Re: [R] Tcl\tk not supported on this system

This is covered in the "R Installation and Administration" manual. You need to specify the location of your tclConfig.sh and tkConfig.sh files. Patrick Richardson Biostatistician - Laboratory of Translational Medicine Van Andel Research Institute Gra

Re: [R] Test of Homogeneity of Variances

What are your hypotheses? Once you state what they are, interpretation should be straightforward. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Daren Tan Sent: Friday, August 22, 2008 11:18 AM To: [EMAIL PROTECTED] Subject: [R] Test of Homogeneity of

Re: [R] XP/Vista/Office 2007/IE Compatibility question

http://cran.r-project.org/bin/windows/base/rw-FAQ.html (for the first two questions anyway) _ Patrick Richardson Biostatistician - Program of Translational Medicine Van Andel Research Institute - Webb Lab 333 Bostwick Avenue NE Grand Rapids, MI 49503

Re: [R] Help understanding lrm function of Design library

I found Professor Harrell's book answered most of my questions as it contains discussion of both Hmisc and Design libraries . http://www.amazon.com/Regression-Modeling-Strategies-Frank-Harrell/dp/0387952322/ref=sr_1_2?ie=UTF8&qid=1250596657&sr=8-2 Patrick -Original Message- From: r-help-

[R] Transform data for repeated measures

I have a dataset that I'm trying to rearrange for a repeated measures analysis: It looks like: patient basefev1 fev11h fev12h fev13h fev14h fev15h fev16h fev17h fev18h drug 201 2.46 2.68 2.76 2.50 2.30 2.14 2.40 2.33 2.20a 202 3.50 3.95 3.65 2.93 2.53 3.04

[R] Error message in Design library

This was working a few weeks ago, but perhaps the package has been updated since then. model.1 <- lrm(response ~ p_value, data=c_abl_oncogene_1_RTK) When I run the following command . . . . prediction.1 <- predict(model.1, type=c("fitted")) I get the following error message. . . . Error in predi

Re: [R] Bartlett Test

?bartlett.test >From the help page "If x is a list, its elements are taken as the samples or >fitted linear models to be compared for homogeneity of variances. In this >case, the elements must either all be numeric data vectors or fitted linear >model objects, g is ignored, and one can simply u

Re: [R] Normal distribution

?shapiro.test -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Noela Sánchez Sent: Thursday, October 01, 2009 12:47 PM To: r-help@r-project.org Subject: [R] Normal distribution Hi, I am dealing with how to check in R if some data

Re: [R] Normal distribution

Sent: Thursday, October 01, 2009 1:18 PM To: Richardson, Patrick Cc: Noela Sánchez; r-help@r-project.org Subject: Re: [R] Normal distribution Hi, I think you can also use a qq-plot to do the same, no? You won't get a statistic score + p.value, but perhaps you're more of a visual person? :-)

[R] Greater than less than in "ifelse"

I'm trying to categorize a continuous variable (yes, I know that's horrible, but I'm trying to reproduce some exercises from a textbook) and don't really know an efficient way to do this. I have a data frame that looks like: surv_time relapse sex log_WBC rx 1 35 0 11.45

Re: [R] Warning message when Loading package svMisc in R 2.10.0

svMisc was built and submitted to CRAN under 2.9.2. If you are trying to use it within TINN, TINN will still work. The package needs to be built under 2.10 and resubmitted. I'm sure Phillipe will get to it in due time. Best regards, Patrick -Original Message- From: r-help-boun...@r-pr

[R] Setting Repositories in the .Rprofile file

Is there any way to select (during startup) all repositories by modifying the Rprofile.site file? If so, could someone let me know the syntax to use (or direct me to where I can find it)? Thank you, Patrick This email message, including any attachments, is for th...{{dropped:9}}

Re: [R] how to import data from excel to R

Well, first of all it doesn't look like you're trying to read an excel file as the file you are trying you specify is "data.txt" not "data.xls". Try: library(gdata) ?read.xls HTH, Patrick -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On

Re: [R] glm fit

Interesting. Now the fifth homework question you have posted here. As was stated before (by several members) this is not a homework forum. Patrick -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of mathallan Sent: Friday, May 08, 2

Re: [R] Why can't I use ADF.test?

Since you provided no code, the following is just a guess, Try: install.packages("uroot") library(uroot) Then try your analysis again. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of DongHongwei Sent: Wednesday, June 24, 2009 3:

Re: [R] install.package("TinnR") - there is no package called 'TinnR'

Hi Martin, If all else fails, you could download the package from http://cran.r-project.org/web/packages/TinnR/index.html and install as a .zip file from within R. That is bizarre that R cannot find the package. I've had no problems downloading and installing. Best regards, Patrick -

[R] Separating variables in read.table

If I have a table (we'll call it, "test") containing two columns (as below): i x1 x2 x3 x4 x5 y 0 1.125 0.232 7.160 0.0859 8.905 1.5563 7 0.920 0.268 8.804 0.0865 7.388 0.8976 15 0.835 0.271 8.108 0.0852 5.348 0.7482 22 1.000

[R] Separating variables in read.table

If I have a table (we'll call it, "test") containing seven columns (as below): i x1 x2 x3 x4 x5 y 0 1.125 0.232 7.160 0.0859 8.905 1.5563 7 0.920 0.268 8.804 0.0865 7.388 0.8976 15 0.835 0.271 8.108 0.0852 5.348 0.7482 22 1.000

Re: [R] Separating variables in read.table

] Separating variables in read.table Richardson, Patrick [Fri, Apr 17, 2009 at 09:31:35PM CEST]: > If I have a table (we'll call it, "test") containing seven columns (as below): > > i x1 x2 x3 x4 x5 y > 0 1.125 0.232 7.160 0.0859

Re: [R] Rhelp

Please read the posting guide at http://www.R-project.org/posting-guide.html and repost your question. You have not provided the information need to properly address your difficulties. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf

[R] Cannot update.packages (error message)

When trying to update (various) packages using update.packages() I get the following error message for various packages package 'fBasics' successfully unpacked and MD5 sums checked Error in unpackPkg(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib) : malformed bundle DESCRIPTION file, no Contains f

[R] R-2.9.0 malformed bundle DESCRIPTION file, no Contains field

When trying to update (various) packages using update.packages() I get the following error message for various packages package 'fBasics' successfully unpacked and MD5 sums checked Error in unpackPkg(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib) : malformed bundle DESCRIPTION file, no Contai

Re: [R] Cannot update.packages (error message)

e- From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de] Sent: Tuesday, April 28, 2009 10:01 AM To: Richardson, Patrick Cc: r-help@r-project.org Subject: Re: [R] Cannot update.packages (error message) Richardson, Patrick wrote: > When trying to update (various) packages using update.p

Re: [R] Cannot update.packages (error message)

e, no Contains field > Best regards, Patrick -Original Message- From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de] Sent: Tuesday, April 28, 2009 11:01 AM To: Richardson, Patrick Cc: r-help@r-project.org Subject: Re: [R] Cannot update.packages (error message) Richardson,

Re: [R] Kolmogorov-Smirnov test

This is the third homework question you have asked the list to do for you. How many more should we expect? The posting guide is pretty clear in that: " Basic statistics and classroom homework: R-help is not intended for these." -Original Message- From: r-help-boun...@r-project.org [m

[R] Variable Combinations in Regression

Let's say I have 8 variables and I want to generate all combinations of those variables (In pairs, threes fours, etc) to run in multiple linear regression. Is there a built-in function to do that in R? Or at a minimum, how could I take those variables and generate all possible combinations. Th

[R] Selective Plot Color

Is there a way (with a simple plot) to select all observations greater than a certain value and plot them with a different color than the rest of the observations in the plot? (i.e. for all observations greater than 10, I want to plot them in red, but the rest of the observations remain black. W

[R] Multiple Ploting Colors

I'm trying to use multiple plotting colors in my code. My first "ifelse" statement successfully does what I want. However, now I want anything less than -4.5 to be green and the rest black. I want another "col" argument but can only use one. How could I go about getting separate colors for anyth

Re: [R] Multiple Ploting Colors

Steve, That worked perfectly. Thank You! Best regards, Patrick -Original Message- From: Steve Lianoglou [mailto:mailinglist.honey...@gmail.com] Sent: Monday, July 12, 2010 12:55 PM To: Richardson, Patrick Cc: r-help@r-project.org Subject: Re: [R] Multiple Ploting Colors Hi, On Mon

Re: [R] Extreme Value Regression model

Well, RSiteSearch("extreme value regression) turns up quite a few relevant posts including one on package "XReg". . . for extreme value regression. Patrick -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Shubha Vishwanath Karanth

Re: [R] Intel i7 utilization

Costas, Take a look at this post that I found to be very helpful. The walkthrough is very easy to follow. http://psyccomputing.blogspot.com/2010/04/compiling-64-bit-r-2101-with-mkl-in.html I'm not sure if the i7 is supported however you can always replace export FFLAGS="-march=core2 -O3" export

Re: [R] how to analyze time series structures?

would you like coffee with that? From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of ensark [EMAIL PROTECTED] Sent: Sunday, June 01, 2008 5:30 PM To: r-help@r-project.org Subject: [R] how to analyze time series structures? hı, I am preparing undergrad

Re: [R] print and read.table commands

?read.table And don't forget the " at the end of your filename HTH -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Adams Sent: Monday, June 02, 2008 2:34 PM To: r-help@r-project.org Subject: [R] print and read.table commands Hello to everyone, I

Re: [R] samr result

Could you post your code so we can see what you are trying to do? Thanks, Patrick From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Eleni Christodoulou [EMAIL PROTECTED] Sent: Tuesday, June 10, 2008 11:20 AM To: r-help@r-project.org Subject: [R] sam

Re: [R] p-value

Something like. . . > midpoint <- c(132968364, 135945080, 156539568, 157817896, + 162399496, 168344072, 173146584, 176302744, + 182878168, 183946152, 185068720, 190791232, + 84317660, 93708872, 106810172, 12684, + 148519056, 150945112, 155771432, 181069984, + 87104384 + ) > shapiro.test(

Re: [R] 3D histogram

Try ?hist -and- ?plot.histogram You should find what you need there. Cheers, Patrick -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of sumit gupta Sent: Friday, June 20, 2008 8:46 AM To: r-help@r-project.org Subject: [R] 3D histogram Hii.. Could anyo

Re: [R] 3D histogram

Actually, have a look at the rgl package and this link http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/r/3d_bar_chart/ It points to bar charts, but there is some valuable info on 3D histograms as well. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED

Re: [R] Insurance data in library(MASS)

Try ?relevel -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of choonhong ang Sent: Tuesday, February 24, 2009 2:33 PM To: r-help@r-project.org Subject: Re: [R] Insurance data in library(MASS) Hi, In the result shown, the District

Re: [R] Sort help

http://www.ats.ucla.edu/stat/R/faq/sort.htm A great tutorial about sorting data in R. HTH, _ Patrick Richardson Biostatistician - Program of Translational Medicine Van Andel Research Institute - Webb Lab Grand Rapids, MI 49503 -Original Message-

Re: [R] read SAS file

Did you load the "foreign" library first? Try: library(foreign) read.xport("cft2008R") HTH, Patrick -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of b g Sent: Monday, November 10, 2008 1:29 PM To: r-help@r-project.org Subject: [R] read SAS file Looke

[R] Legend Position

List, Is there any way to specify the position of the legend from within the following code? If so, how can I do it. As it stands it in the bottom left corner and I want to move it to the top right. I'm not sure if I can use the default "plot" or if I need to go with the lattice package. Sugg

[R] Dendrogram labels

Is there any way to change the orientation of the labels on the end of the dendrograms to horizontal rather than vertical? If so, how can I do that. _ Patrick Richardson Biostatistician - Program of Translational Medicine Van Andel Research Institute

[R] Dendrogram labels

Is there any way to change the orientation of the labels on the end of the dendrograms to horizontal rather than vertical? If so, how can I do that. Below is my code, but I'm not sure which argument(s) I can use to change the label(s) (if it is possible to do). a <- hclust(z, method = "comple

Re: [R] Dendrogram labels

ional Medicine Van Andel Research Institute - Webb Lab 333 Bostwick Avenue NE Grand Rapids, MI 49503 ph. 616.234.5787 -Original Message- From: Fan Yang [mailto:[EMAIL PROTECTED] Sent: Friday, November 21, 2008 2:28 PM To: Richardson, Patrick Cc: 'r-help@r-project.org' Subject: Re:

[R] Comparing survival curves with "survdiff" "strata" help

ExpeRts, I'm trying to compare three survival curves using the function "survdiff" in the survival package. Following is my code and corresponding error message. > survdiff(Surv(st_months, status) ~ strata(BOR), data=mydata) Error in survdiff(Surv(st_months, status) ~ strata(BOR), data = mydata)

[R] Comparing survival curves with "survdiff" "strata" help

ExpeRts, I'm trying to compare three survival curves using the function "survdiff" in the survival package. Following is my code and corresponding error message. > survdiff(Surv(st_months, status) ~ strata(BOR), data=mydata) Error in survdiff(Surv(st_months, status) ~ strata(BOR), data = mydata)

[R] Clustering with Mahalanobis Distance

Dear R ExpeRts, I'm having memory difficulties using mahalanobis distance to trying to cluster in R. I was wondering if anyone has done it with a matrix of 6525x17 (or something similar to that size). I have a matrix of 6525 genes and 17 samples. I have my R memory increased to the max and am

[R] Error message when starting TINN-R

When R starts I get the following error message Warning message: In grep(paste("[{]TclEval ", topic, "[}]", sep = ""), tclvalue(.Tcl("dde services TclEval {}")), : argument 'useBytes = TRUE' will be ignored Has anyone else run into this issue and is there any way to can fix this? Thanks, Patri

Re: [R] Error message when starting TINN-R

ember 12, 2008 9:34 AM To: Richardson, Patrick Cc: 'r-help@r-project.org' Subject: Re: [R] Error message when starting TINN-R And the *Error* message was (that was a warning)? The warning comes from some contributed code, probably in Tinn-R. Please find out where it is and ask the maint