Re: [R] Question about lme (mixed effects regression)

__ 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. -- Bert Gunter Genentech Nonclinical Biostatistics

Re: [R] Question about lme (mixed effects regression)

not sure now - does ranef(fm1) give the (total) slope and intercept values directly for each group or not? Thanks a lot for clarifying - because I might well have been wrong. Dimitri On Mon, Oct 18, 2010 at 5:57 PM, Bert Gunter gunter.ber...@gene.com wrote: Dmitri: Not quite sure what you

Re: [R] covariance matrix

Unintelligible -- to me anyway. You will have to explain what you mean more explicitly and with greater clarity -- at least for my feeble mind-- to get help. -- Bert Gunter On Fri, Oct 22, 2010 at 11:01 AM, Marcelo Lima mlim...@gmail.com wrote: Dear all, I generated a covariance matrix and I

Re: [R] question in using nlme and lme4 for unbalanced data

://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] Returning highs and lows in R

://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. -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r

Re: [R] transfer string to expression

-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. -- Bert Gunter Genentech Nonclinical Biostatistics

Re: [R] Plots inside a Plot

, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ 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

Re: [R] avoiding too many loops - reshaping data

-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ 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] anova(lme.model)

-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ 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] anova(lme.model)

Diversity            1    14   1.53025  0.2364 Management           2    30   6.01972  0.0063 Species              3   163  51.86699  .0001 Height               1   163  30.08090  .0001 Diversity:Height     1   163  12.57603  0.0005 -- Bert Gunter Genentech Nonclinical Biostatistics

Re: [R] How to eliminate this for loop ?

. -- Bert Gunter Genentech Nonclinical Biostatistics 467-7374 http://devo.gene.com/groups/devo/depts/ncb/home.shtml __ 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] How to eliminate this for loop ?

it. __ 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. -- Bert Gunter Genentech Nonclinical

Re: [R] standardized/studentized residuals with loess

]] __ 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. -- Bert Gunter Genentech Nonclinical

Re: [R] User input after opening graphing device

/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] repeated measure test

/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] Surprising behavior using seq()

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. -- Bert Gunter Genentech Nonclinical Biostatistics

Re: [R] dnorm and qnorm

http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE

Re: [R] How to plot effect of x1 while controlling for x2

... and/or perhaps ?coplot in base R graphics or ?xyplot in trellis. -- Bert Gunter On Mon, Nov 15, 2010 at 2:25 PM, Greg Snow greg.s...@imail.org wrote: Look at Predict.Plot (and TkPredict) from the TeachingDemos package. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center

Re: [R] aspect ratio 1 and blank space

and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ 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] Vectors out of lists?

with his comments is wrong. Cheers, Bert Bert Gunter Genentech Nonclinical statistics __ 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] Help with lmer, nested data and repeated measures

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. -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help

Re: [R] Logistic regression with factorial effect

. __ 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. -- Bert Gunter Genentech Nonclinical Biostatistics

Re: [R] generalized linear regression - function glm - dismissed predictors - more information about simulated data

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. -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r

Re: [R] Sample covariance matrix in R

__ 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. -- Bert Gunter Genentech Nonclinical

Re: [R] Is it possible to make a matrix to start at row 0?

/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. -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r-project.org mailing

Re: [R] Comparing two functions

languages like C or Fortran (or Java?). Cheers, Bert Gunter Genentech Nonclinical Statistics ** His approach also has the advantage of explicitly passing the function you want to masterf rather than forcing R to look for it (in the environment in which masterf was defined). More typically

Re: [R] how to use by() ?

) Greg __ 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. -- Bert

Re: [R] reference text variables as column name to plot

, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ 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

Re: [R] Adding noise

-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ 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

Re: [R] Outlier statistics question

. -- Bert Gunter Genentech Nonclinical Biostatistics __ 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

Re: [R] What is the degrees of freedom in an nlme model

: there may be no good way to do what you want. Note to experts: Please view this post as an invitation to correct my errors and provide authoritative info. Cheers to all, Bert Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r

Re: [R] What is the degrees of freedom in an nlme model

job. -- You need to consult with your local statistician. This forum is not the appropriate venue for difficult statistical questions that require intimate familiarity with the data and an understanding of the scientific questions of interest. -- Bert Gunter Genentech Nonclinical Statistics

Re: [R] [R-pkgs] New package list for analyzing listsurveyexperiments

Rich: I suspect it's a cultural relic of the storage is scarce era that begat C and R in the first place. Cutesiness. Culture is hard to change, but I think you make a very salient point! -- Bert Bert Gunter Genentech Nonclinical Statistics -Original Message- From: r-help-boun...@r

Re: [R] [R-pkgs] New package list for analyzing listsurveyexperiments

-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Hadley Wickham Sent: Thursday, July 15, 2010 12:15 AM To: Yves Rosseel Cc: r-help@r-project.org; richard_rauber...@merck.com Subject: Re: [R] [R-pkgs] New package list for analyzing

Re: [R] Objects within environment

complain, try writing some documentation yourself. It's damn hard! ;) Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics __ 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] Tutorial Tinn-R

-- it is for R, not TINN-R. Perhaps someone will be able to tell you where to post TINN-R questions. I just had to struggle to figure it out and get it set up; but I use it all the time as a pseudo- IDE. Bert Gunter Genentech Nonclinical Statistics -Original Message- From: r-help-boun

Re: [R] Reconciling 2 datasets

Have you read AN INTRODUCTION TO R? ?%in% Bert Gunter Genentech Nonclinical Statistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of chipmaney Sent: Friday, July 23, 2010 3:39 PM To: r-help@r-project.org Subject: [R

Re: [R] Outlier detection in bimodal distribution

before -- what is the scientific context? What is the scientific question? I suspect you need to seek the help of a local statistician before you sweep possibly important data under the outlier rug. Bert Gunter Genentech Nonclinical Biostatistics On Mon, Jul 26, 2010 at 5:40 AM, Tim Smith tim_smith_

Re: [R] Sample size calculation for non-normal population with unknown mean and SD

a parametric form. My guess is that your distribution is right-skew but not Poisson -- probably more like a truncated Poisson. But of course I have no idea what sorts of documents you've got, so how would I know? Bert Gunter Genentech Nonclinical Biostatistics On Mon, Jul 26, 2010 at 1:28 PM, Majonu

Re: [R] specifying an unbalanced mixed-effects model for anova

effects models, so just walking you through a lme model specification is not likely to help. Bert Gunter On Tue, Jul 27, 2010 at 8:24 PM, Murat Tasan mmu...@gmail.com wrote: hi all - i'm having trouble using lme to specify a mixed effects model. i'm pretty sure this is quite easy

Re: [R] finding the next highest number in an array

... just a note: you don't have to first sort the vector to do this: x - sample(1:7) x [1] 3 5 7 6 2 4 1 which(x==min(x[x4])) [1] 2 Bert Gunter Genentech Nonclinical Biostatistics On Wed, Jul 28, 2010 at 3:12 AM, Raghu r.raghura...@gmail.com wrote: Hi I have a sorted array

Re: [R] looking for setdiff equivalent on dataset

not work if the data frame contain calculated numeric values which theoretically (infinite precision) are equal but are not exactly due to finite precision. For example, try: 0 %in% pi/2 If this is what you have, then you have to do something fancier working directly with the numeric values. Bert

Re: [R] Problems with normality req. for ANOVA

can, have a look at Jack Youden's classic paper Enduring Values, which comments to some extent on these issues, here: http://www.jstor.org/pss/1266913 Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics On Mon, Aug 2, 2010 at 10:32 AM, David Winsemius dwinsem...@comcast.netwrote

Re: [R] Problems with normality req. for ANOVA

My sympathies, but I don't think it's the business of list contributors to facilitate stupidity. Confidence interval for the p-value is nonsense. You could try sensitivity analyses via simulation, though. Cheers, Bert Gunter Genentech Nonclinical Biostatistics On Mon, Aug 2, 2010 at 11:31 AM

Re: [R] Using apply for logical conditions

of the frame. Whence one concludes that the f argument must be vectorized for the Reduce to work on the columns of the data frame as you expect. e.g. Reduce(min,data.frame(a=1:3,b=4:6)) [1] 1 but Reduce(pmin,data.frame(a=1:3,b=4:6)) [1] 1 2 3 Cheers, Bert Gunter Genentech Nonclinical Biostatistics

Re: [R] Using apply for logical conditions

Just for fun, here are another couple of versions that work for data frames. For Reduce with | do.call(pmax,c(mydata,na.rm=TRUE)) 0 and for do.call(pmin,c(mydata,na.rm=TRUE)) 0  Cheers, Bert Gunter Genentech Nonclinical Biostatistics On Mon, Aug 2, 2010 at 2:28 PM, Joshua Wiley jwiley.ps

Re: [R] Collinearity in Moderated Multiple Regression

-- and this ignorance gets them into a world of trouble. -- Bert Bert Gunter Genentech Nonclinical Biostatistics On Tue, Aug 3, 2010 at 12:57 PM, Dennis Murphy djmu...@gmail.com wrote: Hi: On Tue, Aug 3, 2010 at 6:51 AM, haenl...@gmail.com wrote: I'm sorry -- I think I chose a bad example

Re: [R] Collinearity in Moderated Multiple Regression

about the basic concepts. Bert Gunter Genentech Nonclinical Biostatistics On Tue, Aug 3, 2010 at 1:42 PM, Michael Haenlein haenl...@escpeurope.eu wrote: Thanks for all your comments! @Dennis: Are there any thresholds that I can use to evaluate the Variance Inflation Factor? I think I learned

Re: [R] REmove level with zero observations

Actually, you probably want to remove the remaining level -- that is, remove the variable altogether, since if it has only a single value its effect is indistinguishable from the overall mean. Again, complying with the posting guide would be advisable. Bert Gunter Genentech Nonclinical

Re: [R] nlme: constraints on fixed effects?

Is there a way to set constraints on the fixed effects parameters? Yes. (I suggest you read and follow the posting guide to get a better answer). Bert Gunter Genentech Nonclinical Statistics On Tue, Aug 3, 2010 at 11:11 AM, Marston, Sarah sarah.mars...@otsuka.com wrote: Dear R Help

Re: [R] split / lapply over multiple columns

, albeit with different syntax. Alternatively, his reshape package (?melt,?cast therein) may also suffice, depending on what you are trying to do. Cheers, Bert Gunter Genentech Nonclinical Biostatistics On Tue, Aug 3, 2010 at 9:06 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 3, 2010

Re: [R] plot the dependent variable against one of the predictors with other predictors as constant

I am thinking about using 'predict' command to generate the prediction of z with the new data.frame but there should be a better way. I'm puzzled. Why would you think that? This is the canonical way to do predictions in R. Bert Gunter Genentech Nonclinical Statistics

Re: [R] Arbitrary number of covariates in a formula

be useful for this. -- Bert Gunter Genentech Nonclinical Biostatistics On Wed, Aug 11, 2010 at 10:53 AM, Mendolia, Franco fmendo...@mcw.edu wrote: I could do that. However, the function f that I mentioned below is part of a bigger program and is nested inside another function, say function

Re: [R] normality tests

?RsiteSearch or consult package sos. Learn how to use R's search resources! -- Bert Gunter Genentech Nonclinical Statistics On Wed, Aug 11, 2010 at 8:21 PM, Geoffrey Smith g...@asu.edu wrote: Hello, does anyone know how to compute the following two normality tests using R: (1) the Kiefer

Re: [R] Re : How to compare the effect of a variable across regression models?

sense in such a world -- and then studies need to be carefully designed -- happenstance data are rarely sufficient -- to quantify them. .. Not what scientists like to hear, I think, but this is the reality. Further comments and criticisms welcome, of course. Cheers, Bert Gunter Genentech

Re: [R] Re : Re : How to compare the effect of a variable across regression models?

statistician to help you gain some clarity. Thanks again, David Biau. De : Bert Gunter gunter.ber...@gene.com À : Biau David djmb...@yahoo.fr Cc : Frank Harrell f.harr...@vanderbilt.edu; r help list r-help@r-project.org Envoyé le : Ven 13 août 2010, 18h

Re: [R] 'panel.smooth' error

. -- Bert Gunter Genentech Nonclinical Biostatistics 467-7374 http://devo.gene.com/groups/devo/depts/ncb/home.shtml __ 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

Re: [R] Why does Bootstrap work for one of similar models but not for the other?

] survival_2.35-8 svSocket_0.9-48 lattice_0.18-3 MASS_7.3-5 What does getOption(digits) give you just before you run each bootstrap? Bert Gunter Genentech nonclinical Statistics On Thu, Aug 19, 2010 at 12:50 AM, Reiko Akiyama reiko.akiy...@ebc.uu.se wrote: Dear all, Could anyone help me figure

Re: [R] csv vs. data frame

-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. -- Bert Gunter Genentech Nonclinical Biostatistics 467-7374 http://devo.gene.com

Re: [R] Surface generated as product of two curves

more informative imho). -- Bert Gunter Genentech Nonclinical Statistics On Fri, Aug 20, 2010 at 8:23 AM, mau...@alice.it mau...@alice.it wrote:  I have the following data table:     [,1] [,2] [,3] [,4] [,5] [1,] 2575 1927 1754  581  354 [2,] 1156  810  730  541  237 [3,]  417  297  199  125

[R] Regex exercise

elegant solution from a true regex expert. (Special note to Thomas Lumley: This seems one of the few instances where eval(parse..)) may actually be appropriate.) Cheers to all, Bert -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r

[R] Addendum to regex query

... I forgot to add: Base R regex functionality only. No special string packages or functions (like gsubfn). I'm sure those would help, but that's not what I'm after. -- Bert -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r-project.org

Re: [R] Regex exercise

 5  3  4  5  6  4  8  5  6  7 10 -- Bert Gunter Genentech Nonclinical Biostatistics 467-7374 http://devo.gene.com/groups/devo/depts/ncb/home.shtml __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] change order of plot panels in faceted ggplot/qplot

This is easy to do in xyplot (latice package) via the index.cond and skip arguments. Don't know about ggplot though. -- Bert On Mon, Aug 23, 2010 at 11:02 AM, Alison Macalady a...@kmhome.org wrote: Hi, I have a 5-paneled figure that i made using the facet function in qplot (ggplot).  I've

Re: [R] multiple assignments ?

. Using lists and list operations usually allows both to be done more efficiently and conveniently in one step. -- Bert Gunter Genentech Nonclinical Statistics On Tue, Aug 24, 2010 at 8:19 AM, r.ookie r.oo...@live.com wrote: Do you mean something like this?  n - 5  (vec1 - matrix(rep(1, n

Re: [R] multiple assignments ?

, Room 1.04 University of East Anglia Norwich, UK NR4 7TJ +44 (0) 1603 591412 -Original Message- From: Bert Gunter [mailto:gunter.ber...@gene.com] Sent: Tuesday, August 24, 2010 4:39 PM To: r.ookie Cc: Maas James Dr (MED); r-help@r-project.org Subject: Re: [R] multiple assignments

Re: [R] Random slopes in lmer

??? You were provided exactly what you requested. I think you either need to read up on what random effects models mean or more clearly communicate what YOU mean. (It's unclear to me, anyway). -- Bert Gunter Genentech Nonclinical Statistics On Thu, Aug 26, 2010 at 8:57 AM, Samantha Patrick

Re: [R] non-linear plot parameters

modeled, fitted, and compared as functions of temperature -- provided that the design permits this (i.e. provides sufficient precision for the characterizations/comparisons). If you don't know how to do this, seek further statistical help. -- Bert Gunter Genentech Nonclinical Statistics

Re: [R] AIC using nls function

are nonlinear. A detailed understanding and explanation of exactly what this means exceeds my understanding. Doug Bates's PhD thesis and subsequent papers (+ others, no doubt) go into this. Cheers, Bert Gunter Genentech Nonclinical Statistics On Fri, Aug 27, 2010 at 7:45 AM, John Ludlam ludlam.j

Re: [R] How to calc ratios base on current and previous row?

Your question is unclear. If the calculation of B[3] now depends on the newly calculated value of B[2], then the answer is no: you must loop. If B[3] is based on the original B[2] value, then the answer is yes, and the solution is just a matter of simple indexing, which I leave as an exercise. --

Re: [R] Brown-Forsythe test of equality of MEANS

way ANOVA on *zij*: In particular, it is NOT a substitute for the normal ANOVA F statistic for when there are unequal variances, and when there is evidence of non-normality. -- Bert Gunter Genentech Noclinical Statistics [[alternative HTML version deleted

Re: [R] Brown-Forsythe test of equality of MEANS

Thanks. I stand corrected, then. -- Bert On Mon, Aug 30, 2010 at 1:45 PM, JRG loesl...@verizon.net wrote: On 30 Aug 2010 at 13:25, Bert Gunter wrote: Inline below. -- Bert Wrong. There *is* a Brown-Forsythe test of equality of means given heterogeneity of variance. [Kirk's

Re: [R] simultaneous estimation

I would hazard the guess that this would be better estimated as a multivariate time series (e.g. AR1) in which the covariance between the two innovation components was NOT assumed to be 0 (nor were their variances assumed to be the same). The R time series task view lists packages to do this, but

Re: [R] Brown-Forsythe test of equality of MEANS

Learned Folks: Well, I've already advertised my ignorance about these matters, so I have nothing to lose by plunging ahead with further Questionable advice. From the references cited, Brown-Forsythe originated in the statistical medieval age -- that is, prior to large scale, cheap computing (to

Re: [R] Detecting Growth Trends

Error of the 3rd kind, (right answer to wrong question), I think. So what if the test rejects --- then what? I think the poster is looking for some kind of smoother. ?loess, ?smooth.spline and about 400 others may be useful. -- Bert Gunter Genentech Nonclinical Statistics On Tue, Aug 31, 2010

Re: [R] Why is vector assignment in R recreates the entire vector ?

will not create a copy if it can avoid it (usually?). Search the list archives for call by value, copy arguments, etc. for authoritative answers. -- Bert Gunter Genentech Nonclinical Statistics Which is actually doing this: x- `[-`(x, list=10, values=NA) # The actual call Assuming this can

Re: [R] [Q] Goodness-of-fit test of a logistic regression model using rms package

a long time ago (in a galaxy far away), Often, even the data aren't sufficient. (This a cryptic statistical in joke; example for the in-crowd: is it an outlier or an indication of curvature?). Cheers, Bert Bert Gunter Genentech Nonclinical Statistics On Wed, Sep 1, 2010 at 12:22 PM, Frank Harrell

Re: [R] Linear models (lme4) - basic question

Why should height be a random effect? I suspect you may need a tutorial on what a random effect in a mixed model is. I see no obvious reason why one would cluster on height. Perhaps if you clarify, it may become obvious either what your concerns are (and that your model is correct) or that you

Re: [R] Linear models (lme4) - basic 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. -- Bert Gunter Genentech Nonclinical Biostatistics 467-7374 http

Re: [R] general question on binomial test / sign test

://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics 467-7374 http://devo.gene.com/groups/devo/depts/ncb/home.shtml __ R-help@r-project.org

[R] Way OT: Does PSA testing reduce prostate cancer mortality?

... For those who are interested, enjoy. Cheers, Bert Bert Gunter Genentech Nonclinical Statistics __ 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] R package to identify model

Another task for the ESP package? Bert Gunter Genentech Nonclinical Statistics On Tue, Sep 7, 2010 at 4:29 AM, netrunner giovanna.va...@gmail.com wrote: Dear all, I would like to know if there is a R package performing model identification? thank you! -- View this message in context

Re: [R] Saving/loading custom R scripts

in a profile file. Cheers, Bert Gunter Genentech Nonclinical Statistics On Wed, Sep 8, 2010 at 8:20 AM, Joshua Wiley jwiley.ps...@gmail.com wrote: Hi, Just create a file called .Rprofile that is located in your working directory (this means you could actually have different ones in each

Re: [R] 'par mfrow' and not filling horizontally

code. -- Bert Gunter Genentech Nonclinical Biostatistics 467-7374 http://devo.gene.com/groups/devo/depts/ncb/home.shtml __ 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] Replace NAs in one column with data from another column

with() would seem to be useful here: m$z - with(m,ifelse(is.na(z), x, z)) (I believe the timing is similar, but haven't checked) -- Bert On Wed, Sep 8, 2010 at 11:22 AM, Dimitris Rizopoulos d.rizopou...@erasmusmc.nl wrote: one way is the following: m - data.frame(x = rnorm(100), y =

Re: [R] Data.frames : difference between x$a and x[, a] ? - How set new values on x$a with a as variable ?

Well, let's see if the following helps or just adds to the confusion. First lists are vectors of mode list . But they are general recursive structures (in fact, completely general). Second, data frames are lists: each column of a data frame is a component (member) of the list with the additional

[R] OT: Is randomization for targeted cancer therapies ethical?

targeted therapies appear to be more effective. While the context may be new, the debate, itself, is not: Tukey wrote (or maybe it was talked -- I can't remember for sure) about this about 30 years ago. I'm sure many other also have done so. Cheers, Bert -- Bert Gunter Genentech Nonclinical

Re: [R] Passing a function as a parameter...

, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ 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] How to pass a model formula as argument to with.mids

@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. -- Bert Gunter Genentech Nonclinical Biostatistics

Re: [R] Opening a .R file with R (Windows)

/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] R-Square for Robust Regression Model

-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. -- Bert Gunter Genentech Nonclinical Biostatistics

Re: [R] 'all subsets' fitting algorithm for Bayesian approach

-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. -- Bert Gunter Genentech Nonclinical Biostatistics 467-7374 http://devo.gene.com

Re: [R] Debye function

@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. -- Bert Gunter Genentech Nonclinical Biostatistics

Re: [R] Debye function

OOPs. I Only read Spencer's reply. Sorry for repeating the poster's original comment. -- Bert On Mon, Oct 4, 2010 at 10:10 AM, Bert Gunter bgun...@gene.com wrote: Well, not really ... Google on R package Debye . The 5th hit lists the gsl package with the debye() function. Moral: DO make

Re: [R] Inheritance and automatic function call on script exit

and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ 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] Source awareness?

-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ 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

Re: [R] Hausman test for endogeneity

. -- Bert Gunter Genentech Nonclinical Biostatistics __ 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

Re: [R] repeatability/intraclass with nested levels

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. -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r

Re: [R] How do I tell whether two vectors are identical?

://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. -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r

Re: [R] Pasting function arguments and strings

://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. -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r

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