this to a standard error of C. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __

Re: [R] transcan() from Hmisc package for imputing data

2005-01-12 Thread Frank E Harrell Jr
frame with the NA values filled up? Or is there any other function that i could use? Thank you avneet It's in the help file for transcan. But multiple imputation is much better, and transcan does not do multiple imputation as well as the newer Hmisc function aregImpute. -- Frank E Harre

Re: [R] Kolmogorov-Smirnof test for lognormal distribution with estimated parameters

2005-01-12 Thread Frank E Harrell Jr
l confidence intervals. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLE

Re: [R] Standard error for the area under a smoothed ROC curve?

2005-01-12 Thread Frank E Harrell Jr
Dan Bolser wrote: On Wed, 12 Jan 2005, Frank E Harrell Jr wrote: Dan Bolser wrote: Hello, I am making some use of ROC curve analysis. I find much help on the mailing list, and I have used the Area Under the Curve (AUC) functions from the ROC function in the bioconductor project... http

Re: [R] empirical (sandwich) SE estimate in lme ()?

2005-01-14 Thread Frank E Harrell Jr
//stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __

Re: [R] Omitting constant in ols() from Design

2005-01-17 Thread Frank E Harrell Jr
constant? I can't use lm(), because robcov() needs an object from the Design() series. Or is there a different way to go about this? Tobias Muhlhofer ols does not support this. Sorry. -- Frank E Harrell Jr Professor and Chair School of Medicine Department

Re: [R] bwplot: how not to draw outliers

2005-01-17 Thread Frank E Harrell Jr
affecting the scale), you will have to modify the panel.bwplot function in addition to using the above. --sundar You may also want to try library(Hmisc) library(lattice) bwplot(..., panel=panel.bpplot) ?panel.bpplot -- Frank E Harrell Jr Professor and Chair School of

Re: [R] (no subject)

2005-01-20 Thread Frank E Harrell Jr
(parametric model) ? Thanks Virginie In the Design package look at the pphsm function that converts a survreg Weibull fit (fitted by the psm function which is an adaptation of survreg) to PH form. -- Frank E Harrell Jr Professor and Chair School of Medicine

Re: [R] Cross-validation accuracy in SVM

2005-01-20 Thread Frank E Harrell Jr
hz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt Unive

Re: [R] logistic regression 3D-plot

2005-02-03 Thread Frank E Harrell Jr
ntour' to get other types of graphs plot(f, sun=NA, trees=NA, fun='plogis') # probability scale -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University

Re: [R] logistic regression 3D-plot CORRECTION

2005-02-03 Thread Frank E Harrell Jr
library(Design) d <- datadist(mydata); options(datadist='d') f <- lrm(incidence ~ sun*trees) # lrm is for binary or ordinal response plot(f, sun=NA, trees=NA) # add method='image' or 'contour' to get other types of graphs plot(f, sun=NA, trees=NA, fun='plogis') # probability scale Correction: fun

Re: [R] Reading Dates in a csv File

2005-02-03 Thread Frank E Harrell Jr
cter" to the specified formal class" but I do not know and have not figured out how to do that. Any suggestion(s) would be greatly appreciated. Thanks, Charles The csv.get function in the Hmisc package may do most of what you want. -- Frank E Harrell Jr Professor and Chair Schoo

Re: [R] no. at risk in survfit()

2005-02-04 Thread Frank E Harrell Jr
can get them? Thanks The Design package's survplot function can print n.risk over equally spaced time points. You might see an easy way to print this by looking at the code. -Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Depar

Re: [R] Programming/scripting with "expressions - variables"

2005-02-07 Thread Frank E Harrell Jr
te data but don't store with(test(data, ),{...})# reference variables in temporary dataset If we know what your ultimate goal is, there may be a much better approach than the test function. In many cases, you do not need to create new variables at all. Franc -- Frank E Harrell

Re: [R] Re:logistic regression

2005-02-08 Thread Frank E Harrell Jr
ation. . -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do rea

Re: [R] Re:logistic regression

2005-02-08 Thread Frank E Harrell Jr
unctions available at the Bioconductor website. There was also some code sent around on the list a few months back for calculating trapeziodal AUC, se's from ROC, and comparing two ROC curves...search the archives if interested, or I can probably dig them out for you offline... Cheers, Joe Quot

Re: [R] Forward Stepwise regression based on partial F test

2005-02-24 Thread Frank E Harrell Jr
redictive accuracy and that violates every aspect of statistical inference, you are on the right track. See http://www.stata.com/support/faqs/stat/stepwise.html for details. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics V

Re: [R] Teaching R in 40 minutes. What should be included?

2005-02-26 Thread Frank E Harrell Jr
uuld be some extended view of available ressources (manuals, FAQ, community) as a starter to learn, use and program R by themselves. I think this would do for a 40 minutes presentation without taking the risk to deter people due to overcomplexity. regards Thomas -- Frank E Harrell Jr

<    1   2   3   4   5   6   7   >