Re: [R] How to modify function for list

2007-10-03 Thread Chung-hong Chan
Thanks for your answer. But I have a strange question that I don't know how to explain and I really don't know how to spot the problematic part. Suppose I have a long list of age, gender and bmi from a data.frame called msltdata. age - msltdata$age gender - msltdata$data bmi -msltdata$bmi

[R] standard errors of regression coefficients

2007-10-03 Thread Alexander Moreno
Hi, If I have two vectors x and y and I do lm(y~x) and now I want to define variables that are the standard errors of the slope and intercept, how do I do that? Thanks, Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing

Re: [R] standard errors of regression coefficients

2007-10-03 Thread Jeffrey Robert Spies
stderr_int - summary(lm(y ~ x))$coefficients[1,2] stderr_slope - summary(lm(y ~ x))$coefficients[2,2] Jeff. On Oct 3, 2007, at 3:01 AM, Alexander Moreno wrote: Hi, If I have two vectors x and y and I do lm(y~x) and now I want to define variables that are the standard errors of the slope

Re: [R] How to modify function for list

2007-10-03 Thread Chung-hong Chan
Yes, I tried. Wrong calculation. On 10/3/07, Stefan Grosse [EMAIL PROTECTED] wrote: On Wednesday 03 October 2007 08:23:15 Chung-hong Chan wrote: CC CC Suppose I have a long list of age, gender and bmi from a data.frame CC called msltdata. CC CC age - msltdata$age CC gender -

Re: [R] Error loading DCluster

2007-10-03 Thread Martin Maechler
BL == Birgit Lemcke [EMAIL PROTECTED] on Mon, 1 Oct 2007 17:30:16 +0200 writes: BL When I try to load the DCluster package I get the BL following error message (R 2.5.1; PowerBook G4; Mac OS X BL 10.4.10) BL (Load needed package) Lade n�tiges Paket: spdep BL (error:

Re: [R] R routines vs. MATLAB/SPSS Routines

2007-10-03 Thread Stefan Grosse
On Tuesday 02 October 2007 22:54:48 Matthew Dubins wrote: MD in what respects do R routines work faster/more efficiently/more MD accurately than those of MATLAB/SPSS. There has been a benchmark: http://www.sciviews.org/benchmark/index.html but thats quite old old, it would be interesting to

[R] can you help me with empirical probability

2007-10-03 Thread becki Davenport
I found you online... Can you help with empirical probability? Hi Partha. I really liked your email that you sent me, it really inspired me. I have been breezing through the chapters, and doing quite well, You should be a teacher. After all the time my college instructor spent with the

[R] Avoiding overfitting in gam(mgcv)

2007-10-03 Thread kanno
Dear listers, I'm using gam(from mgcv) for semi-parametric regression on small datasets(10 to 200 observations), and facing a problem of overfitting. According to the help, it is suggested to avoid overfitting by inflating the effective degrees of freedom in GCV evaluation with increased gamma

Re: [R] R routines vs. MATLAB/SPSS Routines

2007-10-03 Thread Patrick Burns
I don't think it is so much that the R routines work faster/more efficiently/more accurately but that the user works faster/more efficiently/ more accurately. Patrick Burns [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User)

Re: [R] How to modify function for list

2007-10-03 Thread Duncan Murdoch
On 03/10/2007 2:23 AM, Chung-hong Chan wrote: Thanks for your answer. But I have a strange question that I don't know how to explain and I really don't know how to spot the problematic part. Suppose I have a long list of age, gender and bmi from a data.frame called msltdata. age -

[R] regression tree output

2007-10-03 Thread Tom Brewer
Dear All, Some simple interpretation assistance. I am producing regression trees, based on a set of 10 continuous predictors. Have cross validated to fit the model to minimum deviance, prior to summary output. I have not found a source that clearly states the meaning of the residual mean

Re: [R] How to add legend for image()?

2007-10-03 Thread Jim Lemon
zhijie zhang wrote: Dear friends, The following is an example to explain my question. I want to get a legend which will show the z-values according to different colors in image() function. x-sort(runif(10)) #x-coordinates y-sort(runif(10)) #y-coordinates z-matrix(runif(100),nrow=10)

Re: [R] How to modify function for list

2007-10-03 Thread Chung-hong Chan
Yeah, it works fine now. I think I need to modify my function to check for factor. Regards, C On 10/3/07, Duncan Murdoch [EMAIL PROTECTED] wrote: On 03/10/2007 2:23 AM, Chung-hong Chan wrote: Thanks for your answer. But I have a strange question that I don't know how to explain and I

Re: [R] R routines vs. MATLAB/SPSS Routines

2007-10-03 Thread Prof Brian Ripley
On Wed, 3 Oct 2007, Patrick Burns wrote: I don't think it is so much that the R routines work faster/more efficiently/more accurately but that the user works faster/more efficiently/ more accurately. And in particular a user can do many informative/insightful/penetrating

[R] leaps: regsubsets, formula including interactions

2007-10-03 Thread Jonne Zutt
Hi R-list members, Could somebody explain to me the meaning of the '.' in the formula SumTL~. below? I could not find it in the help pages. I'm guessing it is substituted by v1+v2+v3+.. for all independent variables vi. Furthermore, I would like to add interaction effects to the model, is this

[R] P-value

2007-10-03 Thread Emre Unal
How can i print only the P-Value of the kolmogorov smirnov test? ks.test(VeriSeti1, VeriSeti2) Two-sample Kolmogorov-Smirnov test data: VeriSeti1 and VeriSeti2 D = 0.5, p-value = 0.4413 alternative hypothesis: two-sided This expression gives me the whole test results, i need only

Re: [R] How to avoid overfitting in gam(mgcv)

2007-10-03 Thread Ariyo Kanno
I appreciate your quick reply. I am using the model of the following structure : fit - gam(y~x1+s(x2)) ,where y, x1, and x2 are quantitative variables. So the response distribution is assumed to be gaussian(default). Now I understand that the data size was too small. Thank you. Best Wishes,

[R] R-2.6.0 is released

2007-10-03 Thread Peter Dalgaard
I've rolled up R-2.6.0.tar.gz a short while ago. This is a development release which contains a number of new features. In particular, the handling of data with a large number of identical strings should be more memory-efficient. Also, a number of mostly minor bugs have been fixed. See the

[R] Change title size in plot(model)?

2007-10-03 Thread bernhard.mueller
I want to use the plot(model) function to generate Tukey-anscomb and Q-Q plots of a lm(). I manage to change all labels but the main one which apparently is neither main or sub. So far I have tried as par setting: cex (changes symbol size within the plot), cex.main (no effect), cex.sub (no

Re: [R] P-value

2007-10-03 Thread Chung-hong Chan
ks.test(x,y)[2] On 10/3/07, Emre Unal [EMAIL PROTECTED] wrote: How can i print only the P-Value of the kolmogorov smirnov test? ks.test(VeriSeti1, VeriSeti2) Two-sample Kolmogorov-Smirnov test data: VeriSeti1 and VeriSeti2 D = 0.5, p-value = 0.4413 alternative hypothesis:

Re: [R] mcv package gamm function Error in chol(XVX + S)

2007-10-03 Thread Simon Wood
Thanks for sending the data... The problem is triggered by only having one observation per district, so that you have a random effect for each datum. This causes the correlation of the parameter estimates/predictions for the smooth term to become so high that covariance matrix of the smooth

Re: [R] How to avoid overfitting in gam(mgcv)

2007-10-03 Thread Simon Wood
On Wednesday 03 October 2007 10:49, Ariyo Kanno wrote: I appreciate your quick reply. I am using the model of the following structure : fit - gam(y~x1+s(x2)) ,where y, x1, and x2 are quantitative variables. So the response distribution is assumed to be gaussian(default). Now I understand

Re: [R] Change title size in plot(model)?

2007-10-03 Thread Duncan Murdoch
On 03/10/2007 5:41 AM, [EMAIL PROTECTED] wrote: I want to use the plot(model) function to generate Tukey-anscomb and Q-Q plots of a lm(). I manage to change all labels but the main one which apparently is neither main or sub. So far I have tried as par setting: cex (changes symbol size

Re: [R] Change title size in plot(model)?

2007-10-03 Thread Prof Brian Ripley
On Wed, 3 Oct 2007, [EMAIL PROTECTED] wrote: I want to use the plot(model) function to generate Tukey-anscomb and Q-Q plots of a lm(). I manage to change all labels but the main one which apparently is neither main or sub. So far I have tried as par setting: cex (changes symbol size within

Re: [R] P-value

2007-10-03 Thread Frede Aakmann Tøgersen
Try str(ks.test(VeriSeti1, VeriSeti2)) # see ?str then ks.test(VeriSeti1, VeriSeti2)$p.value Med venlig hilsen Frede Aakmann Tøgersen -Oprindelig meddelelse- Fra: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] På vegne af Emre Unal Sendt: 3. oktober 2007 11:32 Til:

Re: [R] Plotmath integral gets horrible with URWPalladio

2007-10-03 Thread Paul Murrell
Hi Paul Smith wrote: Dear All, With the following code: pdf(file=figure.pdf,family=URWPalladio) plot(0,0,type=n) text(0,0,expression(integral(f(x)*dx, a, b))) dev.off() the integral symbol gets horrible. With other fonts, the same does not occur. Is there some way of using

Re: [R] Plotmath integral gets horrible with URWPalladio

2007-10-03 Thread Paul Smith
On 10/3/07, Paul Murrell [EMAIL PROTECTED] wrote: With the following code: pdf(file=figure.pdf,family=URWPalladio) plot(0,0,type=n) text(0,0,expression(integral(f(x)*dx, a, b))) dev.off() the integral symbol gets horrible. With other fonts, the same does not occur. Is there some

[R] Sample selection problem

2007-10-03 Thread stat stat
I want to get a sample of some arbitrary size from a population having only two values 0 and 1 with replacement, but with different probability for selection. For example 0 will be selected with probability 0.4 and 1 with 0.6. I could use sample function i.e. sample(c(0,1), 30, T) to get this,

[R] Reimplement order somehow

2007-10-03 Thread XpeH
Hello, I have a script in R language that makes sorting using the order() method of R language. What I need is to reimplement this method in any other language (PHP, Perl, Python, Java maybe). First I tried to reimplement it in php, here is some numbers that i need to sort:

[R] Error in lm.fit(

2007-10-03 Thread Peter Lauren
I am using R.2.4.1 on Windows XP 5.1 (SP 2). I have the following line in my R code. Analysis=anova(lm(PM ~ x)) It works the first 60 or so times it is called but then I get the following error message. Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 0 (non-NA) cases

[R] r-package RDCOMClient

2007-10-03 Thread Marcin Kopaczynski
hi, i was trying to perform a function from the RDCOMClient package. to make it short: i tried to run the example in ?.COM, namely e - COMCreate(Excel.Application) books - e[[Workbooks]] as soon as e[[Workbooks]] is called, the RGUI crashes. debugging the function .COM reveals that somehow the

Re: [R] r-package RDCOMClient

2007-10-03 Thread Gabor Grothendieck
I have generally found that both RDCOMClient and rcom do work although around the time of new R versions one might be ready for it before the other so try both. On 10/3/07, Marcin Kopaczynski [EMAIL PROTECTED] wrote: hi, i was trying to perform a function from the RDCOMClient package. to make

Re: [R] Reimplement order somehow

2007-10-03 Thread XpeH
Hello, Thierry Thank you for the fast reply actually my php script is not correct, the correct logic is R script, by writing this peace of code in php I tried to do the same logic that R script does. But this php programm algorirm probably is not correct so results are incorrect also. I am

Re: [R] How to avoid overfitting in gam(mgcv)

2007-10-03 Thread Ariyo Kanno
Sorry, let me fix 1 sentence. Here I try to mean by overfitting that GCV was significantly SMALLER than the mean square error of prediction of the validation data, which was randomly selected and not used for regression. Thank you for valuable advices. I'm sorry Dr. N. Wood that by mistake I

Re: [R] How to avoid overfitting in gam(mgcv)

2007-10-03 Thread Simon Wood
Here I try to mean by overfitting that GCV was significantly SMALLER than the mean square error of prediction of the validation data, which was randomly selected and not used for regression. --- so you could try increasing gamma until this is no longer the case. -- Simon Wood,

Re: [R] R 'function' as subroutine

2007-10-03 Thread Gabor Grothendieck
1. you could place the commands in a file and source the file each time you want to run it or it might be good enough to place it on the clipboard and then just do source(clipboard) 2. Thomas Lumley's defmacro in R News 1/3 could be used Neither of these two require that you do anything special

Re: [R] How to avoid overfitting in gam(mgcv)

2007-10-03 Thread Ariyo Kanno
Thank you for valuable advices. I'm sorry Dr. N. Wood that by mistake I sent this reply firstly to your personal e-mail address. I will use the min.sp argument when the data size is very small. I'd like to know if there is any criteria for selecting min.sp. I compared gamma=1.0 and 1.4, and I

Re: [R] error installing gsl pkg

2007-10-03 Thread Robin Hankin
Hello Randy I get emails like this quite a lot. The most likely problem is in the installation of the gsl library. To verify that it is in fact installed, try to compile and run the little Bessel function example given in gsl-ref, section 2.1. Get this working first. If it works, this means

Re: [R] How to avoid overfitting in gam(mgcv)

2007-10-03 Thread Ariyo Kanno
Thank you for your advices. I will try even increased gamma values, and all-out cross-validations. 2007/10/3, Frank E Harrell Jr [EMAIL PROTECTED]: Ariyo Kanno wrote: Sorry, let me fix 1 sentence. Here I try to mean by overfitting that GCV was significantly SMALLER than the mean square

Re: [R] How to avoid overfitting in gam(mgcv)

2007-10-03 Thread Frank E Harrell Jr
Ariyo Kanno wrote: Sorry, let me fix 1 sentence. Here I try to mean by overfitting that GCV was significantly SMALLER than the mean square error of prediction of the validation data, which was randomly selected and not used for regression. Thank you for valuable advices. If your test

[R] error installing gsl pkg

2007-10-03 Thread Randy Heiland
Newbie here (to R) and running Linux... install.packages(gsl,~/R) ... trying URL 'http://cran.wustl.edu/src/contrib/gsl_1.8-4.tar.gz' Content type 'application/x-tar' length 57051 bytes opened URL == downloaded 55Kb * Installing *source* package

Re: [R] mcv package gamm function Error in chol(XVX + S)

2007-10-03 Thread Simon Wood
Dae-Jin, Thanks for your (offline) persistance: you are right the problem is with `gamm'. There was a dimension dropping error in `formXtViX' (called by `gamm') for group sizes of 1 (as occurs when you have a random effect per observation). This will be fixed in mgcv_1.3-28. best, Simon On

Re: [R] R 'function' as subroutine

2007-10-03 Thread Ted Harding
Thanks for the suggestions, Gabor! On 03-Oct-07 12:52:51, Gabor Grothendieck wrote: 1. you could place the commands in a file and source the file each time you want to run it or it might be good enough to place it on the clipboard and then just do source(clipboard) Using the file solution is

Re: [R] Reimplement order somehow

2007-10-03 Thread Vladimir Eremeev
Vladimir Eremeev wrote: XpeH wrote: I am trying to understand how the order method in R language works, and then I'd like to do the same in some other language. 1. Type order in R command prompt (without ( and )) and press enter. This will print you the body of this function, so

[R] Odp: Error in lm.fit(

2007-10-03 Thread Petr PIKAL
Hi [EMAIL PROTECTED] napsal dne 03.10.2007 14:56:19: I am using R.2.4.1 on Windows XP 5.1 (SP 2). Upgrade R. Version 2.6.0 is imminent. I have the following line in my R code. Analysis=anova(lm(PM ~ x)) It works the first 60 or so times it is called but then I get the following

[R] variance explaine by each term in GLS model

2007-10-03 Thread Debbie Russell
Dear all Sorry to bother you. I have a GLS model: modela-gls(pop2~pop1-1 + ccs + pop1:ccs,data=data2,corr = corSpher(c(5, 0.5 ),form = ~ latitude + longitude, nugget = TRUE), method = ML) I was wondering how I can work out how much variance is explained by the model AND by each term. Any

[R] offset in survreg

2007-10-03 Thread Ming-Wen An
Hello, I have a question regarding the use of an offset term with survreg(), in the Survival library. In particular, I am trying to figure out on what scale the offset term should be. Here's a simple example with no censoring and no coefficients: - y = rlnorm(1000, meanlog = 10, sdlog

Re: [R] Calculating proportions from a data frame rather than a table

2007-10-03 Thread John Kane
--- Farrel Buchinsky [EMAIL PROTECTED] wrote: How do you create a table from a data frame? I tried as.table( name.of.data.frame) but it bombed out. I will include the exact error message in my next posting. If I recall correctly, it said that the data.frame could not be coerced to a

Re: [R] Save and load workspace in R: strange error.

2007-10-03 Thread Tony Plate
Did you check whether 'junk4.RData' was created and what its length was - maybe an empty file is being created. Is there some sort of quota or permissions problem? My suggestion would be to look at the size and permissions on the directory and the file. If you need more help, I would

[R] Making a table: collapsing across sub-strings

2007-10-03 Thread Dieter Vanderelst
Hi list, I'm currently processing textual data and I would really appreciate some help with one off my problems. I have a set of strings and I want to count how often each of this strings appears in this set. This is not very difficult and can be done as: TB-table(my_set) plot(TB) However, I

Re: [R] Making a table: collapsing across sub-strings

2007-10-03 Thread jim holtman
How do you determine if one string is a subset of another? Does it only match at the beginning, or anywhere? How large is your set of strings? Can you use table as you describe and then determine what the groupings of subsets are and then just add the numbers together? You can use grep/regexpr

[R] inverse of matrix made by low.tri function

2007-10-03 Thread kevinchang
Hi all, I am using R trying to get a inverse matrix of (X^T)X , but I keep getting the error message like: no b argument and no default value for sprintf(gettext(fmt, domain = domain), ...) . # my code

Re: [R] Strange names when creating a data.frame: Difference between - and =

2007-10-03 Thread John Kane
To everyone who answered Many thanks for the explanations. I think I see what is happening now __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] Save and load workspace in R: strange error.

2007-10-03 Thread Hongxiao Zhu
Tony, Thanks for return. Actually, the data object 'junk4.RData' was created but have size 0. It seems no data was saved. But the real data that I want to load have data in it, which I can't load use my own user account. But if using other people's user account under the same system, it can be

Re: [R] Apparently Conflicting Results with coxph

2007-10-03 Thread Terry Therneau
I thought about this some more, and I'm not sure that possibility is to blame. In my time-dependent model, I don't think I'm doing anything different than is done for transplant in the Stanford Heart Study (the often used example for this kind of time-dependent covariate). As in my case,

Re: [R] error installing gsl pkg

2007-10-03 Thread Randy Heiland
Robin, Thanks much for the reply. It turns out, for reasons which are still unknown to me, that on this machine, doing the following: % g++ bessel.cpp -o bessel -lgsl -lgslcblas will tell me it can't find -lgsl, in spite of its path being on my LD_LIBRARY_PATH. So, being explicit solves

Re: [R] Save and load workspace in R: strange error.

2007-10-03 Thread Tony Plate
Sounds like you are having permissions problems. And as you're using a mix of Unix and WinXP, you might be suffering from some strange permissions settings. WinXP allows a very rich set of permissions which for many exotic combinations have no corresponding mapping to the much simpler

Re: [R] error installing gsl pkg

2007-10-03 Thread Dirk Eddelbuettel
On 3 October 2007 at 12:25, Randy Heiland wrote: | Thanks much for the reply. It turns out, for reasons which are still | unknown to me, that on this machine, doing the following: | | % g++ bessel.cpp -o bessel -lgsl -lgslcblas | | will tell me it can't find -lgsl, in spite of its path

Re: [R] R 'function' as subroutine

2007-10-03 Thread Duncan Murdoch
On 10/3/2007 7:56 AM, (Ted Harding) wrote: Hi Folks, The question I'm asking, regarding the use of function definitions in the context described below, is whether there are subtle traps or obscure limitations I should watch out for. It is probably a rather naive question... Quite often,

[R] ggplot2: problem with geom_errorbar and geom_abline

2007-10-03 Thread James D Forester
Hi all, I have run into what appears to be a bug in ggplot2; however, I am new to the ggplot syntax, so I might be missing a key element. The main issue is that I cannot get geom_abline to plot when colour is used to identify group in the main plot. When I remove colour, geom_abline works

[R] New package to read and write SAS Transport (XPORT) files

2007-10-03 Thread Gregory R. Warnes
Metrum Institute and Random Technologies LLC are pleased to announce the availability of the SASxport package. The new SASxport package provides the ability to directly read, list, and write SAS 'xport' files, including proper handling of custom SAS formats. (This extends existing

Re: [R] corMatrix crashes R 2.5.1 (windows XP) with corARMA structure

2007-10-03 Thread Uwe Ligges
This is reproducible with R-2.6.0 for me. You might want to report it to R-Core, the maintainer of that package. Uwe Ligges Benjamin Tyner wrote: R-helpers, n - 100 arcoefs - c(0.8) macoefs - c(-0.6) p - length(arcoefs) q - length(macoefs) require(nlme) tmp -

[R] Checking for adequate disk space

2007-10-03 Thread Sundar Dorai-Raj
Hi, all, (version info at end) I'm running a script which takes input files, does some analysis, and writes the output to csv files. Last night I ran the script (it took ~6.5 hours) thinking all would go well since it ran on a subset of the data without issue. However, when I returned this

Re: [R] R 'function' as subroutine

2007-10-03 Thread Gabor Grothendieck
On 10/3/07, Duncan Murdoch [EMAIL PROTECTED] wrote: On 10/3/2007 7:56 AM, (Ted Harding) wrote: Hi Folks, The question I'm asking, regarding the use of function definitions in the context described below, is whether there are subtle traps or obscure limitations I should watch out for.

Re: [R] GARCH simulations

2007-10-03 Thread Giovanni Petris
It shouldn't be hard, using the definition of GARCH(1,1). Giovanni Date: Tue, 02 Oct 2007 17:14:27 -0400 (EDT) From: [EMAIL PROTECTED] Sender: [EMAIL PROTECTED] Importance: Normal Precedence: list User-Agent: SquirrelMail/1.4.6 Hey, Is there any way to simulate a GARCH(1,1) data

Re: [R] accuracy of pt for x close to 0

2007-10-03 Thread Charles C. Berry
On Wed, 3 Oct 2007, skylab gupta wrote: Hello, I have been playing around with the statistical distributions in R, and overall I think the accuracy is very good. However, it seems that for the Student's t distribution, the CDF loses accuracy when evaluated at values close to zero. For

Re: [R] Speeding up simulation of mean nearest neighbor distances

2007-10-03 Thread hadley wickham
It looks like you can pass a vector of neighbourhoods to nndist. nndist(rpp, k=2:10) Although you get some warnings, the answers appear to be the same. all.equal(t(sapply(2:10, function(i) nndist(rpp, k=i))), nndist(rpp, k=2:10)) This might be quite a lot faster, depending on how much work is

[R] help with stepclass (klaR)

2007-10-03 Thread Silvia Lomascolo
I use Windows, R version 2.5.1 When I try to run stepclass (klaR) I get an error message/warning saying: 1: error(s) in modeling/prediction step in: cv.rate(vars = c(model, tryvar), data = data, grouping = grouping, ... Actually, I look 16 warnings of this type. Can anyone tell me what this

Re: [R] Factor levels.

2007-10-03 Thread Rolf Turner
On 3/10/2007, at 5:48 PM, Peter Dalgaard wrote: Rolf Turner wrote: I have factors with levels ``Unit, Achieved, and Scholarship; I wish to replace these with U, A, and S. So I do fff - factor(fff,labels=c(U,A,S)) This works as long as all of the levels are actually present in

Re: [R] R routines vs. MATLAB/SPSS Routines

2007-10-03 Thread Rolf Turner
On 3/10/2007, at 8:30 PM, Patrick Burns wrote: I don't think it is so much that the R routines work faster/more efficiently/more accurately but that the user works faster/more efficiently/ more accurately. Well said, O Wise and Ancient One!!! :-) :-) :-)

Re: [R] Factor levels.

2007-10-03 Thread Rolf Turner
On 4/10/2007, at 7:50 AM, Peter Dalgaard wrote: Rolf Turner wrote: Does it even work? (What if it is the first or the 2nd level that is absent? Yes it works. What's the problem? To beat it to death: if the second level of fff is absent then fff will consist entirely of 1's

Re: [R] Factor levels.

2007-10-03 Thread Peter Dalgaard
Rolf Turner wrote: P.S. ***Are*** there any risks/dangers in following Christos Hatzis' suggestion of simply doing levels(fff) - c(U,A,S) ??? Not if the levels are right to begin with. Problems only arise if fff somehow becomes a two-level factor, e.g. if you do

[R] Nomogram

2007-10-03 Thread motaveiga
Hi R users. I have a model of cox that already it is estimated (I have only the model estimated, I haven't data), how can I determine a nomogram with R? Is it posible to do nomograms in Design package? I think that's only when the model (Cox Regression in this case) is before estimated

Re: [R] Reimplement order somehow

2007-10-03 Thread XpeH
I have found how to reimplement order method from R language in PHP: ?php $str = 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13

[R] Shading area under density curves

2007-10-03 Thread rominger
Hello, I have a question regarding shading regions under curves to display 95% confidence intervals. I generated bootstrap results for the slope and intercept of a simple linear regression model using the following code (borrowed from JJ Faraway 2005): attach(allposs.nine.d)

[R] Forcing zero intercept in two predictor case - stat question not R question

2007-10-03 Thread Leeds, Mark \(IED\)
When one is doing simple regression and needs to force a zero intercept ( for whatever reason. I realize it's a controversial issue ), then subtracting the means of the left hand side and the right hand side from themselves does the trick. Does anyone know if there is a similar trick when the

Re: [R] Shading area under density curves

2007-10-03 Thread Marc Schwartz
On Wed, 2007-10-03 at 14:21 -0700, [EMAIL PROTECTED] wrote: Hello, I have a question regarding shading regions under curves to display 95% confidence intervals. I generated bootstrap results for the slope and intercept of a simple linear regression model using the following code

Re: [R] Calculating proportions from a data frame rather than a table

2007-10-03 Thread Farrel Buchinsky
No. Not really.What you have done seems to be similar to what I could do with the reshape library. rawer-melt(coinfection,id.var=study) # please refer to my post immediately before this. I am still unable to make use of prop.table and margin.table functions. On 10/3/07, Deepayan Sarkar [EMAIL

Re: [R] Nomogram

2007-10-03 Thread Frank E Harrell Jr
[EMAIL PROTECTED] wrote: Hi R users. I have a model of cox that already it is estimated (I have only the model estimated, I haven't data), how can I determine a nomogram with R? Is it posible to do nomograms in Design package? I think that's only when the model (Cox Regression in

Re: [R] Calculating proportions from a data frame rather than a table

2007-10-03 Thread Deepayan Sarkar
On 10/3/07, Farrel Buchinsky [EMAIL PROTECTED] wrote: Thank you. It comes close but not exactly what I wanted. I had to scrap my column that contained character values. That column noted the name of the study. Let me try show you here Best if viewed in courier font coinfection

[R] help with mclust

2007-10-03 Thread Lo, Ken
Dear all, I am attempting to model some one-dimensional data using Gaussian mixture model with mclust. Generally, the data that I have have 3 overlapping populations (with one of them being the majority, and the other two combining to less than 15%) and for some reason, mclust consistently

Re: [R] Forcing zero intercept in two predictor case - stat questionnot R question

2007-10-03 Thread Leeds, Mark \(IED\)
Hi john : I just checked it with a simple example before I saw your email and that does work. Thanks and I apologize to you and the list for the question. -Original Message- From: John Fox [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 03, 2007 6:06 PM To: Leeds, Mark (IED) Cc:

Re: [R] Calculating proportions from a data frame rather than a table

2007-10-03 Thread Farrel Buchinsky
Thank you. It comes close but not exactly what I wanted. I had to scrap my column that contained character values. That column noted the name of the study. Let me try show you here Best if viewed in courier font coinfection study HPV6 HPV11 CoInfect other 1 Wiatrak 2004 3123

[R] Trouble with znorm

2007-10-03 Thread Harshal D Dedhia
I am trying to normalize a dataframe of dimensions(1,1) using znorm from the dprep package. What I get back is the same data, and nothing has been normalized. Wondering if there is a known bug I am running into or am I missing something? Cheers! Harshal [[alternative HTML version

[R] FW: help with mclust

2007-10-03 Thread Lo, Ken
No HTML this time. Sorry Dear all, I am attempting to model some one-dimensional data using Gaussian mixture model with mclust.  Generally, the data that I have have 3 overlapping populations (with one of them being the majority, and the other two combining to less than 15%) and for some

Re: [R] Calculating proportions from a data frame rather than a table

2007-10-03 Thread Farrel Buchinsky
Incidentally, the feature becomes really powerful when one uses functions such as addmargins together with prop.table as in coinf.table -as.matrix(coinfection) prop.table(coinf.table,1) # to see proportions from each HPV type per study addmargins(coinf.table)# to see totals within study and

Re: [R] ggplot2: problem with geom_errorbar and geom_abline

2007-10-03 Thread Ben Bolker
James D Forester wrote: Hi all, I have run into what appears to be a bug in ggplot2; however, I am new to the ggplot syntax, so I might be missing a key element. The main issue is that I cannot get geom_abline to plot when colour is used to identify group in the main plot. When I

[R] ??clusplot

2007-10-03 Thread Haiyong Xu
Hi there, I want to do classify some 2-dimensional points into four clusters by pam() in the cluster package. However, I encountered some problems. 1. How can I change the xlab and ylab instead of the default Component 1 and Component 2? When I put xlab option in the function, it always

Re: [R] Odp: Error in lm.fit(

2007-10-03 Thread Peter Lauren
Hi, I checked my code and found that it was actually a subsequent call to lm.fit() (which only gets called occasionally) where the problem occurred. I found that I was accidentally passing a matrix called PMs instead of the vector PM. Sorry about that. Thanks, Peter. --- Petr PIKAL [EMAIL

[R] linewidth in Rgraphviz

2007-10-03 Thread Ben Bolker
I'm an Rgraphviz newbie trying to figure out how to do some things/whether they are possible. Apparently graphviz does allow you to modify line widths of edges: see https://mailman.research.att.com/pipermail/graphviz-interest/2001q2/51.html (although it looks a little obscure even in

[R] as.numeric(FALSE) fails after loading the Matrix package

2007-10-03 Thread Bernd Weiss
Dear all, is this a bug? as.numeric(FALSE) [1] 0 library(Matrix) Loading required package: lattice as.numeric(FALSE) Error in UseMethod(as.double) : no applicable method for as.double Regards, Bernd version _ platform i386-pc-mingw32 arch i386 os

[R] tcltk question

2007-10-03 Thread Tae-Hoon Chung
Is there any requirement for TclTk support for R? When I tried to call the tcltk library, it failed with the following message: library(tcltk) Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system Error in library(tcltk) : .First.lib failed for

Re: [R] as.numeric(FALSE) fails after loading the Matrix package

2007-10-03 Thread Bernd Weiss
Bernd Weiss schrieb: Dear all, is this a bug? as.numeric(FALSE) [1] 0 library(Matrix) Loading required package: lattice as.numeric(FALSE) Error in UseMethod(as.double) : no applicable method for as.double After doing a complette reinstallation (uninstalling R, deleting all

Re: [R] FW: help with mclust

2007-10-03 Thread Tatiana Benaglia
Hi Ken, I know your question was specifically about the mclus, but you can also try to fit a univariate gaussian mixture using the normalmixEM in the mixtools package. library(mixtools) out = normalmixEM(data, k=3) That's what I got for your sample: out$lambda [1] 0.119 0.647 0.234