[R] best.svm

Hi I am trying to fit an svm to predict speech recognition errors. I am using best.svm like this: svm.model = best.svm(data[1:3000,1:23],data[1:3000,24],tunecontrol = tune.control()) I got this: > print(svm.model) Call: best.svm(x = data[1:3000, 1:23], tunecontrol = tune.control(), dat

Re: [R] 21 CFR Part 11 Compliance and R

21 CFR Part 11 is mostly about data audit trails (tracking changes and electronic signatures) and validation of software. Most of this involves documentation and the creation of documentation LOCALLY at YOUR site, regarding YOUR processes and operating procedures. R satisfies most of what is need

Re: [R] How to convert a character string to a number

Dear Andreas, On May 23, 2005, at 4:56 AM, Kraft, Andreas wrote: Hi everyone, I have a simple problem but don´t know how to solve it. I read in a table from a text file that looks like that: -3,932200E-01 -2,00E-01 4,95E-02 -3,932099E-01 -1,00E-01 3,96E-02 ... -3,9313

RE: [R] Returning from a function

Use invisible(NULL) as the last line. Andy > From: Laura Holt > > Hello again. > > I have a function that plots a series and adds some > interesting items to the > plot. > > Fair enough. > > The last statement in the function is > return() > > When the function is executed, NULL appears a

[R] Returning from a function

Hello again. I have a function that plots a series and adds some interesting items to the plot. Fair enough. The last statement in the function is return() When the function is executed, NULL appears at the end, which is ok. Is there any way to prevent NULL from appearing, or is that just as

Re: [R] website reference for building R packages

it is the first link if you type "making packages" into the google search box here: http://maths.newcastle.edu.au/~rking/R/ -s. Laura Holt wrote: Hi R People: A few weeks ago, someone put a link to a website for "how to" for building R packages. It was very nice. But of course, I have

[R] website reference for building R packages

Hi R People: A few weeks ago, someone put a link to a website for "how to" for building R packages. It was very nice. But of course, I have misplaced the link. Does anyone still have that, please? It was someone from the University of Chicago, I believe. Thanks in advance. Sincerely, La

[R] contourLines() starts a plot device

I want to use contourLines() to get contour line coordinate vectors, but I don't want to make a plot. However contourLines() insists on opening a graphics device. Is there a way tell it not to do this? > version platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-

[R] lme4 package and importIntoEnv errors

I've used packages for some years now and seldom had any trouble using the tgz files. Now I've come across something I've never seen before. > version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major2 minor1.0 year 2005 month

RE: [R] How to break an axis?

I think you may wish to look at the plotrix package, assumming that you have taken care of the issues involved in breaking an axis and that your plots don't result in misleading information. I think to use the axis break you would have to calculate your own labels and rescale the data, as it lo

[R] How to break an axis?

Dear list, I need to plot four almost horizontal lines with y-values around 1,3,4, 400. If I plot them directly, the first three lines will be indiscernible so I am thinking of breaking y-axis into two parts, one with range (0,5), another (395,400). Is there an easy way to do this? I can think of

[R] Re: S4 method inheritance

On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote: > Finally, I'm a bit concerned that one article mentioned that S4 > inheritance, in practice, is used mostly for data, not methods (Thomas > Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I > shouldn't travel? > Hmm, mayb

RE: SV: [R] Documentation of S3 and S4 classes, inheritance

I don't think you quite said what you meant ... > I thought if you wanted C to inherit from A and B you could, in S3, > just >class(aCObject)<- c('C', 'A', 'B') > While the ordering is arbitrary, that's usually the case with multiple > inheritance. > I assume you meant, "I thought if you

RE: [R] R annoyances

Bogdan Romocea <[EMAIL PROTECTED]> wrote: > Hypothetically, if whatever=T/F were forbidden and only > whatever=TRUE/FALSE were allowed, all the code could be fixed with > a simple sed script: [deleted] As Bogdan is lobbying hard for disallowing T/F, I wanted to speak up for the other side. Please

Re: SV: [R] Documentation of S3 and S4 classes, inheritance

On Tue, 2005-05-24 at 00:31 +0200, Søren Højsgaard wrote: > >One of the things that S3 is lacking is clearly multiple inheritance, I thought if you wanted C to inherit from A and B you could, in S3, just class(aCObject)<- c('C', 'A', 'B') While the ordering is arbitrary, that's usually the ca

SV: [R] Documentation of S3 and S4 classes, inheritance

I am sure that I do not have the answer to your question - but I would like to add to your views regarding the S4-issue. I've been involved in the gRbase package for graphical modelling in R. The first version was implemented in S4 but now we have made a roll-back to using S3 methods. While,

Re: [R] comparing glm models - lower AIC but insignificant coefficients

Constantinos Antoniou wrote: Hello, I am a new R user and I am trying to estimate some generalized linear models (glm). I am trying to compare a model with a gaussian distribution and an identity link function, and a poisson model with a log link function. My problem is that while the gau

Re: [R] Documentation of S3 and S4 classes, inheritance

On 5/23/05, Ross Boylan <[EMAIL PROTECTED]> wrote: > I'd like to have a class A that computes a likelihood, and a subclass B > that computes the same likelihood by sometimes throws in an additional > term (B includes measurement error). > > So B's likelihood needs to call A's, and then (sometimes)

Re: [R] Calling R from R and specifying "wait until script is finished"

I don't know about efficient, but here is a way that I find to be practical, with around 100 R scripts. I create a master R script (I call it "Runall.r"). It begins like this: ## Execute me with R --save < Runall.r >& Runall.log hc <- TRUE if (hc) sink('Runall.out') t0runall <- Sys.time() ca

[R] Documentation of S3 and S4 classes, inheritance

I'd like to have a class A that computes a likelihood, and a subclass B that computes the same likelihood by sometimes throws in an additional term (B includes measurement error). So B's likelihood needs to call A's, and then (sometimes) multiply by an additional term. It sounds as if, in the S3

Re: [R] Error handling

On 5/23/05, Carsten Steinhoff <[EMAIL PROTECTED]> wrote: > Hi, > > I have written an R-Procedure that automatically does a ML-Fit for some > datasets to a few > selected distributions. After any optimization the function writes the > estimated parameters into a variable. > My problem is now that s

[R] Error handling

Hi, I have written an R-Procedure that automatically does a ML-Fit for some datasets to a few selected distributions. After any optimization the function writes the estimated parameters into a variable. My problem is now that sometimes the optimization failes and my program stops with an error mes

RE: [R] 21 CFR Part 11 Compliance and R

To further add to and perhaps clarify Frank's remark: 21 CFR Part 11 defines certain requirements for electronics records. A general requirement relevant for statistical software used in submissions is, I presume (quoted): " Persons who use closed systems to create, modify, maintain, or transmi

Re: [R] 21 CFR Part 11 Compliance and R

Richard Haney wrote: I have used S-PLUS, R, MATLAB and SAS for many years, and I am actually quite happy to use any of these four languages. The reason may in part involve my using the various languages for the purposes to which they seem most suited. Hence there are many things for which I

Re: [R] transform normally distributed random terms to gamma distributed random terms

1. The help page for ?rgamma says E(g) = shape*scale = shape/rate and var(g) = shape*scale^2 = shape/rate^2. These are different from what I read in your email. Could you please check the help page more carefully? 2. If this does not solve your problem, PLEASE do read the posting gu

[R] comparing glm models - lower AIC but insignificant coefficients

Hello, I am a new R user and I am trying to estimate some generalized linear models (glm). I am trying to compare a model with a gaussian distribution and an identity link function, and a poisson model with a log link function. My problem is that while the gaussian model has significantly

[R] 21 CFR Part 11 Compliance and R

I have used S-PLUS, R, MATLAB and SAS for many years, and I am actually quite happy to use any of these four languages. The reason may in part involve my using the various languages for the purposes to which they seem most suited. Hence there are many things for which I would not use SAS or

[R] transform normally distributed random terms to gamma distributed random terms

Hi, I have normally distributed random terms u~N(0,1). I want to get gamma distributed random terms g~(scale,shape) with E(g)=1=shape/scale and var(g)=theta=1/scale=1/shape. How can I reach my goal? The following way doesn't work: use the distribution function of u to get U(0,1)- distributed

[R] dist equivalent

Hi, The goal is to use Pearson's Phi coefficient to create a similarity matrix from a matrix. The problem is that the DIST command doesn't do it, and I don't know how manipulate the R language well enough to create a substitute. The question is simple: what is a basic way of using custom formu

Re: [R] installing R and Rcmdr onMacOS 10.3.9

Hi John, It does work on my Mac. I'm helping Karla to get it running on hers. Rob On May 23, 2005, at 11:32 AM, John Fox wrote: Dear Karla, It's likely that you don't have Tcl/Tk installed on your Mac. I know that it's possible to get the Rcmdr working on a Mac, but that doing so require

RE: [R] installing R and Rcmdr onMacOS 10.3.9

Dear Karla, It's likely that you don't have Tcl/Tk installed on your Mac. I know that it's possible to get the Rcmdr working on a Mac, but that doing so requires some additional steps. I'm not a Mac user, so I'm afraid that I can't be of much direct help. If someone who's using the Rcmdr on a Mac

RE: [R] colors and palettes and things...

Dear Jeff, Some time ago, Don McQueen posted to r-help a nice function for displaying the named colours. You'll find it at . As well, if you're using R for Windows, the various named colours are defined in the file rgb.txt in R's etc dire

[R] Left truncation in shared frailty models with time-varying covariates

Hi! I want to estimate a shared gamma frailty model with left truncated data. I use a parametric baseline hazard so that I can use simple ML estimation. As I have a big data set it is ok to assume piecewise constant baseline hazards. As my data are left truncated I have modified the definition

RE: [R] colors and palettes and things...

1. I faced the same issue and came up with the code below. 2. See rainbow(). allcol <- colors() png("Rcolors.png",width=1100,height=3000) par(mai=c(0.4,0.5,0.3,0.2),omi=c(0.2,0,0,0),cex.axis=0.1,pch=15,bg="white") plot(1,1,xlim=c(1,10),ylim=c(1,66),col=allcol[1],cex=4) axis(1,at=NULL,labels=FALSE

[R] Can't reproduce clusplot princomp results.

Dear R folk: Perhaps I'm just dense today, but I am having trouble reproducing the principal components plotted and summarized by clusplot. Here is a brief example using the pluton dataset. clusplot reports that the first two principal components explain 99.7% of the variability. But this is no

[R] installing R and Rcmdr onMacOS 10.3.9

I have been trying to install the new, patched R 2.1.0a along with the Rcmdr on my mac. I got the basic R package installed, but in Project Manager, the tcltk package will not install. When I downloaded the Rcmdr binary package from the Berkeley site, it did not show up on the package inst

RE: [R] colors and palettes and things...

Colors predefined in R follow closely colors predefined in in HTML language. See: http://users.rcn.com/giant.interport/COLOR/1ColorSpecifier.html http://www.brobstsystems.com/colors1.htm http://www.geocities.com/html4kids/colors.htm And probably countless other websites defining them. Jarek

RE: [R] Trouble with drplot

I suppose that was the problem. I had my control values included as concentration of 0. My impression was that if I put "no fit" in the OK column they would be ignored when graphing. However, I guess that is not the case, because when I took them out the plot worked. Thanks a lot. Gene -Or

Re: [R] Backslash

Josef Eschgfaeller wrote: Why sometimes one has to put a double backslash in regular expressions, but often simple backslashes work too? Is only a \ required for giving a metacharacter its usual meaning? The general reason is that both R and grep use \ as an escape character. If you want to s

Re: [R] Trouble with drplot

Does your data (that you want to plot have any "Inf" or "-Inf" values? Ales Ziberna - Original Message - From: <[EMAIL PROTECTED]> To: Sent: Monday, May 23, 2005 5:16 PM Subject: [R] Trouble with drplot Hi, I am a newbie with R, so I hope my question isn't too stupid. I am trying t

[R] colors and palettes and things...

After trying to find if there was a color picker in the FAQs and the help, I thought I would send a post here. I was overwhelmed with all the wonderful color choices R has predefined (discovered after typing in colors()) but can't figure out what they all (by name) look like. Is there a color picke

[R] R Reference Card (especially useful for Newbies)

Newbies (and others!) may find useful the R Reference Card made available by Tom Short and Rpad at http://www.rpad.org/Rpad/Rpad-refcard.pdf or through the "Contributed" link on CRAN (where some other reference cards are also linked). It categorizes and organizes a bunch of R's basic, most used

[R] Trouble with drplot

Hi, I am a newbie with R, so I hope my question isn't too stupid. I am trying to generate dose-response curves using the "drfit" package. I have formatted my CSV files to the correct format, and have no trouble running drfit to get a summary of my data. The problem is that when I try to use "drp

Re: [R] formals or args question

formals() returns a list, so you could try this: a <- function(p, r) p + r names(formals(a)) I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32

Re: [R] formals or args question

Ahh. Thanks a lot! works great. :-p Ales Ziberna wrote: names(formals(fun)) You need the names of the elements of the list formals produces, not their content! Ales Ziberna - Original Message - From: "BJ" <[EMAIL PROTECTED]> To: Sent: Monday, May 23, 2005 4:45 PM Subject: [R] form

Re: [R] formals or args question

names(formals(fun)) You need the names of the elements of the list formals produces, not their content! Ales Ziberna - Original Message - From: "BJ" <[EMAIL PROTECTED]> To: Sent: Monday, May 23, 2005 4:45 PM Subject: [R] formals or args question Hello again, thank you again for

[R] formals or args question

Hello again, thank you again for all of your help. I am trying to get the arguments for a function, in a way that I can handle them. If I do args(fun), it doesnt really do what I want. If I use formals(fun) i get output like: $a $r $s Now, lthis is supposedly a list, but if i say formals

Re: [R] constraints

On Sun, 22 May 2005, Arne Henningsen wrote: constrOptim by two inequality constraints: a - b >= 0 and b - a >= 0 However, I guess that the solver prefers the first way ;-) It is not possible. The starting value must be in the interior of the feasible region (because the constraints are im

Re: [R] comparison operator, decimals, and signif()

On Sat, 21 May 2005, Nick Drew wrote: What does signif() do to my object called "testMean" so that the comparison now evaluates to TRUE? signif(testMean, 3) == 82.9 [1] TRUE It rounds to 3 significant digits. An even more reliable approach is round(testMean*10) == 829 since 829 is an

[R] dse1 package simulate example

Hi, I am trying to use the simulate function in the dse1 package to generate VAR (multivariate) models. I *think* the first example gives a simple VAR(2) time series, here is the code. > AR <- array(c(1, .5, .3, 0, .2, .1, 0, .2, .05, 1, .5, .3) ,c(3,2,2)) > VAR <- ARMA(A=AR, B=diag(1

[R] R 2.1 installation on Mac OS 10.2

Hi, I am trying to install R 2.1 from source on a Mac 10.2.8, Darwin Kernel Version 6.8 According to the FAQ at http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html I proceeded in the following manner: ./configure --with-blas='-framework vecLib' --with-lapack --with-aqua This resulte

Re: [R] Maps, Eastern Europe

Ray Brownrigg wrote: > Unfortunately the world databases for the maps package are very old > (early 1990's) and have not been updated since, except for minor > typographical errors in country names. Note that Czechoslovakia is > there (as is USSR!). Also, it currently satisfies my needs, which i

Re: [R] Dickey-Fuller Test

hello i ammended the code. it was in some package. dont know which? try tseries. this might be of help. adf.test.1<-function (x,kind=3,k = trunc((length(x)- 1)^(1/3))) { #kind = the kind of test undertaken #kind = 1 ==> No constant no trend #kind = 2 ==> Constant #kind = 3 ==> Constant and tre

Re: [R] Dickey-Fuller Test

tseries (adf.test) On Monday 23 May 2005 12:27, Amir Safari wrote: > Hi All , > Could you please tell using which library ,Dickey-Fuller Test can be run? > Thanks a lot > > __ > > > > [[alternative HTML version deleted]] > > __

Re: [R] Dickey-Fuller Test

On Mon, 23 May 2005 03:27:49 -0700 (PDT) Amir Safari wrote: > > > Hi All , > Could you please tell using which library, Dickey-Fuller Test can be > run? Thanks a lot That depends: in which *library* have you installed the tseries *package*? (Look at the archives for the difference between lib

[R] Dickey-Fuller Test

Hi All , Could you please tell using which library ,Dickey-Fuller Test can be run? Thanks a lot __ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.

[R] How to convert a character string to a number

Hi everyone, I have a simple problem but don´t know how to solve it. I read in a table from a text file that looks like that: -3,932200E-01 -2,00E-01 4,95E-02 -3,932099E-01 -1,00E-01 3,96E-02 -3,932000E-01 0,00E+00 3,96E-02 -3,931899E-01

[R] Problem with label name in mosaics plot

Dear all R-help, I have a problem with label name in mosaics plot if I use more 4 variables. Let see with my toy example. library(vcd) toy.mosaics <- array(c(96,44,1,138,64,2,117,56,6,75,48,5,72,49,6,83,60,8,140, 43,1,171,65,4,152,58,9,101,51,9,102,58,10,111,67,16,24,

[R] confidence interval and cross validation

I've obstained the mean square error of prediction, using a 10 fold cross validation for a linear multiple regression model (I've used errortest, from package ipred), how can I calculate the confidence interval? And, could I use test set of cross validation to calculate correlation and concordan

[R] Backslash

Why sometimes one has to put a double backslash in regular expressions, but often simple backslashes work too? Is only a \ required for giving a metacharacter its usual meaning? --- u=grep('\\{[\\-u]x',a,perl=T) # equivalent to u=grep('\{[\-u]x',a,perl=

[R] using lme in csimtest

Hi group, I'm trying to do a Tukey test to compare the means of a factor ("treatment") with three levels in an lme model that also contains the factors "site" and "time": model = response ~ treatment * (site + time) When I enter this model in csimtest, it takes all but the main factor "treatm

Re: [R] skewness and kurtosis in e1071 correct?

This is probably an issue over definitions rather than the correct answer. To me skewness and kurtosis are functions of the distribution rather than the population, they are equivalent to expectation rather than mean. For the normal distribution it makes no sense to estimate them as the distribut

[R] Re: Finding the right number of clusters

Philip I have been using the kgs function in the maptree package, although you still need to decide on a weighting factor. Mike White __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide!