[R] How does one plot the -log(log(survival))

R 2.8.1 Windows XP How does one plot the -log(log(survival)) from a coxph? Survfit does not seem to be up to the task. Thanks, John John David Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10

[R] Comparing COXPH models, one with age as a continuous variable, one with age as a three-level factor

value. Is there any way to get anova to produce p values? Thank you, John Sorkin ANOVA results are pasted below: anova(fitCont,fitCat) Analysis of Deviance Table Model 1: Surv(Time30, Died) ~ Rx + Age Model 2: Surv(Time30, Died) ~ Rx + AgeGrp Resid. Df Resid. Dev Df Deviance 162

[R] Generating plots with two lines, each line plotted with a different color

=c(1,2),lwd=2) Thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of Maryland School of Medicine Claude D. Pepper OAIC, University of Maryland Clinical Nutrition Research Unit, and Baltimore VA Center Stroke of Excellence

[R] dependency ‘Matrix’ is not availabl e when installing Rcmdr

R 2.8.1 Windows XP Any suggestions for addressing the problem listed below, obtained when installing Rcmdr The downloaded packages are in C:\Documents and Settings\jsorkin\Local Settings\Temp\RtmpaxlG6g\downloaded_packages updating HTML package descriptions Warning message: dependency

[R] Package or packages for randomization in a clinical trial

Can anyone recommend a package that can be used to randomize subjects? I am looking for a generalized package, or several packages that can accomplish unrestricted randomization (i.e. simple random assignment) restricted randomization including stratified randomization, blocked randomization,

Re: [R] upgrade to 2.5

Why do you wish to upgrade to 2.5, it is not the current release! You should upgrade to 2.8.1. John John David Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC

[R] R editor that will work with Rcmdr

R 2.8.1 Windows XP Fedora Linux. I would like a suggestion for an editor that will help format my R code that can be used with Rcmdr. Is there anything I need to know about running or installing an editor when using Rcmdr? I run R on both Windows and Linux (Fedora). Thank you, John John

Re: [R] R editor that will work with Rcmdr

Dalgaard [mailto:p.dalga...@biostat.ku.dk] Sent: March-05-09 8:29 AM To: John Fox Cc: 'John Sorkin'; r-help@r-project.org Subject: Re: [R] R editor that will work with Rcmdr John Fox wrote: Dear John, I'm not entirely sure what you have in mind. Any editor or IDE that communicates

Re: [R] Inefficiency of SAS Programming

Terry's remarks (see below) are well received however, I take issue with one part of his comments. As a long time programmer (in both statistical programming languages and traditional programming languages), I miss the ability to write native-languages in R. While macros can make for difficult

Re: [R] Inefficiency of SAS Programming

-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing) Frank E Harrell Jr f.harr...@vanderbilt.edu 2/27/2009 12:52 PM John Sorkin wrote: Terry's remarks (see below) are well received however, I take issue with one part of his comments. As a long time programmer (in both

[R] Problems installing RODBC as part of Rcmdr and as separate package

/RODBC' The downloaded packages are in /tmp/RtmpA1nKF2/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages(RODBC) : installation of package 'RODBC' had non-zero exit status John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics

Re: [R] Problems installing RODBC as part of Rcmdr and as separatepackage

) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing) Marc Schwartz marc_schwa...@comcast.net 2/20/2009 10:39 AM on 02/20/2009 09:27 AM John Sorkin wrote: Fedora 10 R 2.8.1 I hope someone can tell me the meaning of error I received trying to install RODBC

Re: [R] Problems in Recommending R

In any redesign we need to remember that a good user interface that works with as many browsers as possible should be the primary design criteria. We don't need eye candy. John John David Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division

Re: [R] logLik for poisson models

Antonio, Given the model you used, the log link means you are modeling log(expected value of y)=intercept If you had an independent variable e.g. x model - glm(y ~ x, family=poisson()) you would be modeling log(expected value of y)=intercept+x John John David Sorkin M.D., Ph.D. Chief,

[R] Odd behaviour of subset indexing (x:y).

, NA x[iS+1:iE] [1] 3 4 5 NA Thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of Maryland School of Medicine Claude D. Pepper OAIC, University of Maryland Clinical Nutrition Research Unit, and Baltimore VA Center Stroke

Re: [R] reading data from Excel Spread sheet

Kiran, One, not very elegant way, to solve your problem is to first save the Excel spreadsheet as a CSV file (open the Excel file in Excel and the use file-save as CSV, i.e. xxx.CSV) and then use read.csv() John John David Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of

Re: [R] Some clarificatins of anova() and summary ()

Ben, You were quite correct to indicate that Tanmoy should not use the listserver to get answers to his class assignments. Never the less, I do have some sympathy for him. The help pages for the R functions summary, anova, drop1, do not discuss the critically important issue addressed by

[R] means of a column within groups of a data frame

R 2.8.0 windows XP I would like to divide the rows of data frame into five groups and then get the mean of one column within the five groups. I have accomplished this using the code below, but I hope there is an easier way, i.e. some function that I can call # create five groups.

[R] glm error message when using family Gamma(link=inverse)

R 2.5 windows XP I am getting an error from glm() that I don't understand. Any help or suggestions would be appreciated. N.B. 1=AAMTCAREJ=327900 summary(data$AAMTCAREJ) Min. 1st Qu. Median Mean 3rd Qu. Max. 1.0404.3 1430.0 6567.0 5457.0 327900.0

Re: [R] glm error message when using family Gamma(link=inverse)

(BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing) Prof Brian Ripley [EMAIL PROTECTED] 12/9/2008 2:11 PM On Tue, 9 Dec 2008, John Sorkin wrote: R 2.5 Please 1) do as the posting guide asks, and quote version numbers

[R] Sink does not send graphs to sink file

Wiindows XP R 2.7 I am using sink() to send the results of my analyses to a text file. Unfortunately my graphs do not become part of the file. Is there anyway that I can have both the text and graphic output of my analyses appear in a file? Thanks, John John David Sorkin M.D., Ph.D. Chief,

[R] Comparing output from linear regression to output from quasipoisson to determine the model that fits best.

R 2.7 Windows XP I have two model that have been run using exactly the same data, both fit using glm(). One model is a linear regression (gaussian(link = identity)) the other a quasipoisson(link = log). I have log likelihoods from each model. Is there any way I can determine which model is a

[R] Overlay two plots on the same device with axes having the same scale.

R 2.6.0 Windows XP I have crated a file containing data with x and y values and have plotted the data using the output of gam. I would like to overlay an x,y plot of the data on top of the line returned by gam. I have succeeded in doing this using par(new=TRUE), unfortunately the y axis of

Re: [R] Linear regression

lm, for example: fit1-lm(y~x,data=mydata) if you enter ?lm in an R session you will get more information. John John David Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene

Re: [R] calculation for standard normal cumulative distribution

I suggest you issue the following command: ?pnorm which will get you to a manual page that will give you information about the following commands: dnorm(x, mean=0, sd=1, log = FALSE) pnorm(q, mean=0, sd=1, lower.tail = TRUE, log.p = FALSE) qnorm(p, mean=0, sd=1, lower.tail = TRUE, log.p =

[R] apply, t-test and p-values

: boo-apply(sample1,1,t.test$t.test,sample2) boo-apply(sample1,1,t.test,sample2)$t.test any suggestions? Thanks John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of Maryland School of Medicine Claude D. Pepper OAIC, University of Maryland

Re: [R] apply, t-test and p-values

16, 2008 at 8:01 AM, John Sorkin [EMAIL PROTECTED] wrote: R 2.7.2 Windows XP I am using apply to compute a series of Student's t-test from two matrices, sample1 and sample2. boo-apply(sample1,1,t.test,sample2) I want to pick of the p-values from the tests, but can't seem to get

Re: [R] apply, t-test and p-values PREVIOUS SUGGESTION DID NOT WORK

On Thu, Oct 16, 2008 at 8:01 AM, John Sorkin [EMAIL PROTECTED] wrote: R 2.7.2 Windows XP I am using apply to compute a series of Student's t-test from two matrices, sample1 and sample2. boo-apply(sample1,1,t.test,sample2) I want to pick of the p-values from the tests, but can't seem

Re: [R] Fw: Logistic regresion - Interpreting (SENS) and (SPEC)

Jumping into a thread can be like jumping into a den of lions but here goes . . . Sensitivity and specificity are not designed to determine the quality of a fit (i.e. if your model is good), but rather are characteristics of a test. A test that has high sensitivity will properly identify a

Re: [R] Fw: Logistic regresion - Interpreting (SENS) and (SPEC)

[EMAIL PROTECTED] 10/13/2008 2:35 PM John Sorkin wrote: Jumping into a thread can be like jumping into a den of lions but here goes . . . Sensitivity and specificity are not designed to determine the quality of a fit (i.e. if your model is good), but rather are characteristics of a test

Re: [R] Fw: Logistic regresion - Interpreting (SENS) and (SPEC)

PROTECTED] To: John Sorkin [EMAIL PROTECTED] Cc: r-help@r-project.org; [EMAIL PROTECTED]; [EMAIL PROTECTED] Sent: Monday, October 13, 2008 2:09 PM Subject: Re: [R] Fw: Logistic regresion - Interpreting (SENS) and (SPEC) John Sorkin wrote: Frank, Perhaps I was not clear in my previous Email message

Re: [R] Fw: Logistic regresion - Interpreting (SENS) and (SPEC)

to faxing) Peter Dalgaard [EMAIL PROTECTED] 10/13/2008 6:28 PM John Sorkin wrote: Of course Prof Baer is correct the positive predictive value (PPV) and the negative predictive values (NPV) serve the function of providing conditional post-test probabilities PPV: Post-test probability

[R] List of varying length suitable for use as dimnames

Windows XP R 2.7.2 I need to create a list of varying length of the form SS1 SS2 SS3 . . . SSn I will be using the list for the dimnames of a matrix that will have varying dimensions. Any suggestions for a good way to accomplish this would be appreciated. Thanks, John Confidentiality

[R] List of varying length suitable for use as dimnames

Windows XP R 2.7.2 I would like to create a list of varying length (length n) suitable for use as dimnames for a matrix whose size will vary, i.e. SS1 SS2 SS3 . . . SSn Ansy suggestions for accomplishing this would be appreciated. Thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics

[R] apply

: jj-sapply(c(1,2,3),sample,size=10,replace=TRUE,prob=c(.1,.3,.6)) Suggestions? John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of Maryland School of Medicine Claude D. Pepper OAIC, University of Maryland Clinical Nutrition Research Unit

[R] selecting from a series of integers with pre-determined probabilities

R 2.6 Windows XP I need to select from the integers 1,2,3,4,5 with some pre-determined probability, e.g. probability of selecting 5 80%, probability of selecting 1 or 2 or 3 or 4 20%. Any suggestions for how I might accomplish this? I need to do it very efficiently as I will be doing it

[R] Rcommander installation fails on Fedora 9

: error: expected ‘)’ before ‘object’ make: *** [Classes.o] Error 1 ERROR: compilation failed for package 'party' ** Removing '/usr/lib/R/library/party' John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of Maryland School of Medicine Claude D

Re: [R] Rcommander installation fails on Fedora 9

Distributions.o IndependenceTest.o LinearStatistic.o mvt.o Node.o Predict.o RandomForest.o S3Classes.o Splits.o SurrogateSplits.o TestStatistic.o TreeGrow.o Utils.o -L/usr/lib/R/lib -lRlapack -L/usr/lib/R/lib -lRblas -lgfortran -lm -lgfortran -lm -L/usr/lib/R/lib -lR Thanks, John John Sorkin

[R] Sorting a matrix by a column

R 2.6 Windows XP I have a 100x4 matirx data-matrix(nrow=100,ncol=4) I would like to sort the entire matrix by column two, i.e. data[,2] I looked at the help page for sort() but can not determine how I can use it to sort a matrix on one of the matrix's columns. Thanks, John John David Sorkin

Re: [R] Can I do regression by steps?

Be very careful! When regression is performed by steps, you often will not get the same results as you would get from a single multivariable regression. The explanation for this is not simple, but a simplified explanation is that when you do your first regression, y=f(x1) all the total variance

Re: [R] Can I do regression by steps?

number above prior to faxing) rlearner309 [EMAIL PROTECTED] 7/8/2008 6:25 PM Thanks for the reply. I am awared of the difference, but can I do regression by steps at all? I am not feeling comfortable about it. John Sorkin wrote: Be very careful! When regression is performed by steps, you

[R] Can not load msm package

windows XP R 2.6.0 I have tried to install the msm package several times. Each time the installation appears to work. I then go to PACKAGES-LOAD PACKAGE but the msm package does not appear in the SELECT ONE dialog box. Can someone suggest how I can get msm to run on my system? Thanks, John

[R] package for repeated measures ANOVA with various link functions

for a package that will allow for repeated measures ANOVA in the context of various link functions would be appreciated. Thanks as always, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center

Re: [R] package for repeated measures ANOVA with various link functions REDUX

the correlation structure of the repeated measures from a subject a la SAS proc mixed or by adjusting the parameter estimates using GEE a la proc GENMOD? Perhaps R has a package that accounts for repeated measures in some other manner. Thank you, John Sorkin John Sorkin M.D., Ph.D. Chief

[R] emacs and R

that I might read? In the past I have used R on a Windows XP system and used the built-in windowing interface. Thank you, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of Maryland School of Medicine Claude D. Pepper OAIC

[R] glm: offset

) or as: offset=NumUniqPt I suspect I need to use the log, bu t I can't find any discussion of this in MASS 1994 or on the man page for glm. Thanks John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA

Re: [R] building packages for Linux vs. Windows

language R version.string R version 2.6.1 (2007-11-26) John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR

[R] EMACS and ESS

someone tell me where to go to get the RPMs? If anyone would have a suggestion for an editor other than EMACS to use with R, I would appreciate any suggestions. Thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division

Re: [R] help with R

-project.org/doc/manuals/R-intro.html and do some reading of the introduction document. Once you have done this you should be able to get started using R and will be able to ask a question that we can more easily answer. John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA

Re: [R] help with R

to get started using R and will be able to ask a question that we can more easily answer. John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of Maryland School of Medicine Claude D. Pepper OAIC, University of Maryland Clinical Nutrition

Re: [R] I need arguments pro-S-PLUS and against SAS...

one is absolutely better than the other. John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax

Re: [R] I need arguments pro-S-PLUS and against SAS...

of the entire R community, thank you. With greatest respect and thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524

[R] Using R function in Excel

, e.g. =mysum(A2,A6). Thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913

Re: [R] Packages - a great resource, but hard to find the right one

package finding system. Thanks to all who contributed to the discussion. John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of Maryland School of Medicine Claude D. Pepper OAIC, University of Maryland Clinical Nutrition Research Unit

[R] Packages - a great resource, but hard to find the right one.

packages and the many people who contribute to the R list server. John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of Maryland School of Medicine Claude D. Pepper OAIC, University of Maryland Clinical Nutrition Research Unit, and Baltimore

Re: [R] Packages - a great resource, but hard to find the right one.

Gabor, The URL you cited is helpful, but it is not searchable. It can not be used, for example, to easily determine that MASS can be used for boxcox tranforms. John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of Maryland School

Re: [R] Help with R software

KEYWORDS. John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number

Re: [R] r achives

Might I suggest that the Email deamon include the URL of the archives to the footer it attaches to Email messages. Johh John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of Maryland School of Medicine Claude D. Pepper OAIC, University

Re: [R] Trust p-values or not ?

Listserv mailing list! John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of Maryland School of Medicine Claude D. Pepper OAIC, University of Maryland Clinical Nutrition Research Unit, and Baltimore VA Center Stroke of Excellence

Re: [R] Linear Regression

the components, viz. coeffs-summary(fit1)$coefficients #or RSq-summary(fit1)$r.squared John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore

Re: [R] Linear Regression

OOPPSS, I forgot a right parenthesis fit1-summary(lm(weight~group-1) ) John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524

[R] 3-dimensional graph

Windows XP R 2.3.1 I have a funciton fit1-lm(y~x+z) Is there a function that will produce a 3-dimensional plot of y,x,z? I looked at the help files, but did not find a clean answer to my question. Thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland

Re: [R] data structure with coefficients, and call from lm()

1.887634 0.04372724 43.168382 1.410167e-65 Thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524

Re: [R] data structure with coefficients, and call from lm()

Thank you Moshe, I understand you point, but I would hope that I could use summary to save my self some work. I need to do what I described in my original Email to the list server on tens of regressions. John John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University

Re: [R] data structure with coefficients, and call from lm()

I desire. Of course when used on real data each line will have different values. Again thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR

Re: [R] statistics - hypothesis testing question

Mark, Estimates of R values can be compared using Fishers r to z transform. Perhaps this will do what you wish to do. John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of Maryland School of Medicine Claude D. Pepper OAIC, University

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