Re: [R] what to do if residuals produced by lm() have long tails?

2007-11-29 Thread Prof Brian Ripley
On Thu, 29 Nov 2007, tom soyer wrote: > Hi, > > I am using lm() for regression analysis of my data set. My regression > results look pretty good, i.e., the coefficient is significant and the p > value is much less than 0.05. But when I checked the residuals, both using > qqnorm() and hist(), the d

[R] what to do if residuals produced by lm() have long tails?

2007-11-29 Thread tom soyer
Hi, I am using lm() for regression analysis of my data set. My regression results look pretty good, i.e., the coefficient is significant and the p value is much less than 0.05. But when I checked the residuals, both using qqnorm() and hist(), the distribution does not look normal. It looks like t

Re: [R] vector sprintf argument

2007-11-29 Thread Christos Hatzis
According to the help page sprintf will recycle its arguments: The arguments (including fmt) are recycled if possible a whole number of times to the length of the longest, and then the formatting is done in parallel. Therefore the following works: > sprintf("Number: %d", A) [1] "Number: 3" "Nu

Re: [R] vector sprintf argument

2007-11-29 Thread Moshe Olshansky
The only thing I can think of is: > a <- c(1,2.7,5.19) > F<-c("numeric: %d ","%g ","%8.3f") > x<-sapply(1:length(a),function(i) sprintf(F[i],a[i])) > y<-paste(x,sep="",collapse="") But I am sure that you will get a better advice elsewhere. --- Tom Sgouros <[EMAIL PROTECTED]> wrote: > > Hello

Re: [R] main plot title

2007-11-29 Thread Rolf Turner
On 30/11/2007, at 4:53 PM, marciarr wrote: > > Hello Rolf, > I am sorry for the incovenience. Well, here it goes again! > Let's say, I have a time series for the variable Chl. I wrote a > function > "pgram" that gives me the raw periodogram of the time series. So, this > function uses the value

Re: [R] main plot title

2007-11-29 Thread jim holtman
The answer is exactly the same: deparse(substitute(x)) go to the help page on 'deparse' On Nov 29, 2007 10:53 PM, marciarr <[EMAIL PROTECTED]> wrote: > > Hello Rolf, > I am sorry for the incovenience. Well, here it goes again! > Let's say, I have a time series for the variable Chl. I wrote a fu

Re: [R] main plot title

2007-11-29 Thread marciarr
Hello Rolf, I am sorry for the incovenience. Well, here it goes again! Let's say, I have a time series for the variable Chl. I wrote a function "pgram" that gives me the raw periodogram of the time series. So, this function uses the values of my time series in an algorithm that gives me new x and

[R] using color coded colorbars for bar plots

2007-11-29 Thread James.Dell
Hello R Fundi, The poetic title of this post is a request for help in regard to a "simple" plotting question. I have displayed the mean observations of a series variables using barplot(). On the same figure I have colored the bars to represent the Standard deviation of each variable us

Re: [R] main plot title

2007-11-29 Thread Rolf Turner
On 30/11/2007, at 3:53 PM, marciarr wrote: > > Hi Jim, > Thanks for your answer. > Unfortunately, because the x of my plot function is not actually > waht I need > on my graph's title, your advice does not work. Thanks anyway, > Marcia Jim answered the question you asked. If his advice didn't

Re: [R] main plot title

2007-11-29 Thread marciarr
Hi Jim, Thanks for your answer. Unfortunately, because the x of my plot function is not actually waht I need on my graph's title, your advice does not work. Thanks anyway, Marcia jholtman wrote: > > hopefully this will help you: > > mydata <- 1:10 > my.plot <- function(x) plot(x, main=paste('da

Re: [R] The R Book - great resource for R beginners

2007-11-29 Thread Tom La Bone
IMHO "The R Book" is far better than indicated in that review and should be near the top of the list for beginners looking for a "manual" for R. Tom Katharine Mullen wrote: > > It was reviewed in the most recent R News > (http://www.r-project.org/doc/Rnews/Rnews_2007-2.pdf). > > On Thu, 29 No

Re: [R] vector sprintf argument [SEC=UNCLASSIFIED]

2007-11-29 Thread Crombie, Joe
Hi Tom, Try this: > G <- "Number: %s" > sprintf(G, toString(A)) [1] "Number: 3, 4, 5" Cheers Joe Joe Crombie Biosecurity and Information Sciences Bureau of Rural Science Canberra Australia p: +61 2 6272 5906 e: [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] [mai

Re: [R] MS Excel Data

2007-11-29 Thread Gabor Grothendieck
Or even: clip <- function() read.delim("clipboard", header = is.na(suppressWarnings(as.numeric(scan("clipboard", "", 1) On Nov 29, 2007 7:51 PM, <[EMAIL PROTECTED]> wrote: > Here is a very crude function I use quite often. It tries to recognize > whether you have headers or not by checking

Re: [R] configure the margin of the plot

2007-11-29 Thread Wang, Zhaoming (NIH/NCI) [C]
It looks much better now! Thanks Jim!! -Original Message- From: jim holtman [mailto:[EMAIL PROTECTED] Sent: Thursday, November 29, 2007 7:29 PM To: Wang, Zhaoming (NIH/NCI) [C] Cc: r-help@r-project.org Subject: Re: [R] configure the margin of the plot try this: layout(cbind(1,2)) par(m

Re: [R] main plot title

2007-11-29 Thread jim holtman
hopefully this will help you: mydata <- 1:10 my.plot <- function(x) plot(x, main=paste('dataset =', deparse(substitute(x my.plot(mydata) On Nov 29, 2007 9:05 PM, marciarr <[EMAIL PROTECTED]> wrote: > > Dear R users, > I am having a problem with the main title of a plot. I have written a > fu

[R] main plot title

2007-11-29 Thread marciarr
Dear R users, I am having a problem with the main title of a plot. I have written a function returning a plot and I would like that the main title of this plot shows actually the name of the dataset I have used. So, for instance: if my dataset is called Chl, I would like that my plot to be entitle

Re: [R] The R Book - great resource for R beginners

2007-11-29 Thread Katharine Mullen
It was reviewed in the most recent R News (http://www.r-project.org/doc/Rnews/Rnews_2007-2.pdf). On Thu, 29 Nov 2007, Robert Harris wrote: > Hi all, > > I've recently discovered "The R Book" by Micheal J. Crawley. I am new to R > and I am finding it incredibly useful. > > With my background in m

[R] vector sprintf argument

2007-11-29 Thread Tom Sgouros
Hello all: If I have a vector and a format, I want to do this: > A <- c(3,4,5) > F <- "Number: %d, %d, %d" > sprintf(F,A) This doesn't work because A isn't three arguments, it's just one. Is there a way to peel the vector members out of A so that sprintf can get at them? I would like to do

Re: [R] MS Excel Data

2007-11-29 Thread apjaworski
Here is a very crude function I use quite often. It tries to recognize whether you have headers or not by checking the very first character. If it is numeric, it assumes that there are no headers. The suppressWarnings gets rid of a warning one gets when trying to coerce a character to numeric.

[R] The R Book - great resource for R beginners

2007-11-29 Thread Robert Harris
Hi all, I've recently discovered "The R Book" by Micheal J. Crawley. I am new to R and I am finding it incredibly useful. With my background in math and programming, I expected that I would be able to pick it up quickly, but even after reading several other intro books, I found it was still ha

[R] Controlling Postscript output, size and orientation

2007-11-29 Thread Nathan Vandergrift
I'm trying to get my graphics so that I can use them in LaTeX to create (via ) a pdf presentation. I've tried controlling inner and outer margins and figure size using par(), to no avail. The ps output keeps appearing as a portrait page with a centered figure. Nothing I have been able to do so fa

Re: [R] MS Excel Data

2007-11-29 Thread Bert Gunter
Better yet! Thanks Gabor. -- Bert -Original Message- From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] Sent: Thursday, November 29, 2007 12:10 PM To: Bert Gunter Cc: r-help@r-project.org Subject: Re: [R] MS Excel Data On Nov 29, 2007 3:01 PM, Bert Gunter <[EMAIL PROTECTED]> wrote: > Th

Re: [R] configure the margin of the plot

2007-11-29 Thread jim holtman
try this: layout(cbind(1,2)) par(mar=c(4,4,2,0)) plot(0) par(mar=c(4,0,2,0)) plot(0, yaxt='n', ylab='') On Nov 29, 2007 5:41 PM, Wang, Zhaoming (NIH/NCI) [C] <[EMAIL PROTECTED]> wrote: > I'm trying to put two plots side-by-side in two panels. Since the > y-axis of the two plots is the same, I w

Re: [R] List operations in R

2007-11-29 Thread Rolf Turner
?unname ?unlist cheers, Rolf Turner On 30/11/2007, at 1:07 PM, Srinivas Iyyer wrote: > hello: > > I am very confused when it comes to list operations in > R. > > I seek help in the following problem. > > I have two different vectors > > myIDs - a character vector with no

Re: [R] List operations in R

2007-11-29 Thread jim holtman
To remove the 'names': > x2 <- c('1001_a'='123', '1002_b'='345') > x2 1001_a 1002_b "123" "345" > names(x2) <- NULL > x2 [1] "123" "345" > To append: > z <- letters[1:4] > z [1] "a" "b" "c" "d" > z <- c(z,x2) > z [1] "a" "b" "c" "d" "123" "345" > On Nov 29, 2007 7:07 PM, Srinivas

[R] List operations in R

2007-11-29 Thread Srinivas Iyyer
hello: I am very confused when it comes to list operations in R. I seek help in the following problem. I have two different vectors myIDs - a character vector with no names to their elements x2 - another character vector derived from unlisting a list where an element has both a name and value

[R] configure the margin of the plot

2007-11-29 Thread Wang, Zhaoming (NIH/NCI) [C]
I'm trying to put two plots side-by-side in two panels. Since the y-axis of the two plots is the same, I want to leave out the y-axis of the second plot. And the two plots look quite separate from each other. Is there any way to have them stay closer to each other? I've tried to adjust mar o

Re: [R] How can R be used to solve algebra equations?

2007-11-29 Thread Sundar Dorai-Raj
francogrex said the following on 11/29/2007 1:00 PM: > suppose I have this equation: > (x^2+y^2+3z^3)/(5*z^2*x^3)=0 > > and I want to find x in relation to the other variables which actually is: > > x=sqrt(-3*z^3-y^2) or x=-sqrt(-3*z^3-y^2) > > Can R give me this expression solution? I know th

Re: [R] How to align the text in the legend

2007-11-29 Thread Wang, Zhaoming (NIH/NCI) [C]
Thanks Jim! And it does work!! Zhaoming -Original Message- From: jim holtman [mailto:[EMAIL PROTECTED] Sent: Thursday, November 29, 2007 5:26 PM To: Wang, Zhaoming (NIH/NCI) [C] Cc: r-help@r-project.org Subject: Re: [R] How to align the text in the legend try this when plotting the leg

Re: [R] How can R be used to solve algebra equations?

2007-11-29 Thread Daniel Lakeland
On Thu, Nov 29, 2007 at 01:00:59PM -0800, francogrex wrote: > > suppose I have this equation: > (x^2+y^2+3z^3)/(5*z^2*x^3)=0 > > and I want to find x in relation to the other variables which actually is: > > x=sqrt(-3*z^3-y^2) or x=-sqrt(-3*z^3-y^2) > > Can R give me this expression solution? I

Re: [R] How to align the text in the legend

2007-11-29 Thread jim holtman
try this when plotting the legend: plot(...) par(family='mono') legend('topright', legend=) This should use fixed width fonts for your legend. On Nov 29, 2007 4:20 PM, Wang, Zhaoming (NIH/NCI) [C] <[EMAIL PROTECTED]> wrote: > Can you give me a little more in detail? I'm new to this. > Thank

Re: [R] How can R be used to solve algebra equations?

2007-11-29 Thread Gabor Grothendieck
Yes, try this: > library(Ryacas) Loading required package: XML > x <- Sym("x") > y <- Sym("y") > z <- Sym("z") > Solve((x^2+y^2+3*z^3)/(5*z^2*x^3)==0, x) [1] "Starting Yacas!" expression(list(x == root(-(4 * (y^2 + 3 * z^3)), 2)/2, x == -root(-(4 * (y^2 + 3 * z^3)), 2)/2)) On Nov 29, 2007

Re: [R] How can R be used to solve algebra equations?

2007-11-29 Thread Søren Højsgaard
The Ryacas package might be able to do it... Søren Fra: [EMAIL PROTECTED] på vegne af francogrex Sendt: to 29-11-2007 22:00 Til: r-help@r-project.org Emne: [R] How can R be used to solve algebra equations? suppose I have this equation: (x^2+y^2+3z^3)/(5*z^2*x^

Re: [R] extracting items from R objects and using them in \Sexpr with Sweave--problem with $

2007-11-29 Thread Charles C. Berry
On Thu, 29 Nov 2007, Christopher W. Ryan wrote: > Running R 2.5.1 on WinXP with Tinn-R, and using Sweave via MikTex. > > I am having trouble with the code below: > > > --- > <>= > lowerCI95713 <- t.test(data713, alternative="greater") > lowerCI95

Re: [R] How to align the text in the legend

2007-11-29 Thread Wang, Zhaoming (NIH/NCI) [C]
Can you give me a little more in detail? I'm new to this. Thanks Zhaoming -Original Message- From: jim holtman [mailto:[EMAIL PROTECTED] Sent: Thursday, November 29, 2007 4:05 PM To: Wang, Zhaoming (NIH/NCI) [C] Cc: r-help@r-project.org Subject: Re: [R] How to align the text in the legen

Re: [R] How to align the text in the legend

2007-11-29 Thread jim holtman
Have you tried a non-proportional font like Courier? On Nov 29, 2007 12:14 PM, Wang, Zhaoming (NIH/NCI) [C] <[EMAIL PROTECTED]> wrote: > Hello, > > > > I tried to align lines of text in the legend of a plot. It always > defaults to the central alignment. How can I adjust it to be left > alignmen

[R] How can R be used to solve algebra equations?

2007-11-29 Thread francogrex
suppose I have this equation: (x^2+y^2+3z^3)/(5*z^2*x^3)=0 and I want to find x in relation to the other variables which actually is: x=sqrt(-3*z^3-y^2) or x=-sqrt(-3*z^3-y^2) Can R give me this expression solution? I know there is uniroot, but here I want the "expression" not the value, becaus

Re: [R] How to align the text in the legend

2007-11-29 Thread Wang, Zhaoming (NIH/NCI) [C]
Thanks Petr! I checked both of your suggestions and nothing seems working for me. I don't understand why the well-formatted text string got re-aligned in the legend of plot. This is what I got: Quantitles #Samples 1002759 95 121 50 0 And here is what I'

Re: [R] R as server application

2007-11-29 Thread kchine
Dear Kilian, The most advanced set of tools and frameworks for using R in Server mode has been developed as part of the biocep project: http://www.ebi.ac.uk/microarray-srv/frontendapp/ by using biocep, R can be run as an RMI server exposing a very rich set of remotly accessible methods. you can th

Re: [R] Wireframe graph: black and white shading instead of color

2007-11-29 Thread Deepayan Sarkar
On 11/29/07, David Afshartous <[EMAIL PROTECTED]> wrote: > > > All, > > The code below produces a color 3D graph. I'd like to make it black and > white shading. I tried setting col.regions to FALSE but this just made it > completely white. I want the graph to look exactly as is, except black (or

Re: [R] Anova(car) SS digits

2007-11-29 Thread Tyler Smith
On 2007-11-29, John Fox <[EMAIL PROTECTED]> wrote: > > Anova() creates an object of class "anova" which then gets printed by the > print method for "anova" objects. The reason that the sums of squares for > the type II tests are rounded like this is because of the large value for > the intercept. A

Re: [R] Anova(car) SS digits

2007-11-29 Thread John Fox
Dear Tyler, > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Tyler Smith > Sent: Thursday, November 29, 2007 2:07 PM > To: [EMAIL PROTECTED] > Subject: [R] Anova(car) SS digits > > Hi, > > When I use Anova(car) to produce type III SS, 'Sum Sq' is r

Re: [R] MS Excel Data

2007-11-29 Thread Gabor Grothendieck
On Nov 29, 2007 3:01 PM, Bert Gunter <[EMAIL PROTECTED]> wrote: > This has been discussed on this list many times before. Google on "Import > Excel R". Note also that there are potential problems (loss of digits) due > to Excel "idiosyncracies" depending on what you do. > http://www.burns-stat.com/

Re: [R] MS Excel Data

2007-11-29 Thread Bert Gunter
This has been discussed on this list many times before. Google on "Import Excel R". Note also that there are potential problems (loss of digits) due to Excel "idiosyncracies" depending on what you do. http://www.burns-stat.com/pages/Tutor/spreadsheet_addiction.html provides some details. Finally,

Re: [R] error in utils:::menuInstallPkgs() for R 2.6.1

2007-11-29 Thread Uwe Ligges
Monica Pisica wrote: > Hi, > > I have upgraded on Windows from R 2.5.1 to R2.6.1 and when i've tried to > install packages with utils:::menuInstallPkgs() i've got the following error > (which i never got before) > > Warning: unable to access index for repository > http://cran.hostingzero.c

Re: [R] Question on structuring variances using the lme4 package

2007-11-29 Thread Dieter Menne
Catherine A. Holt u.washington.edu> writes: > I am modeling the effects of an environmental variable (X) on fish recruitment (Y) for several, > ecologically related species (i) using a mixed-effects model. The linear relationship between X and Y > includes a fixed effect that is common across all

[R] extracting items from R objects and using them in \Sexpr with Sweave--problem with $

2007-11-29 Thread Christopher W. Ryan
Running R 2.5.1 on WinXP with Tinn-R, and using Sweave via MikTex. I am having trouble with the code below: --- <>= lowerCI95713 <- t.test(data713, alternative="greater") lowerCI95713.bound <- lowerCI95713$conf.int[1] @ Thus a lower 95\% confi

[R] Wireframe graph: black and white shading instead of color

2007-11-29 Thread David Afshartous
All, The code below produces a color 3D graph. I'd like to make it black and white shading. I tried setting col.regions to FALSE but this just made it completely white. I want the graph to look exactly as is, except black (or grey) and white shading. Is this possible? Cheers, David p.list

[R] error in utils:::menuInstallPkgs() for R 2.6.1

2007-11-29 Thread Monica Pisica
Hi, I have upgraded on Windows from R 2.5.1 to R2.6.1 and when i've tried to install packages with utils:::menuInstallPkgs() i've got the following error (which i never got before) Warning: unable to access index for repository http://cran.hostingzero.com/bin/windows/contrib/2.6 Do you have

[R] Anova(car) SS digits

2007-11-29 Thread Tyler Smith
Hi, When I use Anova(car) to produce type III SS, 'Sum Sq' is reported in integers: > Anova(bot.lm3, type ="III") Anova Table (Type III tests) Response: bottemp Sum Sq DfF value Pr(>F) (Intercept) 45295 1 29436.4440 < 2e-16 fungroup

Re: [R] Working with time series class object

2007-11-29 Thread Antonio , Fabio Di Narzo
tendencias.com.br> writes: > > > Hi > > I have a daily time series dataset, witch is very irregular spaced. Take a look at package zoo, which has detailed vignette. HTH, Antonio. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailm

[R] fatal error from R function "gls"

2007-11-29 Thread Maura E Monville
I would appreciate some help with the followiing error ... what did I do wrong and what is the woraroud. > library(nlme) > glmod <- gls(A ~ T +cosP +cos2P +cos4P +cos5P +sin3P +sin5P +cosP2 +sinP3 +P2, correlation=corAR1(),method="ML") Error: cannot allocate vector of size 491.3 Mb I have a bunc

Re: [R] image() plot with z not in matrix format

2007-11-29 Thread Julian Burgos
Hello Marc, Well, image() requires data values in a regular grid. So you need to interpolate your data to a regular grid before you do your plot. There are many interpolation methods, but a good place to start is to do linear interpolation. You should first use expand.grid() to create the r

Re: [R] MS Excel Data

2007-11-29 Thread AA
The package RODBC by Pr. Ripley is very helpful for this (Thanks To B. Ripley). Also see the package xlsReadWrite (thanks to H.P Suter). The latter is maybe easier to use. Good luck AA. - Original Message - From: "faisal afzal siddiqui" <[EMAIL PROTECTED]> To: Sent: Wednesday, November 2

Re: [R] How to take the ave of two rows in a data frame

2007-11-29 Thread aaront
Would ?aggregate help? affy snp wrote: > >> Dear list, >> I have a data frame like: >> >> > log2.ratios[1:3,1:4] >>ID a1 a2 a3 >> 1 GS1-232B23 -0.0207500 0.17553833 0.21939333 >> 2 RP11-82D16 -0.1896667 0.02645167 -0.03112333 >> 3

[R] Question on structuring variances using the lme4 package

2007-11-29 Thread Catherine A. Holt
I am modeling the effects of an environmental variable (X) on fish recruitment (Y) for several, ecologically related species (i) using a mixed-effects model. The linear relationship between X and Y includes a fixed effect that is common across all species and random effects that vary by species

[R] How to take the ave of two rows in a data frame

2007-11-29 Thread affy snp
> Dear list, > I have a data frame like: > > > log2.ratios[1:3,1:4] >ID a1 a2 a3 > 1 GS1-232B23 -0.0207500 0.17553833 0.21939333 > 2 RP11-82D16 -0.1896667 0.02645167 -0.03112333 > 3 RP11-62M23 -0.1761700 0.08214500 -0.04877000 > 4

[R] Working with time series class object

2007-11-29 Thread lmiceli
Hi I have a daily time series dataset, witch is very irregular spaced. The data is stored in a text file with the fields; day;month;year;stock1 price; stock2 price;...;stockN price The problem is that a script like described below, will result in a not very useful time count in the

[R] Odp: How to align the text in the legend

2007-11-29 Thread Petr PIKAL
Well, did you look at xjust, yjust options of legend? And maybe it would be worth to check adj graphic parameter see ?par Petr [EMAIL PROTECTED] napsal dne 29.11.2007 18:14:55: > Hello, > > > > I tried to align lines of text in the legend of a plot. It always > defaults to the central alignm

Re: [R] How to manipulate a data frame

2007-11-29 Thread affy snp
Thanks a lot, Petr. Allen On Nov 29, 2007 12:12 PM, Petr PIKAL <[EMAIL PROTECTED]> wrote: > Hi > > I just guess what you want but maybe > > rownames(log2.ratios) <-log2ratios$Clone > > changes rownames and then you could get your output (after getting rid of > first column). > > If you just want

Re: [R] Data sets with usage in documentation object but not in code

2007-11-29 Thread Peter Dalgaard
Prof Brian Ripley wrote: > On Thu, 29 Nov 2007, Jonathan Weeks wrote: > > >> All, >> >> I recently made some changes to my package and ran R CMD check, but I >> am getting a warning regarding my data sets. >> >> I am running R 2.6.1 I have an image (.RData) file containing five >> data sets in t

Re: [R] ftable as latex (with Hmisc?)

2007-11-29 Thread Dieter Menne
Dieter Menne wrote: > I tried to create an ftable lookalike of the following data set in > LaTeX/Sweave > with summary(formula,..), but I could not get it to work for count tables; > numeric tables work fine. > summary(formula,...,fun="table") does not give the full cross breakdown. Frank E

Re: [R] coloring leaves in clustering

2007-11-29 Thread Martin Maechler
> "EC" == Eleni Christodoulou <[EMAIL PROTECTED]> > on Thu, 29 Nov 2007 18:25:46 +0200 writes: EC> Hello everyone, EC> I wanted to know if it was possible to change the color of certain leaves in EC> a hclust object in order to make my graph more readable. I know I can co

[R] How to align the text in the legend

2007-11-29 Thread Wang, Zhaoming (NIH/NCI) [C]
Hello, I tried to align lines of text in the legend of a plot. It always defaults to the central alignment. How can I adjust it to be left alignment? Here is the code fragment written in python using Rpy module: text = 'Quantiles #Loci\n' text += '%s %6d\n' % (' 100',tot

[R] Odp: How to manipulate a data frame

2007-11-29 Thread Petr PIKAL
Hi I just guess what you want but maybe rownames(log2.ratios) <-log2ratios$Clone changes rownames and then you could get your output (after getting rid of first column). If you just want an output to spreadsheet without row names column, look at ?write.table especially row.names option. rega

Re: [R] Data sets with usage in documentation object but not in code

2007-11-29 Thread Prof Brian Ripley
On Thu, 29 Nov 2007, Jonathan Weeks wrote: > All, > > I recently made some changes to my package and ran R CMD check, but I > am getting a warning regarding my data sets. > > I am running R 2.6.1 I have an image (.RData) file containing five > data sets in the data subdirectory and an .Rd file for

Re: [R] How to manipulate a data frame

2007-11-29 Thread Ben Bolker
affy snp wrote: > > Dear list, > I have a data frame like: > >> log2.ratios[1:3,1:4] >Clone a1 a2 a3 > 1 GS1-232B23 -0.0207500 0.17553833 0.21939333 > 2 RP11-82D16 -0.1896667 0.02645167 -0.03112333 > 3 RP11-62M23 -0.1761700 0.082

[R] Bootstrap Correlation Coefficient with Moving Block Bootstrap

2007-11-29 Thread Andreas Klein
Hello. I have got two problems in bootstrapping from dependent data sets. Given two time-series x and y. Both consisting of n observations with x consisting of dependent and y consisting of independent observations over time. Also assume, that the optimal block-length l is given. To obtain my bo

Re: [R] Question about using “par”

2007-11-29 Thread Charilaos Skiadas
On top of which, you should expect a setting of mfrow=c(1,2) like you have to only allow you to put two figures in 1 row and 2 columns. Haris Skiadas Department of Mathematics and Computer Science Hanover College On Nov 29, 2007, at 9:35 AM, Dieter Menne wrote: > cathelf hotmail.com> writes:

Re: [R] str() options

2007-11-29 Thread Thompson, David (MNR)
Beautiful! Exactly what I was looking for. Thank you, Gabor >-Original Message- >From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] >Sent: November 27, 2007 05:02 PM >To: Thompson, David (MNR) >Subject: Re: [R] str() options > >On Nov 27, 2007 1:55 PM, Thompson, David (MNR) ><[EMAIL PROT

[R] coloring leaves in clustering

2007-11-29 Thread Eleni Christodoulou
Hello everyone, I wanted to know if it was possible to change the color of certain leaves in a hclust object in order to make my graph more readable. I know I can color certain groups but I would like to enter a vector telling the plot function which leaves to color in which color. Thanks in adv

Re: [R] re lative importance of predictors

2007-11-29 Thread Ulrike Grömping
Hi Robert, relaimpo does work with a (non-robust) linear model, i.e. calculations in relaimpo are using correlations between variables, and it is not possible to incorporate things like the Huber psi function. I am not an expert on robust regression, but I try to answer your question from the rel

Re: [R] how to read in a txt file with some blanks

2007-11-29 Thread affy snp
Hi Jim, Thanks! The pattern for blanks varies. It could be any of scenarios you outlined. Other folks pointed out the problem can be solved by specifying sep="\t" in read.table(). Best, Allen On Nov 28, 2007 10:12 PM, jim holtman <[EMAIL PROTECTED]> wrote: > The question is what do the 'bl

Re: [R] R as server application

2007-11-29 Thread Scionforbai
I found this link: http://jesus-loves-grass.blogspot.com/search/label/R%20server Which points to RSOAP and Rserver. __ 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.

[R] How to manipulate a data frame

2007-11-29 Thread affy snp
Dear list, I have a data frame like: > log2.ratios[1:3,1:4] Clone a1 a2 a3 1 GS1-232B23 -0.0207500 0.17553833 0.21939333 2 RP11-82D16 -0.1896667 0.02645167 -0.03112333 3 RP11-62M23 -0.1761700 0.08214500 -0.04877000 how to make it to

Re: [R] question about warning message in nlme model

2007-11-29 Thread David Atkins
Hi Christine-- The problem (and error msg) arises because you have repeated measures nested in individuals and *exactly* two individuals in every couple. Your syntax below specifies a random intercept and slope, and implicitly, the covariance between those random-effects at the second (or ind

Re: [R] Re commended textbooks for R?

2007-11-29 Thread Max
Thanks guys for the recomendations! :) aaront wrote on 11/29/2007 : > I am currently using: ---John Maindonald and John Braun. Data Analysis and > Graphics Using R--- and find it very useful, note that there now is a 2007 > edition. > > Most of the texts mentioned in the previous link have revie

Re: [R] Recommended textbooks for R?

2007-11-29 Thread Wensui Liu
my favorite is MASS by B. Ripley. I bought it 6 yrs ago and am still browsing it when I have time. On Nov 28, 2007 10:38 AM, Max <[EMAIL PROTECTED]> wrote: > Hi everyone! > > I've recently begun to learn R for my job as the IT department suffers > from lack of funding for new software. I was talki

Re: [R] library(RII)

2007-11-29 Thread John Kane
You need to provide us with some more information. Please see if you can provide us with a simple example of the problem code as is requested in the posting guide. --- Maria del Carmen olvera <[EMAIL PROTECTED]> wrote: > Dear all > > I'm Manme from Spain. I could not solve one problem > , so

[R] rpvm error when loading

2007-11-29 Thread Lenzo, Antonino
Hello, I get this error when issuing the library command (with rpvm) in R: = Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(rpvm) Error in dyn.load(x, as.logical(loc

[R] relative importance of predictors

2007-11-29 Thread robert . ptacnik
Hei Group, I want to compare the relative importance of predictors in a multiple linear regression y~a+bx1+cx2... However, bptest indicates heteroskedasticity of my model. I therefore perform a robust regression (rlm), in combination with bootstrapping (as outlined in J. Fox, Bootstrapping Regres

Re: [R] Re commended textbooks for R?

2007-11-29 Thread aaront
I am currently using: ---John Maindonald and John Braun. Data Analysis and Graphics Using R--- and find it very useful, note that there now is a 2007 edition. Most of the texts mentioned in the previous link have reviews on Amazon. Jared O'Connell-2 wrote: > > This page may be helpful :) > >

[R] Data sets with usage in documentation object but not in code

2007-11-29 Thread Jonathan Weeks
All, I recently made some changes to my package and ran R CMD check, but I am getting a warning regarding my data sets. I am running R 2.6.1 I have an image (.RData) file containing five data sets in the data subdirectory and an .Rd file for each of the data sets in the man subdirectory. When I r

[R] Listing factor levels for elements of letters in an rpart plot

2007-11-29 Thread Cliff Behrens
I would like to create a list of factor levels represented by elements of letters shown in an rpart plot. It seems that the order of levels for a factor are different than the alphabetized order returned a simple list command, e.g., rpartModel$factor_name. I was also wondering how best to mod

Re: [R] Time Series Issues, Stationarity ..

2007-11-29 Thread John C Frain
Look at the R help files for predict.Arima rather than using forecast to forecast an ARIMA model. You might plot your data and the first difference and you should be able to come to a conclusion about stationarity. With your very small data set you need a very parsimonious model. Knowledge about

Re: [R] Question about using “par”

2007-11-29 Thread Dieter Menne
cathelf hotmail.com> writes: > Sorry for bothering your guys again. I am trying to use "par" to put 6 > figures into 3 rows and 2 columns. My code is: > > op <- par(mfrow = c(1, 2)) > xyplot(x1+x2+x3 ~ y, data=resulta, type="l", pch=LETTERS[1:3], lty=c(1:3), > main="For k=3, theata1=1") > xyplot

Re: [R] Survreg(), Surv() and interval-censored data

2007-11-29 Thread Terry Therneau
The question (slightly rephrased) was Why does survreg(Surv(T.1, T.2, type='interval2') ~1, data=x) fail, when x is T.1 T.2 Status 1 0.000 0.62873036 1 2 0.000 2.07039068 1 3 0.000 1.40297214 1 4 0.000 0.09112871 1 5 0.

[R] [R-pkgs] New versions of the caret (3.08) and caretLSF (1.12) packages

2007-11-29 Thread Kuhn, Max
New versions of the caret (3.08) and caretLSF (1.12) packages have been released. caret (short for "Classification And REgression Training") aims to simplify the model building process. The package has functions for data splitting, pre-processing and model tuning, as well as other miscellaneous f

[R] Doing PCA

2007-11-29 Thread Amit Patel
Hi Fellow R enthusiasts I have managed to reshape my data using a much shorter script than before. Woohoo However now I have new problems. The code is below. There are no problems with the create matrix section. The problem code is highlighted in bold. I am trying to do PCA on the data. Here a

[R] Odp: MS Excel Data

2007-11-29 Thread Petr PIKAL
Hi [EMAIL PROTECTED] napsal dne 29.11.2007 04:54:18: > I am using MS Excel (Windos Operating system), how I > import/export data between MS_Excel and R. What data and how often. There are few options from add on packages through ODBC to copy and paste. If you bother to read any documentation a

[R] [R-pkgs] Package dlm version 0.8-1

2007-11-29 Thread Giovanni Petris
I uploaded a new version of package dlm to CRAN. dlm provides functions for maximum likelihood, Kalman filtering and smoothing, and Bayesian analysis of Gaussian linear state space models, also known as Dynamic Linear Models. The most important visible changes from the previous version are th

Re: [R] MS Excel Data

2007-11-29 Thread Prof Brian Ripley
On Wed, 28 Nov 2007, faisal afzal siddiqui wrote: > I am using MS Excel (Windos Operating system), how I > import/export data between MS_Excel and R. Why not read the 'R Data Import/Export' manual? It ships with R, or can be accessed from http://cran.r-project.org/manuals.html . -- Brian D. R

Re: [R] ggplot2 melt function "value"

2007-11-29 Thread hadley wickham
> > Hi:I recently started using the melt function and > > found that it is very useful and powerful,however I > > can't seem to find the way to change the default > > column header "value" to my custom column name. > > melted data are data frames. You can names[..]<-"myvalue" for renaming, but > m

[R] Question about using “par”

2007-11-29 Thread cathelf
Hi, Sorry for bothering your guys again. I am trying to use "par" to put 6 figures into 3 rows and 2 columns. My code is: op <- par(mfrow = c(1, 2)) xyplot(x1+x2+x3 ~ y, data=resulta, type="l", pch=LETTERS[1:3], lty=c(1:3), main="For k=3, theata1=1") xyplot(x1+x2+x3 ~ y, data=resultb, type="l"

[R] MS Excel Data

2007-11-29 Thread faisal afzal siddiqui
I am using MS Excel (Windos Operating system), how I import/export data between MS_Excel and R. Regds Faisal Afzal SIddiqui +92-300-9297089 [EMAIL PROTECTED] Never miss a thing. Make Yahoo your home page

[R] LOCFIT:Automatic bandwidth selection for kernel regression

2007-11-29 Thread learnerminer
Hello all! I have recently started using the LOCFIT package, together with Clive Loader's book. I need to implement some method for automatic (plug-in) bandwidth selection in a multivariate kernel regression. From the book, and the LOCFIT documentation, it is not clear whether this is possible

[R] Boxplots from lme objects

2007-11-29 Thread CG Pettersson
Dear all! W_XP, R 2.6.0 I am evaluating variety trails over several years, where the different cultivars have not been present in the dataset the same number of years. I use lme{nlme} to fit random effect models and estimable{gmodels} to extract the fixed effects. The general model is: lme(y ~

Re: [R] How to perform Bayesian analysis in R?(corrected)

2007-11-29 Thread Ben Bolker
adilshah wrote: > > Dear Members i'm trying to access different packages used for Bayesian > analysis, but > failed to integrate after making the likelihood of the model the model > like this > a= exp(b)/summation(exp(b)) > where 'b' = half of the natural log of 'a' > please If some one knows

Re: [R] R crashes using quantreg censored estimation (method fcen)

2007-11-29 Thread roger koenker
1. As the posting guide advises, queries about packages should be sent in the first instance to the package author/maintainer before posting to the list. 2. As the posting guide also advises, a _minimal_ reproducible example is desirable not one that claims that somewhere in the middle of 1

[R] empty cells in ftable

2007-11-29 Thread temiz
hello when I enter: ftable(xtabs(cnt~jeo+slp+pcurv+asp+hey),data=dt) it gives a frequncy table. But some cells are empty. like this: 192 72 0 3 68 0 4 99 0 5 110 0

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