Re: [R] lmer coefficient distributions and p values

/listinfo/r-sig-mixed-models Also check the latest documentation for lme4 and the lmer() and lmer2() functions at http://cran.r-project.org/ in the Packages ... lme4 pages. Hope this helps Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research

Re: [R] Systematically biased count data regression model

to your situation, and it has plenty of good references Application of Shrinkage Techniques in Logistic Regression Analysis: A Case Study E. W. Steyerberg Statistica Neerlandica, 2001, vol. 55, issue 1, pages 76-88 Steven McKinney Statistician Molecular Oncology and Breast Cancer Program

Re: [R] FW: Selecting undefined column of a data frame (was[BioC]read.phenoData vs read.AnnotatedDataFrame)

States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia

[R] FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)

other attached packages: plotrix lme4 Matrix lattice 2.2-3 0.99875-4 0.999375-0 0.16-2 Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: smckinney +at+ bccrc +dot+ ca tel: 604-675

Re: [R] FW: Selecting undefined column of a data frame (was [BioC]read.phenoData vs read.AnnotatedDataFrame)

base other attached packages: plotrix lme4 Matrix lattice 2.2-3 0.99875-4 0.999375-0 0.16-2 Should this discussion move to R-devel? Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email

Re: [R] FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)

columns selected [.data.frame is one of the most complex functions in R, and does many different things depending on which arguments are supplied. On Fri, 3 Aug 2007, Steven McKinney wrote: Hi all, What are current methods people use in R to identify mis-spelled column names when selecting

Re: [R] FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)

-Original Message- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: Fri 8/3/2007 1:05 PM To: Steven McKinney Cc: r-help@stat.math.ethz.ch Subject: Re: [R] FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame) I've since

Re: [R] FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)

, and as you point out, [.data.frame is one of the most complex functions in R so please bear with me. This change in behaviour has taken away a side-effect debugging tool, discussed below. On Fri, 3 Aug 2007, Steven McKinney wrote: -Original Message- From: Prof Brian

Re: [R] FW: Selecting undefined column of a data frame (was [BioC]read.phenoData vs read.AnnotatedDataFrame)

Hi Bert, -Original Message- From: Bert Gunter [mailto:[EMAIL PROTECTED] Sent: Fri 8/3/2007 3:19 PM To: Steven McKinney; r-help@stat.math.ethz.ch Subject: RE: [R] FW: Selecting undefined column of a data frame (was [BioC]read.phenoData vs read.AnnotatedDataFrame) I suspect

Re: [R] Extracting a website text content using R

-Original Message- From: [EMAIL PROTECTED] on behalf of Am Stat Sent: Wed 8/1/2007 2:19 PM To: r-help@stat.math.ethz.ch Subject: [R] Extracting a website text content using R Dear useR, Just wandering whether it is possible that there is any function in R could let me get the text

[R] Design matrix question

)$A [1] contr.treatment attr(,contrasts)$B [1] contr.treatment How do I get model.matrix to not add that column of zeroes? Why does model.matrix add that column of zeroes? Is this a bug, or a senior moment? Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British

Re: [R] reodering factor

) Coefficients: (Intercept)grp2A 10.66 -10.17 Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: [EMAIL PROTECTED] tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver

Re: [R] Computing an ordering on subsets of a data frame

6 2 1 2 5 2 1 1 4 2 3 3 7 3 2 2 9 3 3 3 8 3 1 1 HTH Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: [EMAIL PROTECTED] tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3

Re: [R] extracting intercept from ppr fit

] 9.973964 a - 210 data$z - evalq(a + atan (x + y) + rnorm (n), data) data.ppr - ppr(z ~ x + y, data=data, nterms =1) data.ppr$yb [1] 209.9773 HTH Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: [EMAIL PROTECTED] tel: 604

Re: [R] Extracting approximate Wald test (Chisq) fromcoxph(..frailty)

, sep = ) invisible(return(list(temp = temp, tmp = tmp))) } Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: [EMAIL PROTECTED] tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver

Re: [R] problem with RCurl install on Unix

packages: DBI 0.1-12 Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: [EMAIL PROTECTED] tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -Original

Re: [R] replacing all NA's in a dataframe with zeros...

TRUE FALSE 6 FALSE TRUE TRUE FALSE FALSE mydata.df[is.na(mydata.df)] - 0 mydata.df V1 V2 V3 V4 V5 1 1 0 1 1 1 2 1 0 0 0 1 3 0 0 1 0 0 4 0 0 0 0 1 5 0 1 0 0 1 6 1 0 0 1 1 Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia

Re: [R] dendrogram - got it , just need to label :)

access to internal node labels/names and being able to extract internal nodes by those labels/names. Best Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: [EMAIL PROTECTED] tel: 604-675-8000 x7561 BCCRC Molecular Oncology

Re: [R] Double-banger function names: preferences and suggestions

of the graphical codes, left-arrow mutated to the underscore of ASCII-1967. It may have had earlier, or other, meanings, but for some early programming languages it was assignment, eg. c ? b + a C is assigned the sum of B and A. Steven McKinney Statistician Molecular Oncology

Re: [R] Google Custom Search Engine for R

Whereas R is very generic, CRAN is much less so. I've had very good luck adding CRAN to my search terms, e.g. try to Google cran 3d scatterplot This produces all R-related hits on the first Google page. Hope this helps Steven McKinney Statistician Molecular Oncology and Breast Cancer

Re: [R] How to plot two graphs on one single plot?

) y2=dnorm(x2, mean=0, sd=1) plot(x1, y1, type='p', xlim=range(x1,x2), ylim=range(y1, y2), xlab='x', ylab='y') points(x2, y2, type='p', col=red, xlab='x', ylab='y') Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email

[R] Bug/problem reporting: Possible to modify posting guide FAQ?

If users post a bug or problem issue to an R-based news group (R-devel, R-help, BioC - though BioC is far more forgiving) they get yelled at for not reading the posting guide and FAQ. Please *_do_* read the FAQ, the posting guide, ... the yellers do say. So I read the BioC FAQ and it says...

[R] How do I modify an exported function in a locked environment?

residing? How do I push it out to replace the exported copy? Is this the proper way to modify a package function? Are there other ways? I've searched webpages, R news, help files and have been unable to find out how to get this process fully completed. Any guidance appreciated. Steven McKinney

[R] scripts to process array CGH data files from NimbleGen

in and use to create an aCGH object. Any info appreciated. Best Steve McKinney Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list