[R] Odp: Jitter in correlation matrix?

Hi Add sapply(any.data.frame, jitter) into your function. Either sapply(na.omit(.), jitter) or pairs(sapply(..., jitter), ...) Regards Petr [EMAIL PROTECTED] [EMAIL PROTECTED] napsal dne 25.02.2008 00:26:27: Hi, I am just starting to use R for a graduate course, and I like how the

[R] Avoiding overplotting of text.

Hi all, I am plotting some data, and use text() to get variable names next to points on the graph. What is the best way to make sure that these text labels are readable and not overlapping when two datapoints are close? I've tried using jitter(), but the effect is random and doesn't always give a

[R] RWinEdt Install issue

Dear RUsers, I just upgraded from 2.6.0 to 2.6.2 and tried to reinstall the RWinEdt patch to work with WinEdt so that I can continue function as I always have but I have run into problems that I don't understand how to fix. Any help would be great. Essentially, I downloaded the latest

Re: [R] Odp: version 2.5.1 and version 2.3.1

Petr PIKAL wrote: Hi I can not help you to run your code in R 2.5.1 but I would recommend to use even more recent R version (2.6.1) Well, 2.6.2 is recent... or even maybe R 2.7.0. That one is heavily under development and I don't think it is the best option for regular users yet.

Re: [R] including data frames in R packages

On Sun, 2008-02-24 at 18:05 -0800, dxc13 wrote: useR's, Does any one know if there is a size limitation on the data frames that can be included in R packages. I have a data set in a text file that I would like to include in a package I am building and it is 8.5 MB in size. Will this be

[R] addreg help

Hello! Im having a bit of a problem creating martingale-residuals for my aalen additive model. Is it even possible in R to do that? My code for the additive model is the following: ruff -addreg(Surv(E$stop,E$delta) ~E$Zh +E$Zr +E$PSA +E$Treatment) summary(ruff)plot(ruff) If it had been a cox

Re: [R] To get more digits in precision of predict function of randomForests

Nagu wrote: Hi, I am using randomForests for a classification problem. The predict function in the randomForest library, when asked to return the probabilities, has precision of two digits after the decimal. I need at least four digits of precision for the predicted probabilities. How do

Re: [R] RWinEdt Install issue

Alexander Nervedi wrote: Dear RUsers, I just upgraded from 2.6.0 to 2.6.2 and tried to reinstall the RWinEdt patch to work with WinEdt so that I can continue function as I always have but I have run into problems that I don't understand how to fix. Any help would be great.

Re: [R] clustering problem

Karin Lagesen wrote: First I just want to say thanks for all the help I've had from the list so far..) I now have what I think is a clustering problem. I have lots of objects which I have measured a dissimilarity between. Now, this list only has one entry per pair, so it is not

Re: [R] How do I use as.Date when day values are missing?

Gabor Grothendieck wrote: In looking at this again here is a slight simplification. Its now only one line: library(chron) x - c(01/00/05, 01/22/06) as.chron(sub(/00/, /15/, x)) + (regexpr(/00/, x) 0) / 2 [1] (01/15/05 12:00:00) (01/22/06 00:00:00) You don't really need chron

Re: [R] including data frames in R packages

dxc13 wrote: useR's, Does any one know if there is a size limitation on the data frames that can be included in R packages. I have a data set in a text file that I would like to include in a package I am building and it is 8.5 MB in size. Will this be problematic? Not as such, no. There

Re: [R] efficient writing of calculation involving each element of 2 data frames.

Vikas N Kumar wrote: Hi I have 2 data.frames each of the same number of rows (approximately 3 or more entries). They also have the same number of columns, lets say 2. One column has the date, the other column has a double precision number. Let the column names be V1, V2. Now I

Re: [R] Avoiding overplotting of text.

Gustaf Rydevik wrote: Hi all, I am plotting some data, and use text() to get variable names next to points on the graph. What is the best way to make sure that these text labels are readable and not overlapping when two datapoints are close? I've tried using jitter(), but the effect is

Re: [R] Avoiding overplotting of text.

I am plotting some data, and use text() to get variable names next to points on the graph. What is the best way to make sure that these text labels are readable and not overlapping when two datapoints are close? I've tried using jitter(), but the effect is random and doesn't always give a

Re: [R] How do I use as.Date when day values are missing?

On Mon, Feb 25, 2008 at 6:03 AM, Peter Dalgaard [EMAIL PROTECTED] wrote: Gabor Grothendieck wrote: In looking at this again here is a slight simplification. Its now only one line: library(chron) x - c(01/00/05, 01/22/06) as.chron(sub(/00/, /15/, x)) + (regexpr(/00/, x) 0) / 2

[R] Exporting a dataframe from R to Excel

I am trying to export a dateframe created in R: Duration_summary V1 2.5 % 97.5 % V4 2.5 %97.5 % [1,] 1 0.46076018 1.128776 1.00 0.5280828 0.9576338 [2,] 0 0. 0.00 1.00 0.1741793 1.2352705 [3,] 1 0.46566719 1.313711 1.00 0.7233312

Re: [R] How do I use as.Date when day values are missing?

On Mon, Feb 25, 2008 at 7:40 AM, Peter Dalgaard [EMAIL PROTECTED] wrote: Gabor Grothendieck wrote: On Mon, Feb 25, 2008 at 6:03 AM, Peter Dalgaard [EMAIL PROTECTED] wrote: Gabor Grothendieck wrote: In looking at this again here is a slight simplification. Its now only one line:

Re: [R] Exporting a dataframe from R to Excel

Where did you get the idea to use sqlUpdate from? sqlSave is how you write a database to a table. I think it would be easier to use write.csv to write a .csv file and import that into Excel. ODBC connections to Excel work much better for reading than for writing. And there are other ways: see

Re: [R] Exporting a dataframe from R to Excel

You have tried write.table? write.table(x, file=file.xls, sep=\t, row.names=F) On 25/02/2008, Nadia Theron [EMAIL PROTECTED] wrote: I am trying to export a dateframe created in R: Duration_summary V1 2.5 % 97.5 % V4 2.5 %97.5 % [1,] 1 0.46076018 1.128776

[R] efficient is.na tabulation?

I am aware of table(is.na(df$var)) but is there an efficient way of create a table that shows the number of missing values in each variable of a data frame? Right now I am forced to create a new variable, varna-is.na(df$var), for each variable of the data frame, bind them to a new data frame

Re: [R] efficient is.na tabulation?

On 2/25/2008 8:59 AM, Angelo Passalacqua wrote: I am aware of table(is.na(df$var)) but is there an efficient way of create a table that shows the number of missing values in each variable of a data frame? Right now I am forced to create a new variable, varna-is.na(df$var), for each

[R] Logical statements and subseting data...

Hi, I'm scratching my head as to why I can't use the subset() command to remove one line of data from a data frame. There is just one row (out of 45840) that I'd like to remove and it can be identified using dim(raw.all.clean) [1] 4584010 subset(raw.all.clean, Height.1 == 0 Height.2

Re: [R] Logical statements and subseting data...

Thanks Thierry, they do both leave me with what I expected. On Mon, Feb 25, 2008 at 2:28 PM, ONKELINX, Thierry [EMAIL PROTECTED] wrote: The negation of Height.1 == 0 Height.2 == 0 was incorrect. Use subset(raw.all.clean, !(Height.1 == 0 Height.2 == 0)) I can see clearly how this expression

[R] how to find the significance F for one-way ANOVA

I am now writing an R code to do the systematic permutation test and the random permutation test. And I encountered a couple of problems which I cannot figure them out. At first, whenever I type permtest in my R2.6.1, it always shows:there is no such a function, I tried again and again

Re: [R] Logical statements and subseting data...

The negation of Height.1 == 0 Height.2 == 0 was incorrect. Use subset(raw.all.clean, !(Height.1 == 0 Height.2 == 0)) or subset(raw.all.clean, Height.1 != 0 | Height.2 != 0) HTH, Thierry ir. Thierry Onkelinx

[R] by function half-working when used in a custom function

Dear R users, I'm trying to save the results of separate logistic regression analyses of a dataset according to a categorical factor. For that, I first used a by function such as following : temp - by( data, data$categorical.factor , function(x) summary( glm( formula = data$var1 ~ data$var2

[R] Read.xport function in package foreign

Hi All, Sorry that I didn't provide enough information. I've been trying to import SAS xport files that contain multiple files using package foreign's read.xport. I first attempted this back in 2005 and had problems. Some of files that were present in the SAS xport file weren't being created

Re: [R] Logical statements and subseting data...

Neil, Maybe this example will make things more clear to you. DF - expand.grid(A = 0:1, B = 0:1) cbind(DF, DF$A != 0, DF$B != 0, DF$A != 0 DF$B != 0, DF$A != 0 | DF$B != 0) A B DF$A != 0 DF$B != 0 DF$A != 0 DF$B != 0 DF$A != 0 | DF$B != 0 1 0 0 FALSE FALSE FALSE

Re: [R] Read.xport function in package foreign

Hi, Gary, I have exchanged data between SAS and R all the time using SASxport package and found no problem at all. It might be worth for you to try. On Mon, Feb 25, 2008 at 10:12 AM, Nelson, Gary (FWE) [EMAIL PROTECTED] wrote: Hi All, Sorry that I didn't provide enough information. I've

[R] anova (repeated measure)

Hi R people, I'm trying to do a Anova with 3 different tests (intra subject), 6 times of measures (intra subject) and 3 groups (inter subject). I want to obtain an Huynh-Feldt epsilon on accuracy with anova(lm(acc.t1~gr.dem),test=Spherical) for test 1 # gr.dem is my group variable

Re: [R] by function half-working when used in a custom function

Please give minimal reproducible examples. The data and a test driver were missing. See last line to every message to r-help. The problem is discussed here: http://tolstoy.newcastle.edu.au/R/help/06/08/32017.html On Mon, Feb 25, 2008 at 10:05 AM, vincent chouraki [EMAIL PROTECTED] wrote: Dear R

[R] Problems with augPlot and for loops

Dear all, I'm a new R user and I find myself in trouble with some of the plot functions. I'm trying to save a sequence of plots to eps files using a for loop, but I get only empty figures. In each iteration of the for loop I fit a nlme model and I'd like to plot its prediction of the dependent

Re: [R] Jitter in correlation matrix?

Hi, thanks so much: pairs(sapply(MAR.omitindep[,c(poldis , polres , ecdis , culres , gcc1 )],jitter,amount=1), lower.panel=panel.smooth, upper.panel=panel.cor) Mehmet. On Mon, 25 Feb 2008 09:05:28 +0100 Petr PIKAL [EMAIL PROTECTED] wrote: Hi Add sapply(any.data.frame, jitter) into

[R] kronecker product in mixed model

Hi, does anyone know how to self-define the variance-covariance structure of the within-subject variance for the mixed models , i.g, yi=Xibeta+Zibi+ei For ei I want to use kronecker product so its variance matrix will be R=V*E, here * represents Kronecker product. Thanks so many.

Re: [R] Minor tick marks

On 2/24/08, Saptarshi Guha [EMAIL PROTECTED] wrote: Hello, Is there a way to add minor tick marks to the Y-axis of a lattice plots? Yes, see http://lmdvr.r-forge.r-project.org/figures/figures.html?chapter=08;figure=08_05;theme=stdBW;code=right -Deepayan

Re: [R] Problems with augPlot and for loops

FAQ Q7.22 (you may not have been aware that you were using lattice). On Mon, 25 Feb 2008, Nicola Buratti wrote: Dear all, I'm a new R user and I find myself in trouble with some of the plot functions. I'm trying to save a sequence of plots to eps files using a for loop, but I get only empty

[R] Extracting variance components from a Manova

I am trying to run a simple nested manova with two levels of nesting, Sires, and Dams within Sires. The goal is to extract the among sires covariance matrix and secondarily, the among Dams within Sires covariance matrix. Both sires and dams are random effects. At present there are four

Re: [R] To get more digits in precision of predict function of randomForests

Thank you Uwe Ligges. Yes. I had only 50 trees. I come across memory problems running for big number of trees. Also, I am going to post my next question in a separate thread, but, it does not harm me to ask here. How do I deal with large datasets when using randomForests. I have approximately,

Re: [R] To get more digits in precision of predict function of randomForests

Nagu wrote: Thank you Uwe Ligges. Yes. I had only 50 trees. I come across memory problems running for big number of trees. Also, I am going to post my next question in a separate thread, but, it does not harm me to ask here. How do I deal with large datasets when using randomForests. I

[R] Running randomForests on large datasets

Hi, I am trying to run randomForests on a datasets of size 50X650 and R pops up memory allocation error. Are there any better ways to deal with large datasets in R, for example, Splus had something like bigData library. Thank you, Nagu __

[R] Parallel R for dummies (on hpc)

Hi, I had access to an hpc cluster, and wanted to parallelize some of my R code. I looked at the snow,nws, rscalapack documentation but was unable to make out how I should submit my job to the hpc, and how I should code a simple program. For example, if I had 10 matrices, and 10 processor how

Re: [R] Kenward-Roger correction in lme

stian at mail.rockefeller.edu stian at mail.rockefeller.edu writes: Hi,I am wondering how to conduct Kenward-Roger correction in the linear mixed model using R. Any idea? Thanks a lot, Suyan Not really possible, I'm afraid. Having already invested a huge amount of time in making lme4

Re: [R] Kenward-Roger correction in lme

Ben Bolker wrote: stian at mail.rockefeller.edu stian at mail.rockefeller.edu writes: Hi,I am wondering how to conduct Kenward-Roger correction in the linear mixed model using R. Any idea? Thanks a lot, Suyan Not really possible, I'm afraid. Having already invested a huge

[R] logLik calculation in gls (nlme)

I'm getting some odd results computing log-likelihoods with gls using splines with increasing degrees of freedom -- the deviance *increases* substantially with increasing df. (Since spline models with increasing df aren't nested, it need not decline monotonically but I would expect it to have

[R] Highlighting different series with colors

Hello, I have a data frame with 3 vectors $x, $y, and $type. I would like to plot $x~$y and having different colors for the corresponding points, one for each level of $type. Would someone know how to do that? Is it possible to then generate a legend automatically? Valentin

Re: [R] Highlighting different series with colors

One option is use lattice: require(lattice) xyplot(x~y, data=your.data, group=type, auto.key=T) On 25/02/2008, Valentin Bellassen [EMAIL PROTECTED] wrote: Hello, I have a data frame with 3 vectors $x, $y, and $type. I would like to plot $x~$y and having different colors for the

[R] Graph Axis

Hi I have data of exchange rates and time, and am trying to draw a graph that will show the rates on the y axis and dates on the x axis. I am using the following code: plot(rate, type='l', xlab='Date', ylab='Rate', main='£ to Euro rate over 5 years')This gives me the graph I want although I

Re: [R] Highlighting different series with colors

Valentin Bellassen vbella at lsce.ipsl.fr writes: Hello, I have a data frame with 3 vectors $x, $y, and $type. I would like to plot $x~$y and having different colors for the corresponding points, one for each level of $type. Would someone know how to do that? Is it possible to then

Re: [R] Graph Axis

You have to convert you date to be a Date class: x - read.table(/tempxx.txt, header=TRUE, as.is=TRUE) x$Date - as.Date(x$Date, %d/%m/%Y) plot(x$Date, x$Rate, type='l') On 2/25/08, Khadija Mohammedali [EMAIL PROTECTED] wrote: Hi I have data of exchange rates and time, and am trying to draw a

Re: [R] Avoiding overplotting of text.

I am plotting some data, and use text() to get variable names next to points on the graph. What is the best way to make sure that these text labels are readable and not overlapping when two datapoints are close? I've tried using jitter(), but the effect is random and doesn't always give

[R] union of two data frames

I have a thirty thousand row data frame imported from excel and a 60,000 row data frame imported from excel. they share a common subset of the same data and I would like to combine the two into one data frame merged together on the data in common. I have looked at the help file for merge and

Re: [R] union of two data frames

You probably need to provide an example here, show us your data.frame column names, and what you mean by 'common subset of the same data' at least. What did you try and what did it do that you didn't expect? stephen sefick wrote: I have a thirty thousand row data frame imported from excel and

Re: [R] union of two data frames

stephen, are you sure you want a union? in db term, union has a specific meaning. it seems to me you want a innerjoin, isn't it? sqldf package is a good one, which will also help you grasp the knowledge of SQL and complete your request as well. On Mon, Feb 25, 2008 at 4:59 PM, stephen sefick

Re: [R] deleting certain observations in a data frame

Thanks Peter: For others who are interested, the first one one with [-indices,] doesn't really do, because the first level of indices are the component names. eg, if I have a data frame with variables, name, DOB, gender, then by using the first choice, I'm merely deleting lists of

Re: [R] union of two data frames

Perhaps this example might help you? I create 2 sample data.frames, take a look at what they contain and then what the merge function gives. Compare with all = FALSE. df1 - data.frame(a = 1:10, b = 11:20) df2 - data.frame(a = c(1:2,98), b = c(11:12, 99)) merge(df1, df2, all = TRUE) Erik

Re: [R] union of two data frames

DateTime var1 var2 var3 var4 var5 var6 . .. . . . . . . . .. . . . .. . . . . 1/5/06 1 2 3 4 5 6 1/6/06 1 2 3 4 5 6 1/7/06

Re: [R] Graph Axis

Hi Jim Thank you for your quick response. This worked great. I am having the same problem again. I have moved on to calculating returns from rates and want to plot returns on the y axis and again dates on the x axis. The code I am using to calculate returns is as follows: rate-x$Rate

Re: [R] union of two data frames

On Mon, Feb 25, 2008 at 5:35 PM, stephen sefick [EMAIL PROTECTED] wrote: DateTime var1 var2 var3 var4 var5 var6 . .. . . . . . . . .. . . . .. . . . . 1/5/06 1 2

Re: [R] union of two data frames

There is a merge function in the zoo package that deals with time series. There have been couple of threats about it recently. Do a search. Specially look for solutions proposed by Gabor Grothendieck regarding merge in those threats. (It was very helpful for me Tnx to Gabor). you could begin by

Re: [R] union of two data frames

On Mon, 25 Feb 2008, stephen sefick wrote: DateTime var1 var2 var3 var4 var5 var6 . .. . . . . . . . .. . . . .. . . . . 1/5/06 1 2 3 4 5 6 1/6/06

Re: [R] union of two data frames

On Mon, 25 Feb 2008, AA wrote: There is a merge function in the zoo package that deals with time series. There have been couple of threats about it recently. Do a search. Exactly. Threats like this: Do a search! RTFM! Or we will kick your ass! But typically we try to avoid threats in threads

Re: [R] Plotting series marked with a symbol on every nth data point, preferably in ggplot...

Maybe someone can help with the ggplot version of this thing? Your best bet is just to wait a couple of weeks until the next version of gglot2 comes out :) Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list

Re: [R] Graph Axis

Plot the x-axis with one less data point: plot(x$Date[-1], returns,) On Mon, Feb 25, 2008 at 5:39 PM, Khadija Mohammedali [EMAIL PROTECTED] wrote: Hi Jim Thank you for your quick response. This worked great. I am having the same problem again. I have moved on to calculating returns from

[R] The meaning of 'z value' and 'Pr(|z|)' in the result of glm

Hi all, I used the function 'glm' to perform logistic regression, and then use 'summary' to display the fitting result. There are 'z value' and 'Pr(|z|)' Do they simpily represent the result of 'z test' ? as I perform the 'z test' for a particular variable following the definition, it

Re: [R] Graph Axis

You might consider using the zoo package since it handles all this automatically: library(zoo) z - read.zoo(Data.txt, format = %d/%m/%Y, header = TRUE) plot(z) plot(diff(log(z))) There are 3 vignettes that come with zoo with more info. On Mon, Feb 25, 2008 at 5:39 PM, Khadija Mohammedali [EMAIL

Re: [R] Plotting series marked with a symbol on every nth data point, preferably in ggplot...

On 2/26/08, hadley wickham [EMAIL PROTECTED] wrote: Maybe someone can help with the ggplot version of this thing? Your best bet is just to wait a couple of weeks until the next version of gglot2 comes out :) Hadley -- http://had.co.nz/ I'm certainly looking forward to it! Cheers, TL

[R] adjusting monthplot() towards a seasonal diagnostic plot for stl()

Hi all, I would like to adjust the monthplot() of an stl() so that for a time-series with freq=12 (months): a) the curve on the panel for the k-th month graphs the seasonal values minus their monthly mean values b) add to the fig. the values of the k-th month of the seasonal + remainder, also

Re: [R] The meaning of 'z value' and 'Pr(|z|)' in the result of glm

Stephen Lau asks: I used the function 'glm' to perform logistic regression, and then use 'summary' to display the fitting result. There are 'z value' and 'Pr(|z|)' The z value is the Wald statistic for testing the hypothesis that the corresponding parameter (regression coefficient) is zero.

[R] load windows file in linux

Hello R users, I have windows XP running Rv2.6.0 and a Solaris OS 10 x86-64 running Rv2.4.0. I transferred several large .rda files from windows to linux because of memory issues. I saved as .rda files on windows. In linux, the files load and have the proper dimensions, but will not index. I

[R] changing format of y-axis (barplot)

Dear all, I have some data.frame and I would like (1) change the format of y=axis to escape of scientific format (like 1e+05...) and (2) label the value or other variable on the top of the bar. df-data.frame(x=1:6,y=c(100,500,1000,25000,50,100)) barplot(df$y,names.arg=df$x) Thanks in

Re: [R] changing format of y-axis (barplot)

bp = barplot(df$y,names.arg=NULL, yaxt=n, ylim=c(0, 110)) text(bp, df$y+15000, paste(Class, 1:6)) axis(2, df$y) b On Feb 26, 2008, at 1:41 AM, milton ruser wrote: Dear all, I have some data.frame and I would like (1) change the format of y=axis to escape of scientific format (like

Re: [R] Parallel R for dummies (on hpc)

Hi Tim, I think you should have a look at this Rmpi Tutorial http://ace.acadiau.ca/math/ACMMaC/Rmpi/ and to Luke Tierney's webpage: http://www.cs.uiowa.edu/~luke/R/cluster/uiowasnow.html Best, Markus Tim Smith schrieb: Hi, I had access to an hpc cluster, and wanted to parallelize some of my

Re: [R] load windows file in linux

On Mon, 25 Feb 2008, Beth Wilmot wrote: Hello R users, I have windows XP running Rv2.6.0 and a Solaris OS 10 x86-64 running Rv2.4.0. I transferred several large .rda files from windows to linux because of memory issues. I saved as .rda files on windows. In linux, the files load and have

[R] [R-pkgs] Course on analysing spatial point patterns

A full set of course notes on 'Analysing spatial point patterns in R' is now available at http://www.csiro.au/resources/pf16h.html The course is based on the package 'spatstat'. It includes a brief introduction to R, a detailed introduction to the 'spatstat' package, and a

[R] OLS standard errors

Hi, the standard errors of the coefficients in two regressions that I computed by hand and using lm() differ by about 1%. Can somebody help me to identify the source of this difference? The coefficient estimates are the same, but the standard errors differ. Simulate data

Re: [R] OLS standard errors

Daniel Malter wrote: Hi, the standard errors of the coefficients in two regressions that I computed by hand and using lm() differ by about 1%. Can somebody help me to identify the source of this difference? The coefficient estimates are the same, but the standard errors differ.