Re: [R] nls model singular gradient matrix parametrization

Your model is over-parametrized: d1*exp(-gt) gives two parameters for one constant. As a result, the least-square surface is flat in one direction, and the gradient matrix is singular. If this is the model you intended, you can simplify it by dropping d1. It is also partially linear (d) so it

Re: [R] problem when calling help.search() a second time

Argument 'rebuild'. The error message will be better in R-devel. Thank you very much, setting argument 'rebuild' to TRUE in help.search() fixed the problem. My Sweave document can include now all the high level plot examples from all base packages intead just from the 'graphics' one. This is

Re: [R] a matrix in a seprate window?

On Thu, 1 Jun 2006, H. Paul Benton wrote: A very simple one but I cannot figure it out. I have a matrix and I want to display it in a seprate window. I would really like it if it worked on both linux and windows. edit.matrix will provide you with a spreadsheet display in a separate window.

[R] basic array question

I have a large array and would like to extract from it the row and column indices just of values for which a particular boolean condition is true. I assume there's a simple way to do this, but I haven't figured it out yet. Any help would be appreciated. Tim

Re: [R] basic array question

Tim Alcon wrote: I have a large array and would like to extract from it the row and column indices just of values for which a particular boolean condition Do you mean a matrix, i.e. exactly 2 dimensions? is true. I assume there's a simple way to do this, but I haven't figured it out yet.

Re: [R] A coding question

xpRt.wannabe wrote: Dear List: I have the follow code: y - replicate(10,replicate(8,sum(rnorm(rpois(1,5) Now I need to apply the following condition to _every_ randomly generated Normal number in the code above: x - max(0,x-15) + max(0,x-90), where x represents the individual

Re: [R] basic array question

Hi On 2 Jun 2006 at 10:26, Uwe Ligges wrote: Date sent: Fri, 02 Jun 2006 10:26:44 +0200 From: Uwe Ligges [EMAIL PROTECTED] Organization: Fachbereich Statistik, Universitaet Dortmund To: Tim Alcon [EMAIL PROTECTED] Copies to:

[R] Multivariate skew-t cdf

Dear All, I am using the pmst function from the sn package (version 0.4-0). After inserting the example from the help page, I get non-trivial answers, so everything is fine. However, when I try to extend it to higher dimension: xi - alpha - x - rep(0,27) Omega - diag(0,27) p1 - pmst(x, xi, Omega,

Re: [R] nls model singular gradient matrix parametrization

Yes! Now I can see it, it's so evident... Thank you so much, m Mihai Nica, ABD Jackson State University ITT Tech Instructor 170 East Griffith Street G5 Jackson, MS 39201 601 914 0361 The least of learning is done in the classrooms. - Thomas Merton Original Message Follows From: Prof

[R] a question about a simply figure

I think there is a question in R. I donot know the reason. This is my data about comulative percentage figure. The result is not right. The first point (no=1,leiji=26.94350) in the plot figure was showen in a lower location. Why? Thanks ! fre no leiji 1 1 26.94350 2 2 46.86401 3

Re: [R] a question about a simply figure

Hi Zhang Jian, If I say plot(t$no,t$leiji), then the lower bound is neatly set at about 25... (I'm not sure how I can measure the bounds on the current plot - but I'm sure it can be found!) You can set the bounds on the y-axis to be between 0 and 100 by saying

[R] nlme: extract covariance matrix of the random effects

Dear all, I am looking for a function to extract, from an nlme object, the estimated variance-covariance matrix of the random effects. many thanks, Bernard, __ [[alternative HTML version deleted]]

Re: [R] nlme: extract covariance matrix of the random effects

Marc Bernard bernarduse1 at yahoo.fr writes: I am looking for a function to extract, from an nlme object, the estimated variance-covariance matrix of the random effects. VarCorr D.Menne __ R-help@stat.math.ethz.ch mailing list

Re: [R] A coding question

Uwe Ligges ligges at statistik.uni-dortmund.de writes: xpRt.wannabe wrote: y - replicate(10,replicate(8,sum(rnorm(rpois(1,5) x - max(0,x-15) + max(0,x-90), where x represents the individual Normal numbers. y - replicate(10, { rp - rpois(8, 5) mysum -

Re: [R] Help with evaluation of expressions

Michael Conklin michael.conklin at markettools.com writes: I have searched through the help files and I have been unsuccessful in solving this problem. I am trying to create a small wrapper function that will go around a call to a plot function and create a windows metafile in the

[R] Running Demos

I see the output of running, for instance, demo(lm.glm) just fine, but how do I view the set of commands and the data that served as the input? Thanks for the help. Edward Downie __ R-help@stat.math.ethz.ch mailing list

Re: [R] variation on vioplot?

I don't think this is exactly what you want but try: par(mfrow=c(1,2)) vioplot(normal, names=Normal, horizontal=TRUE, ylim=c(-12,12)) vioplot(uniform, names =Uniform, horizontal=TRUE, ylim=c(-12,12)) --- Karin Lagesen [EMAIL PROTECTED] wrote: Michael Dondrup [EMAIL PROTECTED] writes: Hi

Re: [R] Running Demos

Try this: file.show(system.file(demo/lm.glm.R, package = stats)) On 6/2/06, Edward Downie [EMAIL PROTECTED] wrote: I see the output of running, for instance, demo(lm.glm) just fine, but how do I view the set of commands and the data that served as the input? Thanks for the help.

Re: [R] Running Demos

The source R files comes with the package for instance, in this case, in a Linux machine you can locate it with: [EMAIL PROTECTED]:~$ locate lm.glm /usr/lib/R/library/stats/demo/lm.glm.R In other OS this will be similar, look for the stats package best P.J. On Fri, 2 Jun 2006, Edward

[R] speed?

dear R wizards: while extolling the virtues of R, one of my young econometrics colleagues told me that he still wants to run ox because [a] his code is written in it (good reason); [b] because ox seems to be faster than R in most benchmarks (huh?). this got me to wonder. language speed can't

[R] Table collumn to single var in lowcase

Dear All, I have read a table using DataTABLE - read.table(mytable.txt, header=T) And get the following data structure Var1 VAR2 VaR3 Var4 ... How can I list all collumn names (in lowcase) and create variables from table collumns. By hand I do var1 -

[R] Problem with mle

R 2.3.0 Linux, SuSE 10.0 Hi I have two problems with mle - probably I am using it the wrong way so please let me know. I want to fit different distributions to an observed count of seeds and in the next step use AIC or BIC to identify the best distribution. But when I run the script below

Re: [R] Table collumn to single var in lowcase

tolower(names(DataTABLE)) Peter Ehlers Milton Cezar wrote: Dear All, I have read a table using DataTABLE - read.table(mytable.txt, header=T) And get the following data structure Var1 VAR2 VaR3 Var4 ... How can I list all collumn names (in lowcase)

[R] Intercept of confidence interval with a constant

Hello, Is there a way for R to determine the point where a confidence interval equals a specified value? For example: x = seq(1:5) y = c(5, 5, 4, 4, 3) lm = lm(y ~ x) p = predict.lm(lm, interval=confidence) matplot(p, type=b) abline(h = 3) I want to answer the question: What is the value of x

Re: [R] a question about a simply figure

I don't understand the question. What's wrong with showing 26.94350 as being less than all the other leiji values? Peter Ehlers zhang jian wrote: I think there is a question in R. I donot know the reason. This is my data about comulative percentage figure. The result is not right. The

Re: [R] Intercept of confidence interval with a constant

Try this: approx(p[,lwr], 1:5, 3) On 6/2/06, Larry Howe [EMAIL PROTECTED] wrote: Hello, Is there a way for R to determine the point where a confidence interval equals a specified value? For example: x = seq(1:5) y = c(5, 5, 4, 4, 3) lm = lm(y ~ x) p = predict.lm(lm, interval=confidence)

Re: [R] Table collumn to single var in lowcase

names(DataTABLE) - tolower(names(DataTABLE)) ?casefold ?names Milton Cezar wrote: Dear All, I have read a table using DataTABLE - read.table(mytable.txt, header=T) And get the following data structure Var1 VAR2 VaR3 Var4 ... How can I list all collumn

Re: [R] speed?

You (and your colleague) might want to have a look at http://www.sciviews.org/benchmark/. It's a bit dated, but still may be a good starting point. Some months ago some one asked about working on getting R to use the GPU for computation on the R-devel list. Don't know if anything came of it.

Re: [R] Table collumn to single var in lowcase

Note that creating separate variables out of your data frame is not really a good idea. However, to answer your question: # this puts it on the path iris.lc - iris names(iris.lc) - tolower(names(iris.lc)) attach(iris.lc) search() # shows where its located print(head(sepal.length)) detach() # get

[R] function environment

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, how can I automatically access the functions that I loaded into a separate environment? save(A,B,file=myfun.r) load(myfun.r,envir=(ENV-new.env())) ls(ENV) [1] A B ?[ turned up that I can access the functions via ENV$A function () { }

Re: [R] Intercept of confidence interval with a constant

Larry Howe wrote: Hello, Is there a way for R to determine the point where a confidence interval equals a specified value? For example: x = seq(1:5) y = c(5, 5, 4, 4, 3) lm = lm(y ~ x) p = predict.lm(lm, interval=confidence) matplot(p, type=b) abline(h = 3) You can do it this

Re: [R] function environment

Try this: attach(as.list(ENV)) search() # shows it on the path A function's environment refers to where variables in the function are looked for if they can't find the variable in the function itself. The environment in which a function itself is located is entirely different. e.g. a - 1 e -

Re: [R] executable file with R

Romain Lorrilliere wrote: Hi, I made an R function, and I want make an executable applet with it. Do you know how it is possible? More details about what you want would be helpful. Here is what I do and it may be useful to you. Under *nix,OSX, etc use bash's here document feature.

Re: [R] speed?

The benchmark report is good stuff - I've been wondering about these speed issues recently myself. Has anyone tried something similar on 64-bit Linux or other OS? I'm contemplating switching to 64-bit Linux if I'll get some dramatic cycle time improvements. Anyone have any experience with this?

Re: [R] function environment

On Fri, 2 Jun 2006, Matthias Braeunig wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, how can I automatically access the functions that I loaded into a separate environment? This is a topic that is probably best suited to R-devel: the explanations are going to get technical, and

Re: [R] function environment

Try save(A, B, file = myfun.r) attach(myfun.r) Your functions will be on the search list. -roger Matthias Braeunig wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, how can I automatically access the functions that I loaded into a separate environment? save(A,B,file=myfun.r)

Re: [R] speed?

Running on 64-bit per se does not make things faster. In fact, from my experience it sometimes makes things slower. The advantage with 64-bit is the extra address space for storing things in memory. Of course, today's 64-bit chips are all faster than recent 32-bit chips, so you will get a

Re: [R] speed?

On Fri, 2 Jun 2006, Roger D. Peng wrote: Running on 64-bit per se does not make things faster. In fact, from my experience it sometimes makes things slower. The advantage with 64-bit is the extra address space for storing things in memory. See the R-admin manual for some additional

Re: [R] how to add point and label to boxplot using bwplot

On 6/1/06, Maria Montez [EMAIL PROTECTED] wrote: Hi. My data contains information for 10 hospitals for 12 different measures. Let's call it x1-x12. I need to create a boxplot for each one of this measures and put them into one page. Each plot also needs to be independent, i.e. cannot use the

Re: [R] Problem with mle

Rainer M KRug RMK at krugs.de writes: R 2.3.0 Linux, SuSE 10.0 Hi I have two problems with mle - probably I am using it the wrong way so please let me know. I want to fit different distributions to an observed count of seeds and in the next step use AIC or BIC to identify the best

[R] doubt with integrate ()

Dear members, I'm getting an error with the integrate function. Searching in the r-help archives, I think this may have something to do with the function (it is not returning a vector but a number), but I don't see exactly what. The function to integrate was defined with a for loop first:

[R] geoR, plot of variog4 lines incomplete

I'm using R for Mac OSX version 1.14 (2129) and the geoR package version 1.6-5 (the current version in the R repository). I'm running R in OS 10.4.6 on a Mac G4 iBook (933MHz, 640 MB DDR SDRAM). I searched the R archive and did not find a posting on this issue. I want to use the variog and

[R] plot with different color

Hi how can I plot a series of number as a line, but with lines above a threshould as one color, and with lines below the threshold as another color. for example, a numeric vector: rnorm(1:100), and plot these numbers in the original order, but lines above the horizontal line at 0 are in red, and

[R] presetting R environment

Hi, Is there a way of presetting my R environment so that, for example everything between -1e-15 and -1e-15 be equal to 0. Thanks in advance Guilaume Blanchet __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

[R] ANCOVA in S-plus/R?

Dear R user: I have a question about doing ANCOVA in S-plus or R. I know that many users use lm to do the regression and check the ANCOVA. But is there a way to get the traditional Table form of the ANCOVA test through S-plus (like what we would get from SPSS or SAS)? The

[R] Clumpy in image Landscape Ecology metrics

Dear R-friends, Is there someone workingo with Landscape Ecology Metrics in R? I´m writing a short routine to compute a Percolation index in a map and I need to identify Clumpy in the image. My input data looks like 000 0011000 0011100 000 0111000

Re: [R] ANCOVA in S-plus/R?

To get the ANCOVA table you need to look at the anova() function. The variables T and L must be factors to get the multi-degree-of-freedom anova tables you are looking for. Order matters. You get the same residual, but the sequential sums of squares differ. bt.aov - aov(E ~ B + T)

Re: [R] plot with different color

Here is one approach. It uses the function clipplot which is shown below (someday I will add this to my TeachingDemos package, the TeachingDemos package is required). An example of usage: x - rnorm(1:100) plot(x, type='l',col='red') clipplot( lines(x, col='blue'), ylim=c(-4,0) ) Hope this

Re: [R] FW: How to create a new package?

To follow up on Bert Gunter's remark about a quicker and dirtier way, here is the R script I use to source every *.r file in a directory and save the results into a workspace. It excludes any files beginning with 00 (for example, itself) from the operations. This simplifies maintaining a

Re: [R] Intercept of confidence interval with a constant

Ah, so I switch y with x, give it x, and ask it for y (which is actually x). Clever. I continue to be impressed with R. Thanks, Larry On Friday June 2 2006 11:23, Gabor Grothendieck wrote: Try this: approx(p[,lwr], 1:5, 3) On 6/2/06, Larry Howe [EMAIL PROTECTED] wrote: Hello, Is

[R] lm() variance covariance matrix of coefficients.

Hi, I am running a simple linear model with (say) 5 independent variables. Is there a simple way of getting the variance-covariance matrix of the coeffcient estimates? None of the values of the lm() seem to provide this. Thanks in advance, Ritwik Sinha [EMAIL PROTECTED] Grad Student Case

Re: [R] lm() variance covariance matrix of coefficients.

summary(object)$cov.unscaled __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

Re: [R] lm() variance covariance matrix of coefficients.

Rolf Turner [EMAIL PROTECTED] writes: summary(object)$cov.unscaled You need to multiply that with sigma. However, vcov(object) is easier. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) --

Re: [R] lm() variance covariance matrix of coefficients.

On Fri, 2 Jun 2006 18:24:57 -0300 (ADT) Rolf Turner wrote: summary(object)$cov.unscaled As the name suggests: this is the unscaled covariance matrix! Use the vcov() extractor method, i.e., vcov(object) which has methods not only for lm but also many other fitted model objects. Z

Re: [R] lm() variance covariance matrix of coefficients.

or more simply and better, vcov(lm.object) ?vcov Note R's philosophy:use available extractors to get the key features of the objects, rather then indexing. This is safer, as it does not depend on the particular structure/implementation, which can change. This is the difference between private

Re: [R] lm() variance covariance matrix of coefficients.

Peter Dalgaard wrote: Rolf Turner [EMAIL PROTECTED] writes: summary(object)$cov.unscaled You need to multiply that with sigma. However, vcov(object) is easier. Well, I thought unscaled meant unscaled --- the plain unvarnished covariance matrix! I figure that multiplying

Re: [R] geoR, plot of variog4 lines incomplete

Mike The source of the problem is not obvious to me from what you've reported and I could ot reproduce in a few tests with other data. Would it be possoble to send me the data-set? Cheers P.J. On Fri, 2 Jun 2006, Michael Fuller wrote: Date: Fri, 2 Jun 2006 14:54:46 -0400 From: Michael

[R] make check errors when checking R1.9.1 build (was RE: Building V2.3.0 on Tru64 V5.1B)

Hi, I am attempting to build R on Alpha servers running Tru64 UNIX. I am having problems building R 2.3.0 so am attempting to build older releases. I have been able to build R 1.9.1 without problem. However make check fails for the following tests: 1. arith.Rout The difference

Re: [R] lm() variance covariance matrix of coefficients.

Rolf Turner [EMAIL PROTECTED] writes: Peter Dalgaard wrote: Rolf Turner [EMAIL PROTECTED] writes: summary(object)$cov.unscaled You need to multiply that with sigma. However, vcov(object) is easier. Well, I thought unscaled meant unscaled --- the plain unvarnished

Re: [R] merge function in R

Em Qui, 2006-06-01 às 05:59 -0700, Ahamarshan jn escreveu: hi list, This question must be very basic but I am just 3 days old to R. I am trying to find a function to merge two tables of data in two different files as one. Does merge function only fills in colums between two table where

Re: [R] plot with different color

Greg, It might be better to use ylim = c(min(x), 0) in place of ylim = c(-4, 0). I don't think plt can take negative values. Peter Ehlers Greg Snow wrote: Here is one approach. It uses the function clipplot which is shown below (someday I will add this to my TeachingDemos package, the

Re: [R] A coding question

Uwe and Ben, Thank you both for your help. To me, both sets of code seem to do the job and should produce the same results. However, as a test I inserted set.seed( ) as follows. Unless I put set.seed( ) in the wrong lines, the results produced by both sets of code turn out to be different. I

[R] time series clustering

Dear Listers: I happened to have a problem requiring time-series clustering since the clusters will change with time (too old data need to be removed from data while new data comes in). I am wondering if there is some paper or reference on this topic and there is some kind of implementation in R?

[R] HTML masked (due to Rpad?)

With an older verion of R (I think 2.2.0) and an older version of Rpad I used to use HTML(go, collapse=false) where go is list of objects returned by a function and this worked great. Now that I have done some upgrading (to R 2.3.1 and Rpad 1.1.0) its not working right. I also get a warning when