Re: [R] How to draw different series for different groups in xyplot

2011-03-13 Thread Dennis Murphy
Hi: Try this: xyplot(y ~ x1 | x2 * x3, groups = x4, data = example, type= c(l, p), pch=c(16, 4), col=c(blue, red), col.line = c('blue', 'transparent'), xlim = c(1.04, 1.26), ylim = c(0, 1.1), xlab = X2, ylab = Y, key = list(space = top, text = list(A),

[R] R hangs when connected via VPN [incl. minimal example]

2011-03-13 Thread Marius Hofert
Dear expeRts, This is a similar post as on R-SIG-MAC [I didn't receive an answer there; not sure if it was the right place to post either]. I'm running R version 2.12.1 (Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)) on a MacBook Pro under Mac OS X 10.6.6. The following minimal example

Re: [R] Lattice: Feature Request

2011-03-13 Thread Deepayan Sarkar
On Sat, Mar 12, 2011 at 1:30 AM, Jim Price price...@hotmail.com wrote: Thanks Peter. This is true, but consider this continuation of my example (which is probably what I should have written originally): my.opts - list(default.args = list(                       as.table = TRUE,            

[R] R 2.13.0 scheduled for April 13

2011-03-13 Thread Peter Dalgaard
This is to announce that we plan to release R version 2.13.0 on Wednesday, April 13, 2011. Those directly involved should review the generic schedule at http://developer.r-project.org/release-checklist.html The source tarballs will be made available daily (barring build troubles) via

Re: [R] Reg : Using R in Web

2011-03-13 Thread Erich Neuwirth
Assuming you are using a Windows based server have a look at statconnWS at rcom.univie.ac.at Warning: statconnWS is NOT open source. It is under development, and it also will work under Linux in the future. The statconnDCOM server also might be an option for you. It is available from the same web

Re: [R] Merge data under conditions

2011-03-13 Thread flymer
Thanks to both of you for your help! Jim, my problem is to match some observations of a time serie (vector 'a' in my example) with theoretical predictions of this process (vector 'b' in my example), with a small time lag between them. -- View this message in context:

Re: [R] how to label lines

2011-03-13 Thread derek
Nice, thank you. -- View this message in context: http://r.789695.n4.nabble.com/how-to-label-lines-tp3350452p3351605.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list

[R] Having a problem with choose.files

2011-03-13 Thread Carl.Finkbeiner
I am relatively new to R, and am having a problem with the following snippet of code, and I do not at all understand why it is behaving this way. I am running Windows XP, with R 2.12.1. I copy and paste these 4 lines into the R Console: t-c(a,b,c) ans-select.list(t)

[R] how to change the margins of a plot area

2011-03-13 Thread Lathouri, Maria
Dear all, I am ploting two boxplot of two chemical variables using the format boxplot(Alkalinity, logAlkalinity, log=y, col=c(lightblue), lwd=0.6, boxwex=0.3) However when I plot like this, the distance between the two boxplots is very big and as well the distance of each boxplot from the plot

Re: [R] R hangs when connected via VPN [incl. minimal example]

2011-03-13 Thread Duncan Murdoch
On 11-03-13 4:34 AM, Marius Hofert wrote: Dear expeRts, This is a similar post as on R-SIG-MAC [I didn't receive an answer there; not sure if it was the right place to post either]. I'm running R version 2.12.1 (Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)) on a MacBook Pro under Mac

Re: [R] Having a problem with choose.files

2011-03-13 Thread Duncan Murdoch
On 11-03-13 7:11 AM, carl.finkbei...@tnsglobal.com wrote: I am relatively new to R, and am having a problem with the following snippet of code, and I do not at all understand why it is behaving this way. I am running Windows XP, with R 2.12.1. I copy and paste these 4 lines into the R Console:

[R] problem with looping formula through table

2011-03-13 Thread herr dittmann
Dear useRs, I am stuck with a piece of code and hope you could give me some pointers. My aim is to calculate the lm-regression coefficients of individual stocks against an index. I am interested in both the coefficient and the pval. While I could do this manually for a select hand full, I hope

[R] A basic question about reshape2

2011-03-13 Thread Jim Carolyn Watkins
Dear R Community: This is a newbie reshare2 question; it starts with read a set of data and to melt it: x = data.frame(I=c(a,b,a,b,b), V=c(2,4,2,5,7)) y = melt(x, id = 1:1) What is wrong with the final dcast step: z = dcast(y, formula = I ~ variable, c(length, mean, median)) Will

Re: [R] how to change the margins of a plot area

2011-03-13 Thread John Kane
Hi Maria, I think we need some sample data and code to really be ablo to help. in the meantime have have a look at ?par for general plotting info. --- On Sun, 3/13/11, Lathouri, Maria m.lathour...@imperial.ac.uk wrote: From: Lathouri, Maria m.lathour...@imperial.ac.uk Subject: [R] how to

[R] Problem implementing 'waldtest' when using 'mlogit' package

2011-03-13 Thread Ghosh, Gaurav
Hi all, I have been working through the examples in one of the vignettes associated with the 'mlogit' package, 'Kenneth Train's exercises using the mlogit package for R.' In spite of using the code unchanged, as well as the data used in the examples, I have been unable to run a Wald test to

Re: [R] A basic question about reshape2

2011-03-13 Thread John Kane
I am not sure about this but I don't see how a melt command helps. See what z = dcast(x, I ~ V, mean) gives you. --- On Sun, 3/13/11, Jim Carolyn Watkins jcwat...@gwi.net wrote: From: Jim Carolyn Watkins jcwat...@gwi.net Subject: [R] A basic question about reshape2 To:

Re: [R] Gnuplot fit function in R

2011-03-13 Thread Stefan
OK, this helps. Seems to be exactly what I need. Thanks. Stefan Am 12.03.2011 um 17:57 schrieb Ben Bolker: Stefan jobmensa at me.com writes: [snip] I'm just wondering if there is a equivalent to the fit function of gnuplot in R? If not, s there any good resource on fitting gaussians

[R] pdf device - different page orientation and different plot sizes

2011-03-13 Thread derek
Hello R, I would like make single pdf file in which the the pages are are of mixed format. Manual states this code (down). The problem is the second {} overwrites the first {}, but I want to append them. require(graphics) require(stats) HBA=read.table(file.txt,header =FALSE,sep = , dec =

[R] Setting the language of Rs error messages

2011-03-13 Thread Alexx Hardt
Hi, My R has been installed on a Ubuntu linux computer in Germany. The error messages I get are in German, for example: In min(magnitudes) : kein nicht-fehlendes Argument für min; gebe Inf zurück I would like those to be displayed in English, for pasting them into google. I tried searching

Re: [R] Setting the language of Rs error messages

2011-03-13 Thread Richard M. Heiberger
Sys.setenv(LANG=DE) 2+a Fehler in 2 + a : nicht-numerisches Argument für binären Operator Sys.setenv(LANG=EN) 2+a Error in 2 + a : non-numeric argument to binary operator On Sun, Mar 13, 2011 at 8:39 AM, Alexx Hardt mikrowelle1...@gmx.de wrote: Hi, My R has been installed on a Ubuntu

Re: [R] Problem implementing 'waldtest' when using 'mlogit' package

2011-03-13 Thread Achim Zeileis
On Sun, 13 Mar 2011, Ghosh, Gaurav wrote: Hi all, I have been working through the examples in one of the vignettes associated with the 'mlogit' package, 'Kenneth Train's exercises using the mlogit package for R.' In spite of using the code unchanged, as well as the data used in the

Re: [R] 'Date' elements within a matrix

2011-03-13 Thread Bogaso Christofer
Thanks everyone for clarifying my query. However I was wondering why that Date character is not preserved within a matrix? Why R forcefully changes that to numeric? I am especially concerned because as per the definition of the matrix, each element needs to be of same class. Is there any other

Re: [R] betareg help

2011-03-13 Thread Achim Zeileis
On Sat, 12 Mar 2011, Vlatka Matkovic Puljic wrote: Maybe I should include data: As Ben said previously: The full data would have been more useful. However, I've had a look at the response and even a regression with an intercept only had the same problem. R betareg(cond ~ 1, data =

[R] Full floor of offices in JLT for sale

2011-03-13 Thread Konstantin
Full floor of offices in JLT for sale Building: JBC 2 (opposite DAMAS) Total size: 10908 sq.ft. 7 offices: 01 – 1502 sq.ft. ; 02 – 1123 sq.ft. ; 03 – 2457 sq.ft. ; 04 – 2232 sq.ft. ; 05 - 1123 sq.ft. ; 06 – 1502 sq.ft. ; 07 – 1093 sq.ft. ; 9 parking spaces Price 550 dhs per sq.ft.

[R] use of ROCR package (ROC curve / AUC value) in a specific case versus integral calculation

2011-03-13 Thread Christine SINOQUET
Hello, I would like to use the ROCR package to draw ROC curves and compute AUC values. However, in the specific context of my application, the true positive rates and false positive rates are already provided by some upstream method. Of course, I can draw a ROC plot with the following

[R] replace with quantile value for a large data frame...

2011-03-13 Thread Ram H. Sharma
Dear R-Experts I am sure this might look simple question for experts, at least is problem for me. I have a large data frame with over 1000 variables and each have different distribution( i.e. have different quantile). I want to create a new grouped data frame, where the new variables where the

Re: [R] Setting the language of Rs error messages

2011-03-13 Thread Alexx Hardt
Am 13.03.2011 15:13, schrieb Richard M. Heiberger: Sys.setenv(LANG=EN) Thanks, this is exactly what I was looking for. Can I somehow configure R to set this variable to EN whenever I start it? __ R-help@r-project.org mailing list

Re: [R] Problem implementing 'waldtest' when using 'mlogit' package

2011-03-13 Thread Mark Difford
On Mar 13, 2011; 03:44pm Gaurav Ghosh wrote: I have been working through the examples in one of the vignettes associated with the 'mlogit' package, 'Kenneth Train's exercises using the mlogit package for R.' In spite of using the code unchanged, as well as the data used in the examples, I

Re: [R] 'Date' elements within a matrix

2011-03-13 Thread David Winsemius
On Mar 13, 2011, at 11:46 AM, Bogaso Christofer wrote: Thanks everyone for clarifying my query. However I was wondering why that Date character is not preserved within a matrix? Why R forcefully changes that to numeric? I am especially concerned because as per the definition of the

Re: [R] Setting the language of Rs error messages

2011-03-13 Thread Richard M. Heiberger
Yes. Add that line to your .Rprofile file. See ?Startup for full details on initialization of an R session. On Sun, Mar 13, 2011 at 10:32 AM, Alexx Hardt mikrowelle1...@gmx.de wrote: Am 13.03.2011 15:13, schrieb Richard M. Heiberger: Sys.setenv(LANG=EN) Thanks, this is exactly what I

Re: [R] replace with quantile value for a large data frame...

2011-03-13 Thread Dimitris Rizopoulos
one way is the following: X1 - c(1:10) X2 - c(11:20) X3 - c(21:30) X4 - c(31:40) X5 - c(41:50) DF - data.frame(X1, X2, X3, X4, X5) as.data.frame(sapply(DF, function (x) { qx - quantile(x) cut(x, qx, include.lowest = TRUE, labels = 1:4) })) You may also have a look at function

Re: [R] betareg help

2011-03-13 Thread Vlatka Matkovic Puljic
Sorry, here is my data (attached). 2011/3/12 Ben Bolker bbol...@gmail.com Vlatka Matkovic Puljic v.matkovic.puljic at gmail.com writes: That was also my first thought. But I guess it has something to do with W and phihat (which I'm struggling to check Again, it would help to post

Re: [R] 'Date' elements within a matrix

2011-03-13 Thread Gabor Grothendieck
On Sun, Mar 13, 2011 at 11:46 AM, Bogaso Christofer bogaso.christo...@gmail.com wrote: Thanks everyone for clarifying my query. However I was wondering why that Date character is not preserved within a matrix? Why R forcefully changes that to numeric? I am especially concerned because as per

Re: [R] how to change the margins of a plot area

2011-03-13 Thread Lathouri, Maria
Dear all I have attached a file in a csv format, with two variables; the code that I am using to plot the boxplots is boxplot(ALKY, CL, ylab=Concentration, lwd=0.7, boxwex=0.4) I hope this will help. Thanks Maria From: John Kane [jrkrid...@yahoo.ca]

[R] using pre-calculated coefficients and LP in coxph()?

2011-03-13 Thread Angel Russo
I need to force a coxph() function in R to use a pre-calculated set of beta coefficients of a gene signature consisting of xx genes and the gene expression is also provided of those xx genes. If I try to use coxph() function in R using just the gene expression data alone, the beta coefficients

Re: [R] Need Assistance in Stacked Area plot

2011-03-13 Thread Hadley Wickham
You might try sending a reproducible example (https://github.com/hadley/devtools/wiki/Reproducibility) to the ggplot2 mailing list. Hadley On Wed, Feb 16, 2011 at 8:41 AM, Kishorenalluri kishorenalluri...@gmail.com wrote: Dear All, I need the assistance to plot the staked area plot using

Re: [R] betareg help

2011-03-13 Thread Vlatka Matkovic Puljic
http://dl.dropbox.com/u/21595123/Book1.csv 2011/3/13 David Winsemius dwinsem...@comcast.net Nothing came through. You need to read the posting guide. On Mar 13, 2011, at 12:59 PM, Vlatka Matkovic Puljic wrote: Sorry, here is my data (attached). 2011/3/12 Ben Bolker bbol...@gmail.com

Re: [R] using pre-calculated coefficients and LP in coxph()?

2011-03-13 Thread Dimitris Rizopoulos
probably you want to use the 'init' argument and 'iter.max' control-argument of coxph(). For example, for the Lung dataset, we fix the coefficients of age and ph.karno at 0.05 and -0.05, respectively: library(survival) coxph(Surv(time, status) ~ age + ph.karno, data = lung, init = c(0.05,

Re: [R] betareg help

2011-03-13 Thread Ben Bolker
The problem seems to be that the algorithm for coming up with a starting guess for the phi (dispersion) parameter is getting a negative number. It's not all that easy to figure this out ... The data set is a little bit nasty (lots of points stacked on the equivalent of (0,0)), but not

[R] Stepwise Discriminant... in R

2011-03-13 Thread Ty Smith
Hello R list, I'm looking to do some stepwise discriminant function analysis (DFA) based on the minimization of Wilks' lambda in R to end up with a composite signature (of metals Al,Sb,Bi,Cr,Ba) capable of discriminating 100% of the source factors (LANDUSE: A,B,C). The Wilks' lambda portion

Re: [R] betareg help

2011-03-13 Thread Achim Zeileis
On Sun, 13 Mar 2011, Vlatka Matkovic Puljic wrote: http://dl.dropbox.com/u/21595123/Book1.csv Thanks. As I suspected. Due to the many 0.001 values, the starting value selection does not work well. In the development version of betareg() I've added a more useful warning message and an ad hoc

Re: [R] using pre-calculated coefficients and LP in coxph()?

2011-03-13 Thread David Winsemius
On Mar 13, 2011, at 1:32 PM, Dimitris Rizopoulos wrote: probably you want to use the 'init' argument and 'iter.max' control- argument of coxph(). For example, for the Lung dataset, we fix the coefficients of age and ph.karno at 0.05 and -0.05, respectively: library(survival)

Re: [R] betareg help

2011-03-13 Thread Achim Zeileis
Ben, thanks for your analysis...I also just sent a message with some similar (and some different) ideas. On Sun, 13 Mar 2011, Ben Bolker wrote: The problem seems to be that the algorithm for coming up with a starting guess for the phi (dispersion) parameter is getting a negative number.

Re: [R] pass character vector in instrument field of get.hist.quote function

2011-03-13 Thread algotr8der
Thank you all. Your solutions work. I suppose it doesnt matter whether I use coredata or not (at least for my current purposes). I have created a user-defined function and have saved it in a .R file in my current working directory. But now I'm not sure how to invoke this function. R complains that

[R] troubles with logistic regression

2011-03-13 Thread gked
hello everyone, I working on the dataset for my project in class and got stuck on trying to run logistic regression. here is my code: data - read.csv(file=C:/Users/fieder.data.2000.csv) # creating subset of men fieder.male-subset(data,data[,8]==1)

[R] chisq.test and cbind

2011-03-13 Thread Simone Santoro
Hi, This is a mixed conceptual/methodological issue. I have 3 years and 2 localities, I want to compare the Sex Ratio series between the two localities. I can do it year by year, for instance: SR2010-data.frame(FAO=c(96,52),JUNC=c(60,42)) SR2010 FAO JUNC 1 96 60 2 52 42

Re: [R] pass character vector in instrument field of get.hist.quote function

2011-03-13 Thread David Winsemius
On Mar 13, 2011, at 2:29 PM, algotr8der wrote: Thank you all. Your solutions work. I suppose it doesnt matter whether I use coredata or not (at least for my current purposes). I have created a user-defined function and have saved it in a .R file in my current working directory. But now I'm

Re: [R] using pre-calculated coefficients and LP in coxph()?

2011-03-13 Thread Angel Russo
Thanks very much Dimitrius and David. I want to compute CPE using pre-calculated beta-model and linear.predictor using the following code. I hope it the code is OK. Let me know. I am also doing some sanity checks. testc$x - scores testc$y - Surv(testdata$time,testdata$status) testfit - coxph(y ~

Re: [R] using pre-calculated coefficients and LP in coxph()?

2011-03-13 Thread Ravi Varadhan
Like David, I too thought that `offset' is the way to do this. I was actually in the midst of testing the differences between using `offset' and `init' when David's email came. Here is what I could figure out so far: 1. If you want to fix only a subset of regressors, but let others be

[R] FW: how to change the margins of a plot area

2011-03-13 Thread Lathouri, Maria
Dear all I am sorry about that; I thought that since in R csv formats are acceptable, it will be here as well. I have attached it in a text format. I hope now it is better. Thank you Maria From: David Winsemius [dwinsem...@comcast.net] Sent: 13 March

Re: [R] using pre-calculated coefficients and LP in coxph()?

2011-03-13 Thread Dimitris Rizopoulos
On 3/13/2011 7:43 PM, Ravi Varadhan wrote: Like David, I too thought that `offset' is the way to do this. I was actually in the midst of testing the differences between using `offset' and `init' when David's email came. Here is what I could figure out so far: 1. If you want to fix only a

Re: [R] using pre-calculated coefficients and LP in coxph()?

2011-03-13 Thread David Winsemius
On Mar 13, 2011, at 2:43 PM, Ravi Varadhan wrote: Like David, I too thought that `offset' is the way to do this. I was actually in the midst of testing the differences between using `offset' and `init' when David's email came. Here is what I could figure out so far: 1. If you want to

Re: [R] pass character vector in instrument field of get.hist.quote function

2011-03-13 Thread Joshua Ulrich
Sorry for the late reply. Here's another approach using quantmod::getSymbols. It implicitly loops over a vector of tickers. require(quantmod) getSymbols(tickers[,1], from=2011-01-01, to=2011-01-31) # If you want to merge all the close prices into one object: ClosePrices - do.call(merge,

[R] An example of using neuralnet to predict infinite steps ahead

2011-03-13 Thread Eduardo M. A. M.Mendes
Hello I am new to R and wonder whether someone out there could send me an example on how to use the package neuralnet to fit a model to data, following the usual procedure, that is, fitting the model using the training set and then using the validation set to check the model. Moreover, the

[R] An example on how to use neuralnet to predict values

2011-03-13 Thread Eduardo M. A. M. Mendes
Hello I am new to R and wonder whether someone out there could send me an example on how to use the package neuralnet to fit a model to data, following the usual procedure, that is, fitting the model using the training set and then using the validation set to check the model. Moreover, the

Re: [R] use of ROCR package (ROC curve / AUC value) in a specific case versus integral calculation

2011-03-13 Thread Jose-Marcio Martins da Cruz
Christine SINOQUET wrote: Hello, I would like to use the ROCR package to draw ROC curves and compute AUC values. However, in the specific context of my application, the true positive rates and false positive rates are already provided by some upstream method. Of course, I can draw a ROC plot

[R] readMat - how to retrieve the variables

2011-03-13 Thread Eduardo M. A. M.Mendes
Hello I have a matlab MAT file that contains one single variable: a. The structure of a is as follows: a.river1.flow (flow values) a.river1.date_flow (date) a.river1.precip (precipitation values) a.river1.date_precip a.river2.flow a.river2.date_flow a.river2.precip a.river2.date_precip I have

Re: [R] Having a problem with choose.files

2011-03-13 Thread Duncan Murdoch
On 11-03-13 7:11 AM, carl.finkbei...@tnsglobal.com wrote: I am relatively new to R, and am having a problem with the following snippet of code, and I do not at all understand why it is behaving this way. I am running Windows XP, with R 2.12.1. I copy and paste these 4 lines into the R Console:

Re: [R] readMat - how to retrieve the variables

2011-03-13 Thread Joshua Wiley
Hi Ed, Can you please provide *at least* the R output from running: str(data) where data is the variable name you stored the results of readMat() in. If it is reasonably small and can be sent as plaintext (I do not know Matlabs file format off hand), you could send us the actual data so we can

[R] devSVG error

2011-03-13 Thread Kyle Covington
I was using devSVG to save plots of trees using the RSVGDevice package for devSVG and tree package for the trees. When I put text into the plot, obviously there are and symbols. These seem to be corrupting the svg file which is XML and makes use of for syntax. Is there any way around this,

Re: [R] readMat - how to retrieve the variables

2011-03-13 Thread Eduardo M. A. M.Mendes
Hi Joshua Many thanks for the prompt reply. I have saved a short version of the matlab file and the output on R is b=readMat(testr.mat) b $a , , 1 [,1] river1 List,2 river2 List,2 attr(,header) attr(,header)$description [1] MATLAB 5.0 MAT-file, Platform: PCWIN, Created on: Sun Mar

Re: [R] R hangs when connected via VPN [incl. minimal example]

2011-03-13 Thread Marius Hofert
Dear Duncan, thanks for your suggestion. I contacted REvolution Computing on this behalf. Rmpi and rlecuyer are loaded automatically, so they are not explicitly needed in the minimal example. I'll post the answer (if I receive one). It's quite an annoying problem if you frequently work on a

Re: [R] readMat - how to retrieve the variables

2011-03-13 Thread Joshua Wiley
On Sun, Mar 13, 2011 at 2:56 PM, Eduardo M. A. M.Mendes emammen...@gmail.com wrote: Hi Joshua Many thanks for the prompt reply. I have saved a short version of the matlab file and the output on R is b=readMat(testr.mat) b $a , , 1       [,1] river1 List,2 river2 List,2 It looks like

[R] confidence intervals for noncentrality parameters

2011-03-13 Thread David Bickel
Is there any quick way to compute confidence intervals for the noncentrality parameter of the noncentral chi-square family? I get an error when installing the Deducer package. I would appreciate any help. David __ R-help@r-project.org mailing list

Re: [R] readMat - how to retrieve the variables

2011-03-13 Thread Eduardo M. A. M.Mendes
Hi Joshua Many thanks. The values of flow can be accessed in a weird way and we can used them for some calculations. Since I am a newbie as far as using R is concerned I wonder whether you could tell me how to create a structure in R that looks like the one I have in matlab (that is, a

[R] install.packages reshape failure

2011-03-13 Thread Geoff Russell
I'm not sure where I should send this, I don't have a bugzilla account, but ... it concerns an interaction between library(reshape) and install.packages() ... My current .Rprofile includes: library(reshape) After which install.packages fails ... e.g., install.packages(quantreg) Warning in

Re: [R] readMat - how to retrieve the variables

2011-03-13 Thread Joshua Wiley
Hi Ed, Here are some different ways of structuring and storing data in R as well as how to access them. Hope this helps, Josh # set.seed(10) ## Option 1a (closest to what you want?) a1a - list(river1 = data.frame(flow =

Re: [R] readMat - how to retrieve the variables

2011-03-13 Thread David Winsemius
On Mar 13, 2011, at 6:42 PM, Eduardo M. A. M.Mendes wrote: Hi Joshua Many thanks. The values of flow can be accessed in a weird way and we can used them for some calculations. Since I am a newbie as far as using R is concerned I wonder whether you could tell me how to create a

Re: [R] install.packages reshape failure

2011-03-13 Thread Joshua Wiley
Hi Geoff, What is your platform and R version? I cannot replicate on either: R version 2.12.1 (2010-12-16) Platform: i386-pc-mingw32/i386 (32-bit) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] reshape_0.8.4 plyr_1.4

[R] Problems getting html files out of R CMD check

2011-03-13 Thread Amos Folarin
Hi, I'm trying to R CMD check a package, however I have hit a snag. There seems to be a problem with the creation of the /html files (the only file that's constructed here is the 00Index.html). I've tested each of the .Rd files independently with R CMD Rdconv, they all happily create html files

Re: [R] readMat - how to retrieve the variables

2011-03-13 Thread Eduardo M. A. M.Mendes
Hi Joshua Many many thanks. Cheers Ed -Original Message- From: Joshua Wiley [mailto:jwiley.ps...@gmail.com] Sent: Sunday, March 13, 2011 8:00 PM To: Eduardo M. A. M.Mendes Cc: R-help@r-project.org Subject: Re: [R] readMat - how to retrieve the variables Hi Ed, Here are some

Re: [R] readMat - how to retrieve the variables

2011-03-13 Thread Eduardo M. A. M.Mendes
Hello there Here is the output of the command structure(list(a = structure(list(structure(list(structure(c(16.259746877453, 17.7125316239611, 17.7801266531401, 18.7370886410339, 18.5622784910323, 19. ), .Dim = c(3683L, 1L)), structure(c(0, 0, 6.7, 46.1, 2, 0, 29.5, 93.7, 4.5, 39.6,

Re: [R] readMat - how to retrieve the variables

2011-03-13 Thread David Winsemius
On Mar 13, 2011, at 7:27 PM, Eduardo M. A. M.Mendes wrote: Hello there Here is the output of the command structure(list(a = structure(list(structure(list(structure(c(16.259746877453, 17.7125316239611, 17.7801266531401, 18.7370886410339, 18.5622784910323, 19. That seems pretty

Re: [R] readMat - how to retrieve the variables

2011-03-13 Thread Eduardo M. A. M.Mendes
Hi there ... means that I have not copied all the data that R showed on the screen. Cheers Ed -Original Message- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: Sunday, March 13, 2011 8:37 PM To: Eduardo M. A. M.Mendes Cc: 'Joshua Wiley'; R-help@r-project.org Subject:

Re: [R] readMat - how to retrieve the variables

2011-03-13 Thread David Winsemius
On Mar 13, 2011, at 7:48 PM, Eduardo M. A. M.Mendes wrote: Hi there ... means that I have not copied all the data that R showed on the screen. I fail to see the point in posting mangled dput output. -- David. Cheers Ed -Original Message- From: David Winsemius

[R] pairwise p-values in KM plots?

2011-03-13 Thread Angel Russo
How can I compute pairwise p-values in Kaplan-meier plots for three or more groups? bin.1-cut(score,c(-1000,-1,1,1000),c(low,intermediate,high)) I use km.coxph.plot currently which reports one p-value. Thanks very much. [[alternative HTML version deleted]]

Re: [R] readMat - how to retrieve the variables

2011-03-13 Thread Eduardo M. A. M.Mendes
So sorry but the data is confidential. Cheers Ed -Original Message- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: Sunday, March 13, 2011 9:16 PM To: Eduardo M. A. M.Mendes Cc: 'Joshua Wiley'; R-help@r-project.org Subject: Re: [R] readMat - how to retrieve the variables

Re: [R] Problems getting html files out of R CMD check

2011-03-13 Thread Duncan Murdoch
On 11-03-13 7:14 PM, Amos Folarin wrote: Hi, I'm trying to R CMD check a package, however I have hit a snag. There seems to be a problem with the creation of the /html files (the only file that's constructed here is the 00Index.html). I've tested each of the .Rd files independently with R CMD

Re: [R] Stepwise Discriminant... in R

2011-03-13 Thread Bill.Venables
If you want to do a stepwise selection there is a function in the klaR package to do it. This is not what you are asking for, though. You want a way of finding the successive error rates as additional variables are added in the forward selection process. As far as I can see you have to do

Re: [R] Plotting symbols and colors based upon data values

2011-03-13 Thread David Winsemius
On Mar 13, 2011, at 8:51 PM, Mark Linderman wrote: David, thank you for your quick reply. I spent a few minutes getting your command to work with some sparse synthetic data, and then spent several hours trying to figure out why my data didn't work (at least for symbols, colors look

Re: [R] troubles with logistic regression

2011-03-13 Thread Bill.Venables
It means you have selected a response variable from one data frame (unmarried.male) and a predictor from another data frame (fieder.male) and they have different lengths. You might be better off if you used the names in the data frame rather than selecting columns in a form such as

[R] Non-constancy of variances in mixed model.

2011-03-13 Thread Ben Ward
Hi, I've been doing an experiment, measuring the dead-zone-diameters of bacteria, when they've been grown with paper diffusion disks of antimicrobial. There are two groups, or treatments - one is bacteria that have been cultured in said antimicrobial for the past year, the other group is of

Re: [R] pairwise p-values in KM plots?

2011-03-13 Thread David Winsemius
On Mar 13, 2011, at 8:33 PM, Angel Russo wrote: How can I compute pairwise p-values in Kaplan-meier plots for three or more groups? bin.1-cut(score,c(-1000,-1,1,1000),c(low,intermediate,high)) I use km.coxph.plot currently which reports one p-value. help(summary.glht, package=multcomp)

Re: [R] How to source a part of the file

2011-03-13 Thread Paul Y. Peng
Many thanks to Jim Holtman and Gabor Grothendieck for your quick responses. Jim's solution works beautifully for my tasks. Thanks. I also tried Gabor's solution based on pipe(). Unfortunately it only works on a linux PC, not on Windows 7/Vista. Submitting the command in Windows results in nothing.

Re: [R] use caret to rank predictors by random forest model

2011-03-13 Thread Xiaoqi Cui
Thanks for your prompt reply! You're right, I didn't add the parameter importance=TRUE when I used function train to fit the random forest model. Once I used the above parameter, everything went well. Also the functions varImp and plot work well too. I noticed caret is really good at

Re: [R] How to source a part of the file

2011-03-13 Thread Gabor Grothendieck
On Sun, Mar 13, 2011 at 11:32 PM, Paul Y. Peng pywp...@gmail.com wrote: Many thanks to Jim Holtman and Gabor Grothendieck for your quick responses. Jim's solution works beautifully for my tasks. Thanks. I also tried Gabor's solution based on pipe(). Unfortunately it only works on a linux PC,

[R] using initialize or using a constructor function

2011-03-13 Thread Laura Smith
Hi I'm trying to learn about S4 methods, classes, etc. Is it better to use initialize or use a construction function, please? Thank you. Laura Smith [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

[R] nlysystemfit and loglikelihood values

2011-03-13 Thread Alex Olssen
Dear R-help, The documentation for systemfit shows that logLik() can be used to obtain loglikelihood values from linear systems estimated by systemfit(). It seems to me that logLik() cannot be used for nlsystemfit(). Does anyone know of any other packages that might let me obtain the

[R] svg malformed on CentOS (epel R)

2011-03-13 Thread Jeroen Ooms
There is an issue with the default svg device on a centos workstation that I am using. It does not result in an error, but it produces malformed svg images. Exactly the same script works just fine on an ubuntu box. On Ubuntu I am using R binary that comes with maverick, on centos I am using the

[R] Serial Date

2011-03-13 Thread Raoni Rosa Rodrigues
Hello R Help, I'm working in a project with a software that register date and time data in serial time format. This format is used by excel, for exemple. In this format, 40597.3911423958 is 2011/2/23 09:23:15. First part is number os days since 1900/1/1, and second part is a fraction of a day.

Re: [R] Plotting symbols and colors based upon data values

2011-03-13 Thread Mark Linderman
David, thank you for your quick reply. I spent a few minutes getting your command to work with some sparse synthetic data, and then spent several hours trying to figure out why my data didn't work (at least for symbols, colors look okay). I have massaged my data to where it is practically

Re: [R] How to source a part of the file

2011-03-13 Thread Paul Y. Peng
Yes, I do have Rtools installed on two Windows PCs I tested, and I used them to build R packages. I use sed all the time with no problems. Thanks for confirming me that it works on your Windows PC. I will test it again and will update you if I find out what's wrong in my pc. On Sun, Mar 13, 2011

[R] recursive do.call

2011-03-13 Thread Jeroen Ooms
I would like to define a recursive equivalent to call or do.call, which takes a vector of multiple function names and 'chains' them, by greedy matching of arguments down the chain. For example, I would like to be able to do: rec.do.call(c(glm,coef,print), list(formula=dist~speed, digits=3,

Re: [R] How to source a part of the file

2011-03-13 Thread Gabor Grothendieck
On Mon, Mar 14, 2011 at 12:07 AM, Paul Y. Peng pywp...@gmail.com wrote: Yes, I do have Rtools installed on two Windows PCs I tested, and I used them to build R packages. I use sed all the time with no problems. Thanks for confirming me that it works on your Windows PC. I will test it again and