[R] set up a blank csv file and write time series to it row by row

Dear Friends. Greetings! I have asked the question of how to set up a blank file and write a list to it as a row for many times, with the number of lists unknown. I have received many beautiful solutions. Thanks go to Professor *Murdoch, Professor *Menne, Professor Grothendieck and Dr. Olshansk

[R] Unexpected behavior in PBSmapping package

Using R 2.5.1 on Windows XP Professional, and PBSmapping package version 2.51, I have encountered some behavior which puzzles me. I am including the package's listed maintainer on this email but also seek the thoughts of the R-help community. I have a set of EventData, which I want to plot as

Re: [R] Help using gPath

Hi Emilio Gagliardi wrote: > Hi Paul, > > I'm sorry for not posting code, I wasn't sure if it would be helpful without > the data...should I post the code and a sample of the data? I will remember > to do that next time! It's important not only to post code, but also to make sure that other

Re: [R] small sample techniques

> -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Nair, > Murlidharan T > Sent: Thursday, August 09, 2007 12:02 PM > To: Nordlund, Dan (DSHS/RDA); r-help@stat.math.ethz.ch > Subject: Re: [R] small sample techniques > > n=300 > 30% taking A relief fro

[R] error message: image not found

I have a R version 2.4 and I installed R version 2.5(current version) on Mac OS X 10.4.10. I tried "dyn.load" to load a object code compiled from C source. I got the following error message: Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/User

Re: [R] Subsetting by number of observations in a factor

Here is an even faster way: > # faster way > x.mg.size <- table(x$mg) # count occurance > x.mg.5 <- names(x.mg.size)[x.mg.size > 5] # select greater than 5 > x.new1 <- subset(x, x$mg %in% x.mg.5) # use in the subset > x.new1 mg data 1 A1 4 A4 5 D5 6 D6 7 A7 8

Re: [R] Tukey HSD

Please see the R-help message http://finzi.psych.upenn.edu/R/Rhelp02a/archive/105165.html __ 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 a

Re: [R] Subsetting by number of observations in a factor

Jim, > Does this do what you want? It creates a new dataframe with those > 'mg' that have at least a certain number of observation. Looks good. I also have an alternative solution which appears to work, so I'll see which is quicker on the big data set in question. My solution: mgsize <- as.dat

[R] compute ROC curve?

Hello, i have continuous test results for dieased and nondiseased subjects, say X and Y. Both are vectors of numbers. is there any R function which can generate the step function of ROC curve automatically? Thanks! [[alternative HTML version deleted]] __

Re: [R] Seasonality

?monthplot ?stl On 8/10/07, Alberto Monteiro <[EMAIL PROTECTED]> wrote: > I have a time series x = f(t), where t is taken for each > month. What is the best function to detect if _x_ has a seasonal > variation? If there is such seasonal effect, what is the > best function to estimate it? > > Fun

Re: [R] Subsetting by number of observations in a factor

Does this do what you want? It creates a new dataframe with those 'mg' that have at least a certain number of observation. > set.seed(2) > # create some test data > x <- data.frame(mg=sample(LETTERS[1:4], 20, TRUE), data=1:20) > # split the data into subsets based on 'mg' > x.split <- split(x, x$

Re: [R] Systematically biased count data regression model

Hi Matthew, You may be experiencing the classic 'regression towards the mean' phenomenon, in which case shrinkage estimation may help with prediction (extremely low and high values need to be shrunk back towards the mean) Here's a reference that discusses the issue in a manner somewhat related t

Re: [R] Systematically biased count data regression model

Here is one other idea. Since we are not doing that well with the entire data set lets look at a portion and see if we can do better there. This line of code seems to show that D is related to T: plot(data) so lets try conditioning D ~ T on all combos of the factor levels library(lattice) xyp

Re: [R] odfWeave processing error, file specific

Aric, Can you send me a reproducible example (code and odt file) plus the results if sessionInfo()? Thanks, Max -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Aric Gregson Sent: Thursday, August 09, 2007 6:56 PM To: r-help@stat.math.ethz.ch Subject: [R

Re: [R] Systematically biased count data regression model

I guess I should not have been so quick to make that conclusion since it seems that 74% of the values in the holdout set are FALSE so simply guessing FALSE for each one would give us 74% accuracy: > table(DD[201:254]) FALSE TRUE 4014 > 40/54 [1] 0.7407407 On 8/9/07, Gabor Grothendieck

Re: [R] small sample techniques

Hi Murli, First of all, regarding prop.test, you made a typo: you should have used prop.test(c(69,90),c(300,300)) which gives you the squared value of 3.4228, and it's square root is 1.85 which is not too far from 1.94. I would use Fisher Exact Test (fisher.test). Two sided test has a p-value of

Re: [R] Systematically biased count data regression model

Matthew, In response to that post, I am afraid I have to disagree. I think a poor model fit (eg 16%) is a reflection of a lot of unmeasured factors and therefore random error in the model. This would explain why overall predictive performance is poor (eg a lot of error in the model) Your sit

Re: [R] Systematically biased count data regression model

Perhaps you don't really need to predict the precise count. Maybe its good enough to predict whether the count is above or below average. In that case the model is 74% correct on a holdout sample of the last 54 points based on a model of the first 200 points. > # create model on first 200 and pre

[R] Subsetting by number of observations in a factor

Hi, I generally do my data preparation externally to R, so I this is a bit unfamiliar to me, but a colleague has asked me how to do certain data manipulations within R. Anyway, basically I can get his large file into a dataframe. One of the columns is a management group code (mg). There may be va

[R] odfWeave processing error, file specific

Hello, I hope there is a simple explanation for this. I have been using odfWeave with great satisfaction in R 2.5.0. Unfortunately, I cannot get beyond the following error message with a particular file. I have copied and pasted into new files and the same error pops up. It looks like the error i

Re: [R] plot table with sapply - labeling problems

Here is a modified script that should work. In many cases where you want the names of the element of the list you are processing, you should work with the names: test<-as.data.frame(cbind(round(runif(50,0,5)),round(runif(50,0,3)),round(runif(50,0,4 sapply(test, table)->vardist sapply(test, fu

Re: [R] Systematically biased count data regression model

Dear all, I received a very helpful response from someone who requested anonymity, but to whom I am grateful. PLEASE do not quote my name or email (I am trying to stay off spam lists) Matthew: I think this is just a reflection of the fact the model does not fit perfectly. The example below is

[R] a question on lda{MASS}

hi, assume val is the test data while m is lda model value by using CV=F x = predict(m, val) val2 = val[, 1:(ncol(val)-1)] # the last column is class label # col is sample, row is variable then I am wondering if x$x == (apply(val2*m$scaling), 2, sum) i.e., the scaling (is it coeff vector?) t

Re: [R] Systematically biased count data regression model

Dear Paul, Thank you very much for your comment. I will apply the 'latent' approach you suggested. Sincerely, Matthew Bowser On 8/9/07, paulandpen <[EMAIL PROTECTED]> wrote: > Matthew > > it is possible that your results are suffering from heterogeneity, it may be > that your model performs we

Re: [R] Memory problem

It seems the problem lies in this line: > try(fit.lme <- lme(Beta ~ group*session*difficulty+FTND, random = > ~1|Subj, Model), tag <- 1); As lme fails for most iterations in the loop, the 'try' function catches one error message for each failed iteration. But the puzzling part is, why does

Re: [R] S4 based package giving strange error at install time, but not at check time

On Thu, 9 Aug 2007, Rajarshi Guha wrote: > Hi, I have a S4 based package package that was loading fine on R > 2.5.0 on both OS X and > Linux. I was checking the package against 2.5.1 and doing R CMD check > does not give any warnings. So I next built the package and installed > it. Though the pack

[R] Tukey HSD

Hi, I was wondering if you could help me: The following are the first few lines of my data set: subject group condition depvar s1 c ver 114.87 s1 c feet114.87 s1 c body114.87 s2 c ver 73.54 s2 c feet64.32 s2 c b

Re: [R] RMySQL loading error

This was just discussed: https://www.stat.math.ethz.ch/pipermail/r-help/2007-August/138142.html On 8/9/07, Clara Anton <[EMAIL PROTECTED]> wrote: > Hi, > > I am having problems loading RMySQL. > > I am using MySQL 5.0, R version 2.5.1, and RMySQL with Windows XP. > When I try to load rMySQL I ge

Re: [R] RMySQL loading error

On Thu, 9 Aug 2007, Clara Anton wrote: > Hi, > > I am having problems loading RMySQL. > > I am using MySQL 5.0, R version 2.5.1, and RMySQL with Windows XP. More exact versions would be helpful. > When I try to load rMySQL I get the following error: > > > require(RMySQL) > Loading required pack

Re: [R] Memory Experimentation: Rule of Thumb = 10-15 Times the Memory

The examples were just artificially created data. We don't know what the real case is but if each entry is distinct then factors won't help; however, if they are not distinct then there is a huge potential savings. Also if they are really numeric, as in your example, then storing them as numeric

Re: [R] small sample techniques

30 is not 30% of 300 (it is 10%), so your prop.test below is testing something different from your hand calculations. Try: > prop.test(c(.30,.23)*300,c(300,300), correct=FALSE) 2-sample test for equality of proportions without continuity correction data: c(0.3, 0.23) * 300 out

[R] S4 based package giving strange error at install time, but not at check time

Hi, I have a S4 based package package that was loading fine on R 2.5.0 on both OS X and Linux. I was checking the package against 2.5.1 and doing R CMD check does not give any warnings. So I next built the package and installed it. Though the package installed fine I noticed the following message

Re: [R] Memory Experimentation: Rule of Thumb = 10-15 Times the Memory

On Thu, 9 Aug 2007, Charles C. Berry wrote: > On Thu, 9 Aug 2007, Michael Cassin wrote: > >> I really appreciate the advice and this database solution will be useful to >> me for other problems, but in this case I need to address the specific >> problem of scan and read.* using so much memory. >>

[R] RMySQL loading error

Hi, I am having problems loading RMySQL. I am using MySQL 5.0, R version 2.5.1, and RMySQL with Windows XP. When I try to load rMySQL I get the following error: > require(RMySQL) Loading required package: RMySQL Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shar

Re: [R] Memory Experimentation: Rule of Thumb = 10-15 Times the Memory

I do not see how this helps Mike's case: > res <- (as.character(1:1e6)) > object.size(res) [1] 3624 > object.size(as.factor(res)) [1] 4224 Anyway, my point was that if two character vectors for which all.equal() yields TRUE can differ by almost an order of magnitude in object.size(),

Re: [R] Memory Experimentation: Rule of Thumb = 10-15 Times the Memory

Try it as a factor: > big2 <- rep(letters,length=1e6) > object.size(big2)/1e6 [1] 4.000856 > object.size(as.factor(big2))/1e6 [1] 4.001184 > big3 <- paste(big2,big2,sep='') > object.size(big3)/1e6 [1] 36.2 > object.size(as.factor(big3))/1e6 [1] 4.001184 On 8/9/07, Charles C. Berry <[EMAIL P

Re: [R] tcltk error on Linux

Seth and Brian, Today and downloaded and installed the latest R-devel and tcltk now works. My suspicion is that Tcl was not on my path when R-devel was installed previously. BTW, I had though that is was a courtesy to cc: the maintainers of a package when writing either R-devel or R-help about

Re: [R] depreciation of $ for atomic vectors

Try this: DF <- data.frame(start=1:5,end=10:6) # apply(DF,1,function(row){ return(row$start + row$end) }) DF$start + DF$end apply(DF, 1, function(row) row[["start"]] + row[["end"]]) apply(DF, 1, function(row) row["start"] + row["end"]) On 8/9/07, Ido M. Tamir <[EMAIL PROTECTED]> wrote: > Dear

[R] depreciation of $ for atomic vectors

Dear All, I would like to know why $ was deprecated for atomic vectors and what I can use instead. I got used to the following idiom for working with data frames: df <- data.frame(start=1:5,end=10:6) apply(df,1,function(row){ return(row$start + row$end) }) I have a data.frame with named columns

Re: [R] Memory Experimentation: Rule of Thumb = 10-15 Times the Memory

On Thu, 9 Aug 2007, Michael Cassin wrote: > I really appreciate the advice and this database solution will be useful to > me for other problems, but in this case I need to address the specific > problem of scan and read.* using so much memory. > > Is this expected behaviour? Can the memory usage

Re: [R] Memory Experimentation: Rule of Thumb = 10-15 Times the Memory

One other idea. Don't use byrow = TRUE. Matrices are stored in column order so that might be more efficient. You can always transpose it later. Haven't tested it to see if it helps. On 8/9/07, Michael Cassin <[EMAIL PROTECTED]> wrote: > > I really appreciate the advice and this database solutio

Re: [R] small sample techniques

n=300 30% taking A relief from pain 23% taking B relief from pain Question; If there is no difference are we likely to get a 7% difference? Hypothesis H0: p1-p2=0 H1: p1-p2!=0 (not equal to) 1>Weighed average of two sample proportion 300(0.30)+300(0.23) --- = 0.265 3

Re: [R] Memory Experimentation: Rule of Thumb = 10-15 Times the Memory

I really appreciate the advice and this database solution will be useful to me for other problems, but in this case I need to address the specific problem of scan and read.* using so much memory. Is this expected behaviour? Can the memory usage be explained, and can it be made more efficient? Fo

Re: [R] Memory Experimentation: Rule of Thumb = 10-15 Times the Memory

Just one other thing. The command in my prior post reads the data into an in-memory database. If you find that is a problem then you can read it into a disk-based database by adding the dbname argument to the sqldf call naming the database. The database need not exist. It will be created by sqld

Re: [R] Memory Experimentation: Rule of Thumb = 10-15 Times the Memory

Another thing you could try would be reading it into a data base and then from there into R. The devel version of sqldf has this capability. That is it will use RSQLite to read the file directly into the database without going through R at all and then read it from there into R so its a complete

Re: [R] small sample techniques

> -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Nair, > Murlidharan T > Sent: Thursday, August 09, 2007 9:19 AM > To: Moshe Olshansky; Rolf Turner; r-help@stat.math.ethz.ch > Subject: Re: [R] small sample techniques > > Thanks, that discussion was

Re: [R] Need Help: Installing/Using xtable package

Ok, I got it now. Just: print(xtable(...),) Thanks! Matt On 8/9/07, Seth Falcon <[EMAIL PROTECTED]> wrote: > Peter Dalgaard <[EMAIL PROTECTED]> writes: > > > M. Jankowski wrote: > >> Hi all, > >> > >> Let me know if I need to ask this question of the bioconductor group. > >> I used the bioco

Re: [R] Need Help: Installing/Using xtable package

Peter Dalgaard <[EMAIL PROTECTED]> writes: > M. Jankowski wrote: >> Hi all, >> >> Let me know if I need to ask this question of the bioconductor group. >> I used the bioconductor utility to install this package and also the >> CRAN package.install function. >> >> My computer crashed a week ago. To

Re: [R] Memory Experimentation: Rule of Thumb = 10-15 Times the Memory

Thanks for looking, but my file has quotes. It's also 400MB, and I don't mind waiting, but don't have 6x the memory to read it in. On 8/9/07, Gabor Grothendieck <[EMAIL PROTECTED]> wrote: > > If we add quote = FALSE to the write.csv statement its twice as fast > reading it in. > > On 8/9/07, Mich

Re: [R] Need Help: Installing/Using xtable package

M. Jankowski wrote: > Hi all, > > Let me know if I need to ask this question of the bioconductor group. > I used the bioconductor utility to install this package and also the > CRAN package.install function. > > My computer crashed a week ago. Today I reinstalled all my > bioconductor/R packages. O

Re: [R] Memory Experimentation: Rule of Thumb = 10-15 Times the Memory

If we add quote = FALSE to the write.csv statement its twice as fast reading it in. On 8/9/07, Michael Cassin <[EMAIL PROTECTED]> wrote: > Hi, > > I've been having similar experiences and haven't been able to > substantially improve the efficiency using the guidance in the I/O > Manual. > > Could

Re: [R] Memory Experimentation: Rule of Thumb = 10-15 Times the Memory

Hi, I've been having similar experiences and haven't been able to substantially improve the efficiency using the guidance in the I/O Manual. Could anyone advise on how to improve the following scan()? It is not based on my real file, please assume that I do need to read in characters, and can't

[R] Need Help: Installing/Using xtable package

Hi all, Let me know if I need to ask this question of the bioconductor group. I used the bioconductor utility to install this package and also the CRAN package.install function. My computer crashed a week ago. Today I reinstalled all my bioconductor/R packages. One of my scripts is giving me the

Re: [R] How to apply functions over rows of multiple matrices

Is sens really what you want? The denominator is the indexes, e.g. if a row in goldstandard were c(0, 0, 1, 1) then you would be dividing by 3+4. Also test[which(gold == 1)] is the same as test[gold == 1] which is the same test * gold since gold has only 0 and 1's in it. Perhaps what you really

[R] Seasonality

I have a time series x = f(t), where t is taken for each month. What is the best function to detect if _x_ has a seasonal variation? If there is such seasonal effect, what is the best function to estimate it? Function arima has a "seasonal" parameter, but I guess this is too complex to be useful.

[R] How to apply functions over rows of multiple matrices

Dear ExpRts, I would like to perform a function with two arguments over the rows of two matrices. There are a couple of *applys (including mApply in Hmisc) but I haven't found out how to do it straightforward. Applying to row indices works, but looks like a poor hack to me: sens <- function(test,

Re: [R] Help using gPath

Hi Paul, I'm sorry for not posting code, I wasn't sure if it would be helpful without the data...should I post the code and a sample of the data? I will remember to do that next time! > grid.gedit(gPath("ylabel.text.382"), gp=gpar(fontsize=16)) OK, I think my confusion comes from the notation

Re: [R] small sample techniques

Thanks, that discussion was helpful. Well, I have another question I am comparing two proportions for its deviation from the hypothesized difference of zero. My manually calculated z ratio is 1.94. But, when I calculate it using prop.test, it uses Pearson's chi-squared test and the X-squared valu

Re: [R] Systematically biased count data regression model

Matthew it is possible that your results are suffering from heterogeneity, it may be that your model performs well at the aggregate level and this would explain good aggregate fit levels and decent predictive performance etc, you could perhaps look at a 'latent' approach to modelling your data,

Re: [R] Subject: Re: how to include bar values in a barplot?

Gabor, Putting the numbers in the bars is an improvement over putting them over the bars, but if the numbers are large relative to the bars, this could still create a "fuzzy" top to the bars making them harder to compare. This also has the problem of the poorly laid out table, numbers are easiest

Re: [R] Subject: Re: how to include bar values in a barplot?

Ted, Thanks for your thoughts. I don't take it as the start of a flame war (I don't want that either). My original intent was to get the original posters out of the mode of thinking they want to match what the spreadsheet does and into thinking about what message they are trying to get across.

[R] Systematically biased count data regression model

Dear all, I am attempting to explain patterns of arthropod family richness (count data) using a regression model. It seems to be able to do a pretty good job as an explanatory model (i.e. demonstrating relationships between dependent and independent variables), but it has systematic problems as a

Re: [R] tcltk error on Linux

Hi Mark, Prof Brian Ripley <[EMAIL PROTECTED]> writes: > On Thu, 9 Aug 2007, Mark W Kimpel wrote: > >> I am having trouble getting tcltk package to load on openSuse 10.2 >> running R-devel. I have specifically put my /usr/share/tcl directory in >> my PATH, but R doesn't seem to see it. I also have

Re: [R] Rcmdr window border lost

Andy Weller wrote: > OK, I tried completely removing and reinstalling R, but this has not > worked - I am still missing window borders for Rcmdr. I am certain that > everything is installed correctly and that all dependencies are met - > there must be something trivial I am missing?! > > Thanks

[R] Memory problem

I got a long list of error message repeating with the following 3 lines when running the loop at the end of this mail: R(580,0xa000ed88) malloc: *** vm_allocate(size=327680) failed (error code=3) R(580,0xa000ed88) malloc: *** error: can't allocate region R(580,0xa000ed88) malloc: *** set a bre

[R] Mac OSX fonts in R plots

I had been looking for information about including OSX fonts in R plots for a long time and never quite found the answer. I spent an hour or so gathering together the following solution which, as far as I have tested, works. I'm posting this for feedback and and archiving. I'd be interested in a

[R] AlgDesign expand.formula()

Can anyone explain why AlgDesign's expand.formula help and output differ? #From help: # quad(A,B,C) makes ~(A+B+C)^2+I(A^2)+I(B^2)+I(C^2) expand.formula(~quad(A+B+C)) #actually gives ~(A + B + C)^2 + I(A + B + C^2) They don't _look_ the same... Steve E ***

[R] Interpret impulse response functions from irf in MSBVAR library

Hello, I am wondering if anyone knows how to interpret the values returned by irf function in the MSBVAR library. Some of the literature I have read indicates that impulse responses in the dependent variables are often based on a 1 unit change in the independent variable, but other sources suggest

Re: [R] ARIMA fitting

On Tue, 7 Aug 2007, [EMAIL PROTECTED] wrote: Hello, I‘m trying to fit an ARIMA process, using STATS package, arima function. Can I expect, that fitted model with any parameters is stationary, causal and invertible? Please read ?arima: it answers all your questions, and points out that the ans

Re: [R] Subject: Re: how to include bar values in a barplot?

Gabor Grothendieck wrote: > You could put the numbers inside the bars in which > case it would not add to the height of the bar: I think the Cleveland/Tufte prescription would be much different: horizontal dot charts with the numbers in the right margin. I do this frequently with great effect.

[R] Help with Filtering (interest rates related)

Dear, r-help, Long time reader, first time poster, I'm working on a paper regarding a term structure estimation using the Kalman Filter Algorithm. The model in question is the Generalized Vasicek, and since there are coupon-bonds being estimated, I'm supposed to make some changes on the Kalman Fi

Re: [R] Subject: Re: how to include bar values in a barplot?

You could put the numbers inside the bars in which case it would not add to the height of the bar: x <- 1:5 names(x) <- letters[1:5] bp <- barplot(x) text(bp, x - .02 * diff(par("usr")[3:4]), x) On 8/9/07, Frank E Harrell Jr <[EMAIL PROTECTED]> wrote: > [EMAIL PROTECTED] wrote: > > Greg, I'm goin

Re: [R] Regsubsets statistics

On Wed, 8 Aug 2007, Markus Brugger wrote: > > Dear R-help, > > I have used the regsubsets function from the leaps package to do subset > selection of a logistic regression model with 6 independent variables and > all possible ^2 interactions. As I want to get information about the > statistics beh

Re: [R] Subject: Re: how to include bar values in a barplot?

[EMAIL PROTECTED] wrote: > Greg, I'm going to join issue with your here! Not that I'll go near > advocating "Excel-style" graphics (abominable, and the Patrick Burns > URL which you cite is remarkable in its restraint). Also, I'm aware > that this is potential flame-war territory -- again, I want

Re: [R] Help using gPath

Hi Emilio Gagliardi wrote: > Hi everyone,I'm trying to figure out how to use gPath and the documentation > is not very helpful :( > > I have the following plot object: > plot-surrounds:: > background > plot.gTree.378:: > background > guide.gTree.355:: (background.rect.345, minor-horizontal

Re: [R] Rcmdr window border lost

OK, I tried completely removing and reinstalling R, but this has not worked - I am still missing window borders for Rcmdr. I am certain that everything is installed correctly and that all dependencies are met - there must be something trivial I am missing?! Thanks in advance, Andy Andy Weller

Re: [R] Countvariable for id by date

Try this: Lines <- "id;dg1;dg2;date; 1;F28;;1997-11-04; 1;F20;F702;1998-11-09; 1;F20;;1997-12-03; 1;F208;;2001-03-18; 2;F32;;1999-03-07; 2;F29;F32;2000-01-06; 2;F32;;2003-07-05; 2;F323;F2800;2000-02-05; " # replace textConnection(Lines) with actual file name DF <- read.csv2(textConnection(Lines),

[R] Lo and MacKinlay variance ratio test (Lo.Mac)

Hi all, I am trying to calculate the variance ratio of a time series under heteroskedasticity. So I know that the variance ratio should be calculated as a weighted average of autocorrelations. But I don't find the same results when I calculate the variance ratio manually and when I compute the M2

[R] interior branch test

Dear R users, Does anyone know which package provide interior branch test for phylogenetic tree with distance based method? Any helps are really appreciated. Thank you. Nora. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/lis

[R] ARIMA fitting

Hello, I‘m trying to fit an ARIMA process, using STATS package, arima function. Can I expect, that fitted model with any parameters is stationary, causal and invertible? Thanks __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listin

Re: [R] Countvariable for id by date

This should do what you want: > x <- read.table(textConnection("id;dg1;dg2;date; + 1;F28;;1997-11-04; + 1;F20;F702;1998-11-09; + 1;F20;;1997-12-03; + 1;F208;;2001-03-18; + 2;F32;;1999-03-07; + 2;F29;F32;2000-01-06; + 2;F32;;2003-07-05; + 2;F323;F2800;2000-02

[R] Term Structure Estimation using Kalman Filter

Long time reader, first time poster, I'm working on a paper regarding a term structure estimation using the Kalman Filter Algorithm. The model in question is the Generalized Vasicek, and since there are coupon-bonds being estimated, I'm supposed to make some changes on the Kalman Filter. Does any

[R] Subject: Re: how to include bar values in a barplot?

Greg, I'm going to join issue with your here! Not that I'll go near advocating "Excel-style" graphics (abominable, and the Patrick Burns URL which you cite is remarkable in its restraint). Also, I'm aware that this is potential flame-war territory -- again, I want to avoid that too. However, this

[R] GLMM: MEEM error due to dichotomous variables

I am trying to run a GLMM on some binomial data. My fixed factors include 2 dichotomous variables, day, and distance. When I run the model: modelA<-glmmPQL(Leaving~Trial*Day*Dist,random=~1|Indiv,family="binomial") I get the error: iteration 1 Error in MEEM(object, conLin, control$niterEM) :

[R] Discriminant scores plot

Hello, How can I plot the discriminant scores resulting from prediction using a dataset and n lda model and its decission boundaries using GGobi and rggobi? Best regards, Dani Daniel Valverde Saubí Grup d'Aplicacions Biomèdiques de la Ressonància Magnètica Nuclear (GABRMN) Departament de Bioquími

Re: [R] Help on R performance using aov function

aov() will handle multiple responses and that would be considerably more efficient than running separate fits as you seem to be doing. Your code is nigh unreadable: please use your spacebar and remove the redundant semicolons: `Writing R Extensions' shows you how to tidy up your code to make i

[R] Help on R performance using aov function

Hi, I’m trying to replace some SAS statistical functions by R (batch calling). But I’ve seen that calling R in a batch mode (under Unix) takes about 2or 3 times more than SAS software. So it’s a great problem of performance for me. Here is an extract of the calculation: stoutput<-file("res_oneWay

Re: [R] substrings

one more, shorter, solution. > a [1] "a b c" "1 2 3" "q- 5" > gsub("\\s.+","",a) [1] "a" "1" "q-" Edna Bell wrote: > > I have a set of character results. If one of the characters is a > blank space, followed by other characters, I want to end at the blank > space. > > I tried strsplit, b

Re: [R] substrings

Is this what you want? > a<-c("a b c","1 2 3","q - 5") > a [1] "a b c" "1 2 3" "q - 5" > sapply(strsplit(a,"[[:blank:]]"),function(x)x[1]) [1] "a" "1" "q" Edna Bell wrote: > > I have a set of character results. If one of the characters is a > blank space, followed by other characters, I want

[R] Countvariable for id by date

Best R-users, Here’s a newbie question. I have tried to find an answer to this via help and the “ave(x,factor(),FUN=function(y) rank (z,tie=’first’)”-function, but without success. I have a dataframe (~8000 observations, registerdata) with four columns: id, d

[R] substrings

Hello again! I have a set of character results. If one of the characters is a blank space, followed by other characters, I want to end at the blank space. I tried strsplit, but it picks up again after the blank. Any help would be much appreciated. TIA, Edna ___

Re: [R] Change in R**2 for block entry regression

David Kaplan wrote: > Hi all, > > I'm demonstrating a block entry regression using R for my regression > class. For each block, I get the R**2 and the associated F. I do this > with separate regressions adding the next block in and then get the > results by writing separate summary() statemen

[R] data() problem solved

Problem solved: sapply(data(package="car")$results[,3], function(x)class(get(x))) sorry for the silliness Hi R Gurus: I'm using the data() function to get the list of data sets for a package. I would like to find the class for each data set; i.e.,data.frame, etc. Using str(), I can find the

[R] using data() and determining data types

Hi R Gurus: I'm using the data() function to get the list of data sets for a package. I would like to find the class for each data set; i.e.,data.frame, etc. Using str(), I can find the name of the data set. However, when I try the class function on the str output, I get "character", since the

[R] Odp: Successively eliminating most frequent elemets

Hi your construction is quite complicated so instead of refining it I tried to do such task different way. If I understand what you want to do you can use > set.seed(1) > T <- matrix(trunc(runif(20)*10), nrow=10, ncol=2) > T [,1] [,2] [1,]22 [2,]31 [3,]56 [4,]

Re: [R] tcltk error on Linux

On Thu, 9 Aug 2007, Mark W Kimpel wrote: > I am having trouble getting tcltk package to load on openSuse 10.2 > running R-devel. I have specifically put my /usr/share/tcl directory in > my PATH, but R doesn't seem to see it. I also have installed tk on my > system. Any ideas on what the problem is

Re: [R] R memory usage

See ?gc ?"Memory-limits" On Wed, 8 Aug 2007, Jun Ding wrote: > Hi All, > > I have two questions in terms of the memory usage in R > (sorry if the questions are naive, I am not familiar > with this at all). > > 1) I am running R in a linux cluster. By reading the R > helps, it seems there are no

Re: [R] cointegration analysis

Hello Dorina, if you apply ca.jo to a system with more than five variables, a *warning* is issued that no critical values are provided. This is not an error, but documented in ?ca.jo. In the seminal paper of Johansen, only cv for up to five variables are provided. Hence, you need to refer to a dif

Re: [R] Reading time/date string

On Thu, 9 Aug 2007, Matthew Walker wrote: > Thanks Mark, that was very helpful. I'm now so close! > > Can anyone tell me how to extract the "value" from an instance of a > "difftime" class? I can see the value, but how can I place it in a > dataframe? as.numeric(time_delta) Hint: you want

Re: [R] Reading time/date string

Thanks Mark, that was very helpful. I'm now so close! Can anyone tell me how to extract the "value" from an instance of a "difftime" class? I can see the value, but how can I place it in a dataframe? > time_string1 <- "10:17:07 02 Aug 2007" > time_string2 <- "13:17:40 02 Aug 2007" > >

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