[R] how to update R10.0 to R11.0 in Ubuntu linux

Dear R-listers, I am new to R in linux. And, I am now confused by updating R in Ubuntu 9.10 linux system. I would like to seek some advice on that problem. I have done what are listed in CRAN linux installation guide: 1. add an entry like deb http://cran.cnr.berkeley.edu/bin/linux/ubuntu

Re: [R] [R-pkgs] New package: `lavaan' for latent variable analysis (including structural equation modeling)

On 05/24/2010 09:53 PM, jlu...@ria.buffalo.edu wrote: Yves Would it by to much to ask of you to supply a copy of your LaTeX for the tikz/pgf? I would like to learn tikz/pgf and your pictures are motivating examples. Joe When I find the time, I will put the complete latex source of the

[R] help required to melt a data frame

I have the raw data with 9 column and 197977 row: dummy State Months Bedroom 1xxxJan 1 2xxxJan 2 3xxxJan 1 4yyyJan 1 5yyyJan 2 6yyyJan 1 7zzzJan 3 8zzzJan 1 9zzzJan 2

[R] Lattice: relation = 'free' in scales

Hello list, I am making graphics for an article which I want to publish. The article is about several methods (to calculate breeding values of individuals) applied in several genetic scenarios (scen1 in the example) and using data from two sources (scen 2 in my example). I want to specify the

[R] Cohen's Kappa for beginners

Hi, I've got two vectors with ratings from two coders, like this: x-c(red, yellow, blue, red) #coder number 1 y-c(red, blue, blue, red) #coder number 2 I want to find Cohen's Kappa using the wkappa function in the psych package. The only example in the docs is using a matrix, which I'm

Re: [R] segplot (latticeExtra)

On Tue, May 25, 2010 at 8:37 AM, Sebastian P. Luque splu...@gmail.com wrote: Hi, I'm having a bit of trouble with 'scales=free' in the segplot() function of latticeExtra.  Say we need panels for each year, showing only those counties that are represented in each one:

[R] Mixed effects models: Losing main effects with interactions

I'm new to R and mixed effects models. Can anyone tell me why, when I look for interactions, I lose a main effect, even when the interaction is non significant? I've tried centering, but that didn't work. Any ideas much appreciated! Best regards Mitch [[alternative HTML version

[R] Merging dataframe with list

I often read SPSS system files (*.sav) into R using the 'read.spss' function from the 'foreign' library. To retain all the meta data, i.e. 'variable labels', I call the function like this: test.sav - read.spss('http://www.cdc.gov/healthyYouth/shpps/2006/spss/envs2006.sav',

[R] Problem with Sweave not recognising \Sexpr{}

I am trying to run the Sweave example at http://www.stat.uni-muenchen.de/~leisch/Sweave/Sweave-Rnews-2002-3.pdf However, the \Sexpr{} code is not being evaluated, although the actual R code within the {} runs ok in R. Below is part of the resulting .tex file. Can anyone help identify the

Re: [R] help required state wise count

On 05/24/2010 10:21 PM, Mohan L wrote: ... in this case the state column becomes the row index. I want the state name as the first column. There may be a way to do it. Hi Mohan, You can do it with this awful kludge, but there must be a better way: dummy-data.frame(

[R] Need Help! Poor performance about randomForest for large data

Hi, dears, I am processing some data with 60 columns, and 286,730 rows. Most columns are numerical value, and some columns are categorical value. It turns out that: when ntree sets to the default value (500), it says can not allocate a vector of 1.1 GB size; And when I set ntree to be a very

Re: [R] Merging dataframe with list

Hi, I definitely have no idea of what to do precisely, but there is something you should know: data.frames ARE lists but where all elements have the same length. I don't know if that would change anything, but it might help you finding an alternative. Ivan Le 5/25/2010 11:24, Stefan

Re: [R] Need Help! Poor performance about randomForest for large data

Hi Jia, without seeing the actual data, it's difficult to give solid options. But it's quite normal this runs for hours : it has to make a whole lot of decisions, and it can grow tremendous large trees with that amount of data. Also the error is quite logic : you just can't store all those huge

[R] how can I read a non-standard XLS file

I have attached a file downloaded from database mirWalk. Apparently it is in XLS format (this is the extension of the downloaded file). However, I cannot open it with OpenOffife spreadsheet program and Excel itself cannot separate the columns as it does when a true XLS file is loaded. I tried to

Re: [R] Fast Matrix Computation

Thanks to everyone who responded! On Sun, May 23, 2010 at 1:32 AM, Jorge Ivan Velez jorgeivanve...@gmail.com wrote: Yes, it should be. Thank you for pointing that out. Apologies for the noise. Regards, Jorge On Sun, May 23, 2010 at 1:07 AM, Berend Hasselman wrote: Jorge Ivan Velez

Re: [R] Time problems (POSIXct)

Thanks Gabor, I suppose that in the example below, you can convet Date to POSIXct as well, can't you? Best, Costas On 20/05/2010 18:08, Gabor Grothendieck wrote: The warning message does tell you exactly what was wrong. You are trying to merge zoo objects that have two different index

Re: [R] Cohen's Kappa for beginners

On 05/25/2010 06:01 PM, Jason Priem wrote: Hi, I've got two vectors with ratings from two coders, like this: x-c(red, yellow, blue, red) #coder number 1 y-c(red, blue, blue, red) #coder number 2 I want to find Cohen's Kappa using the wkappa function in the psych package. The only example in

Re: [R] how can I read a non-standard XLS file

It appears you are using read.xls in gdata. In that case be sure you are using the latest version of gdata on CRAN since there was a problem with one older version. There is more info on read.xls in gdata here and also listed there are alternatives you can try:

Re: [R] Time problems (POSIXct)

Yes, its possible but if you have date data Date class would be the better choice. See R News 4/1. On Tue, May 25, 2010 at 7:26 AM, Research risk2...@ath.forthnet.gr wrote: Thanks Gabor, I suppose that in the example below,  you can convet Date to POSIXct as well, can't you? Best, Costas

Re: [R] how can I read a non-standard XLS file

On 25-May-10 11:12:30, mau...@alice.it wrote: I have attached a file downloaded from database mirWalk. Apparently it is in XLS format (this is the extension of the downloaded file). However, I cannot open it with OpenOffife spreadsheet program and Excel itself cannot separate the columns as

Re: [R] segplot (latticeExtra)

On 25 May 2010 13:07, Sebastian P. Luque splu...@gmail.com wrote: Hi, I'm having a bit of trouble with 'scales=free' in the segplot() function of latticeExtra.  Say we need panels for each year, showing only those counties that are represented in each one: ---cut

[R] Follow-up: how can I read a non-standard XLS file

I am uploading 2 XLS-similar files to server www.alice.it. I expect many people in this mailing list won't understand the instructions for grabbing the files because of the different language (sorry I do not have control on that. Telecom has). But it's really very simple. The message you receive

[R] Fixed Effects Estimations (in Panel Data)

Dear Ivo, thanks a lot for the good words, and sorry for not answering before: I was in fact looking into a related issue, reported by Liviu. Summarizing, - fixed effects estimation in plm is actually done on demeaned data, as customary in the econometric literature (see any textbook, e.g.

[R] website address for the pseuso-XLS files

http://gigamail.rossoalice.alice.it/messages/readMessageFrameset.aspx?DeliveryID=ba40cf18-29db-4404-a3ce-af26f760ecf9 Please, paste the website address above shown in your web browser address field. Make sure the whole string is pasted with no space or any other character. Telecom couldn't

[R] Relative Risk/Hazard Ratio plots for continuous variables

Dear all, I am using Windows and R 2.9.2 for my analyses. I have a large dataset and I am particularly interested in looking at time to an event for a continuous variable. I would like to produce a plot of log(relative risk) or relative risk (also known as hazard ratio) against the continuous

[R] summary of arima in R

Hi, I want to know how to summary arima model in R just as in lm by summary(lm.fit). Then I can assess the model fit of each component, especially when I include regressors in the model. Thanks __ R-help@r-project.org mailing list

[R] summary of arima model in R

Hi, I want to give a summary or anova for arima model in R, as summary, and anova for lm. As including various intervention factors in arima(xreg = ) part, I want to assess the significancy of thse factors. I can do it using interrupted analysis of time series by linear regression, but want to

[R] Selecting Monotone pattern of missingness from a dataframe

Dear R- users,   Pls help me with the following problem. I have a dataset that loooks like the following:   jh-data.frame(  'id'=seq(1,10,1),  'time0'=c(8,5,8,8,9,NA,NA,2,4,5),  'time4'=c(NA,NA,9,8,NA,2,3,2,4,5), 'time8'=c(NA,2,8,NA,5,NA,2,3,NA,4),  

[R] Assigning NA to a rows of a dataframe/datamatrix

Dear R-users,  I have a problem, I have the following dataframe:   d-data.frame(  'y1'=c(1,2,1,2,1,NA,NA), 'y2'=c(1,2,1,1,1,2,1), 'y3'=c(1,NA,1,NA,NA,2,1), 'y4'=c(NA,2,NA,1,1,2,NA), 'a'=c(1,1,1,1,1,1,2) ) where the last variable counts the number of missing values in a row. Now, i want to set

Re: [R] Random Forest for Ecological Prediction under presence of Spatial Autocorrelation

Thank you very much for this suggestion, I was not aware of this package. Apart from this, is suggestion 2 (changing nodesize attribute) a good way to go? Experimenting with sampsize (suggestion 4) has yielded promising results. Kind regards, Andreas Béguin 2010/5/24 Gabor Grothendieck

Re: [R] Relative Risk/Hazard Ratio plots for continuous variables

On 05/25/2010 07:28 AM, Laura Bonnett wrote: Dear all, I am using Windows and R 2.9.2 for my analyses. I have a large dataset and I am particularly interested in looking at time to an event for a continuous variable. I would like to produce a plot of log(relative risk) or relative risk (also

Re: [R] website address for the pseuso-XLS files

Maura, These are html files. Rename the downloaded file(s) to *.html and open with your favourite browser. Follow links from there. -Peter Ehlers On 2010-05-25 6:24, mau...@alice.it wrote:

[R] using the name of an argument in a function

Hi all, In a function, I need to get the name of a variable that has been used to call the function. For example, I want: --- 8 -- toto - 3 fun - function(y){ nameOfY -deparse(substitute(y)) cat(name is ,nameOfY) } fun(toto) # [1] name is toto --- 8 But deparse(substitute(y))

Re: [R] Assigning NA to a rows of a dataframe/datamatrix

On May 25, 2010, at 5:23 AM, john james wrote: Dear R-users, I have a problem, I have the following dataframe: d-data.frame( 'y1'=c(1,2,1,2,1,NA,NA), 'y2'=c(1,2,1,1,1,2,1), 'y3'=c(1,NA,1,NA,NA,2,1), 'y4'=c(NA,2,NA,1,1,2,NA), 'a'=c(1,1,1,1,1,1,2) ) where the last variable counts the number

Re: [R] using the name of an argument in a function

Hi, This is a dangerous game you are playing. I would play with the call stack, i.e sys.calls : setMethod(fun,character, definition = function(y,x,...){ stack - sys.calls( ) stack.fun - Filter( function(.) .[[1]] == as.name(fun), stack ) nameOfY -

Re: [R] website address for the pseuso-XLS files

To be more precise: These seem to be files in XML (Extended Markup Language) format, or a variant thereof, not HTML. This is understood by recent versions of Excel. The xls extension is deceptive here! Maura: You originally wrote Apparently it is in XLS format (this is the extension of the

Re: [R] help required to melt a data frame

I trying to get a new data frame for 1 bedroom using cast. But I am not able to get the below data for 1 Bedroom using cost. State  Jan Feb  xxx   2    0  yyy   2    2  zzz   1    0 What do those numbers represent? Hadley -- Assistant Professor / Dobelman Family Junior Chair Department

Re: [R] help required to melt a data frame

On Tue, May 25, 2010 at 6:59 PM, Hadley Wickham had...@rice.edu wrote: I trying to get a new data frame for 1 bedroom using cast. But I am not able to get the below data for 1 Bedroom using cost. State Jan Feb xxx 20 yyy 22 zzz 10 What do those numbers

Re: [R] Problem with Sweave not recognising \Sexpr{}

I think I have solved the problem. In the Sweave manual it mentions that problems may occur after loading the R2HTML package. I have not recently loaded this package but the proposed solution to problems caused by R2HTML also solves my problem with the evaluation of R code in \Sexpr. It seems

Re: [R] Cohen's Kappa for beginners

Hi, It doesn't seem happy with non-numeric data in the data frame version. Maybe a recode would work? x1 - c(1, 2, 3, 1) y1 - c(1, 3, 3, 1) cohen.kappa(data.frame(x = x1, y = y1)) Call: cohen.kappa1(x = x, w = w, n.obs = n.obs, alpha = alpha) Cohen Kappa and Weighted Kappa correlation

[R] R: website address for the pseuso-XLS files

Thank you. May I know the version of your OO and the operating system it runs on ? I use Linux/SuSE 11.1 running OO 3.0.0.9-1.9 Maura -Messaggio originale- Da: ted.hard...@manchester.ac.uk [mailto:ted.hard...@manchester.ac.uk] Inviato: mar 25/05/2010 15.22 A: r-h...@stat.math.ethz.ch Cc:

Re: [R] Cohen's Kappa for beginners

cohen.kappa(cbind(x,y)) works for me. -Peter Ehlers On 2010-05-25 7:42, Scot W. McNary wrote: Hi, It doesn't seem happy with non-numeric data in the data frame version. Maybe a recode would work? x1 - c(1, 2, 3, 1) y1 - c(1, 3, 3, 1) cohen.kappa(data.frame(x = x1, y = y1)) Call:

Re: [R] how to update R10.0 to R11.0 in Ubuntu linux

Mao Jianfeng jianfeng.mao at gmail.com writes: Dear R-listers, I am new to R in linux. And, I am now confused by updating R in Ubuntu 9.10 linux system. I would like to seek some advice on that problem. I have done what are listed in CRAN linux installation guide: 1. add an entry

Re: [R] R: website address for the pseuso-XLS files

It is OpenOffice 2.0 (as updated to openoffice.org-core, dfsg.2-7etch9 Sat Jan 16 2010) running on Linux (Debian Etch, originally installed Sept 2007), so none of it is particularly recent. The command to view the files is like: oocalc Prostatic_Neoplasm-miRNAs.DiseaseTargets.xls Ted. On

[R] R: R: website address for the pseuso-XLS files

Through clicking on the xls file oocalc (OpenOffice spreadsheet module) is automatically launched. But in my case it cannot load it correctly regardless of my choices (separator, etc..). Maybe I should switch to another Linux distribution. Thank you very much. Maura -Messaggio

Re: [R] R: website address for the pseuso-XLS files

On Tue, May 25, 2010 at 3:09 PM, Ted Harding ted.hard...@manchester.ac.uk wrote: It is OpenOffice 2.0 (as updated to openoffice.org-core, dfsg.2-7etch9 Sat Jan 16 2010) running on Linux (Debian Etch, originally installed Sept 2007), so none of it is particularly recent. The command to view the

Re: [R] Problem with Sweave not recognising \Sexpr{}

 I had the same problem before and I think it has something to do with the R2HTML package. To take care of that problem simply sweave your rnw file like this: Sweave(yourfile.Rnw,syntax=SweaveSyntaxNoweb) and try Sexpr{} again.   Felipe D. Carrillo Supervisory Fishery Biologist Department of the

[R] PRESS and P2 statistics in R

Hello all, Is there any function in R by which I can calculate PRESS and P2 statistics for linear regression in R? Thanks Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] Cohen's Kappa for beginners

Peter, Scot, Jim, and Jason, Thanks for the various solutions to Jason's problem. In the next release of psych I will a) document how to use non-numeric categorical variables (e.g., red, blue, etc.) when using cohen.kappa, b) suggest that cbind does the job (Peter's solution), c) make

Re: [R] PRESS and P2 statistics in R

If you search with the Vignettes button checked at the RSiteSearch destination for prediction error sums of squares you find that the mixOmics package provides a function that returns PRESS. Whether that is a recommended approach to model scoring seems questionable, however. It looks

[R] SEM interaction

Hello all, This is a general stats question--I realize it is an R help list, so tell me to go away if it is inappropriate. I have a 2 X 2 design, and I have specified four identical path models (one for each level of each factor). I want to test for an interaction at each path--essentially

[R] R eat my data

HI, Dear R community, My original file has 1932 lines, but when I read into R, it changed to 1068 lines, how comes? c...@nuuk:~/operon$ wc -l id_name_gh5.txt 1932 id_name_gh5.txt gene_name-read.table(/home/cdu/operon/id_name_gh5.txt, sep=\t, skip=0, header=F, fill=T) dim(gene_name) [1] 1068

Re: [R] Problem with Sweave not recognising \Sexpr{}

What other packages do you have loaded? Sometimes things interfere with each other. Also, what version, os, etc are you working with? (the info asked for in the posting guide). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111

[R] Building correlation matrix

Hi, I am a novice with R, so pardon me if the question is a piece of cake to some of you. Say if I have a stream of data consisting of 3 columns, 1st column is birth date, 2nd is death date and third is weight for each individual. My ultimate goal is to be able to compute the correlation of

Re: [R] R eat my data

Hi Changbin, Try to use this code in R to count the lines of your file without open it length(count.fields(id_name_gh5.txt)) Regards Mohamed Changbin Du a écrit : HI, Dear R community, My original file has 1932 lines, but when I read into R, it changed to 1068 lines, how comes?

Re: [R] R eat my data

On May 25, 2010, at 11:42 AM, Changbin Du wrote: HI, Dear R community, My original file has 1932 lines, but when I read into R, it changed to 1068 lines, how comes? We are being asked to investigate this quest, how? Have you looked at the last line to see if it looks like gene_name?

Re: [R] Lattice: relation = 'free' in scales

Albart, On 2010-05-25 1:51, Albart wrote: Hello list, I am making graphics for an article which I want to publish. The article is about several methods (to calculate breeding values of individuals) applied in several genetic scenarios (scen1 in the example) and using data from two sources

Re: [R] Error during wrapup: cannot open the connection

Follow-up : one of my colleagues (who is not experiencing this problem) noticed that I had an older version of impute than he did, so I have now installed impute_1.22.0, but I still get the same error. thanks, Sheila On Mon, May 24, 2010 at 3:01 PM, Sheila Reynolds

Re: [R] R eat my data

length(count.fields(/home/cdu/operon/id_name_gh5.txt)) [1] 1932 It is 1932 lines when count in R On Tue, May 25, 2010 at 8:52 AM, Mohamed Lajnef mohamed.laj...@inserm.frwrote: Hi Changbin, Try to use this code in R to count the lines of your file without open it

[R] File normalization

Dear all, I have a file with 57 columns (671 time points in each column) File looks like this: 10.279191 -1.203200e-02 -0.166772 6.12080e-02 0.196379 4.591900e-02 0.293689 20.267017 -1.150700e-02 -0.159463 5.85400e-02 0.187775 4.392200e-02 0.280854 30.053778

Re: [R] R eat my data

On Tue, May 25, 2010 at 4:42 PM, Changbin Du changb...@gmail.com wrote: HI, Dear R community, My original file has 1932 lines, but when I read into R, it changed to 1068 lines, how comes? c...@nuuk:~/operon$ wc -l id_name_gh5.txt 1932 id_name_gh5.txt

Re: [R] R eat my data

cheks the comments sent by David! M Changbin Du a écrit : length(count.fields(/home/cdu/operon/id_name_gh5.txt)) [1] 1932 It is 1932 lines when count in R On Tue, May 25, 2010 at 8:52 AM, Mohamed Lajnef mohamed.laj...@inserm.fr mailto:mohamed.laj...@inserm.fr wrote: Hi Changbin,

Re: [R] R eat my data

644727344ABC-2 type transporterABC-2 type transporter 644727345conserved hypothetical proteinconserved hypothetical protein Here is the last two lines of the file id_name_gh5.txt. On Tue, May 25, 2010 at 8:57 AM, David Winsemius dwinsem...@comcast.netwrote: On May 25, 2010,

Re: [R] R eat my data

c...@nuuk:~/operon$ grep '^#' id_name_gh5.txt c...@nuuk:~/operon$ no lines starts with # On Tue, May 25, 2010 at 9:11 AM, Barry Rowlingson b.rowling...@lancaster.ac.uk wrote: On Tue, May 25, 2010 at 4:42 PM, Changbin Du changb...@gmail.com wrote: HI, Dear R community, My original file

Re: [R] SEM interaction

Have you looked into multigroup analysis? Is that what you're after? If so, you can do multigroup analysis in lavaan fairly easily or, if you're using the sem package, drop me a line. I have some scripts that will do multigroup analysis for an equal sample size. See

Re: [R] R eat my data

Without the actual file to look at, this is like playing 20 questions, only not so much fun. However, this kind of problem is most often caused by the presence in your file of something that R interprets as a special character, usually # or ' or . Can you open the file in a spreadsheet? Can you

[R] multivariate nonparametric test

Hi, I am doing my PhD and I usually use SPSS however now I need to do some multivariate nonparametric tests but SPSS don’t work with this. Recently I was aware of R and I saw that is possible using the MNM pack to perform multivariate nonparametric tests. I am learning step by step how to

Re: [R] R eat my data

without any clue about your data-file this is definitely unsolvable. But some things to consider : Where is the dataset coming from? Did you check for special characters? Is there an apostrophe somewhere in a string? (That messed up things for me once). Is the delimiter placed correctly

Re: [R] File normalization

What kind of normalization do you want to do? If you want to divide all columns by the median absolute value, try : apply(some_dataset,2,function(x){ x-median(abs(x)) }) also look at ?scale for normalization using the average and the sd. Cheers Joris On Tue, May 25, 2010 at 6:01 PM,

Re: [R] R eat my data

When I encounter problems like this, I make sure each row has the expected number of columns. Something like the following awk code is useful. awk -F\t '{print NF}' id_name_gh5.txt | sort | uniq -c Note: I'm not sure is the \t will work with the -F switch as above. Kevin Changbin Du wrote:

Re: [R] R eat my data

Have you compared them to tail(gene)_name, 2) Come on, man, show some initiative. On May 25, 2010, at 12:12 PM, Changbin Du wrote: 644727344ABC-2 type transporterABC-2 type transporter 644727345conserved hypothetical proteinconserved hypothetical protein Here is the last

Re: [R] help required to melt a data frame

On Tue, May 25, 2010 at 8:39 AM, Mohan L l.mohan...@gmail.com wrote: On Tue, May 25, 2010 at 6:59 PM, Hadley Wickham had...@rice.edu wrote: I trying to get a new data frame for 1 bedroom using cast. But I am not able to get the below data for 1 Bedroom using cost. State  Jan Feb  

Re: [R] multivariate nonparametric test

Hi Jose, the datafile gets thrown away on the list. But in any case, first step is to get rid of EXCEL and save the data as a csv-file, with the first row being the variable names. Then you use read.table or read.csv to get this in R as a data frame. e.g.: myData -

Re: [R] R eat my data

Thanks you all for the contributions! I will send the data back to the computer guys who collect data yesterday. Actually, the data can be open in excel and txt editor. after replace some ;, gene_name-read.table(/home/cdu/operon/id_name_gh5.txt, sep=\t, skip=0, header=FALSE, fill=TRUE)

Re: [R] help required to melt a data frame

In that case, you probably want: subsets.melt - melt(subsets.dummy,id.vars=c(State,Bedroom, Months)) cast(subsets.melt, State ~ Months, fill = 0, fun = length) Hadley Dear Hadley, subsets.melt - melt(subsets.dummy,id.vars=c(State,Bedroom, Months)) subsets.melt State Bedroom Months 1

Re: [R] Error during wrapup: cannot open the connection

On 05/25/2010 08:52 AM, Sheila Reynolds wrote: Follow-up : one of my colleagues (who is not experiencing this problem) noticed that I had an older version of impute than he did, so I have now installed impute_1.22.0, but I still get the same error. Hi Sheila -- Apparently your 'data' list

Re: [R] Building correlation matrix

On 2010.05.25 11:52:07, Anyi Zhu wrote: Hi, I am a novice with R, so pardon me if the question is a piece of cake to some of you. Say if I have a stream of data consisting of 3 columns, 1st column is birth date, 2nd is death date and third is weight for each individual. My ultimate

Re: [R] File normalization

My code substracts the median absolute value. If you want to divide by it, the code must be : apply(some_dataset,2,function( x){ x/median(abs(x)) }) Thanks to Peter Langfelder for pointing out my mistake. On Tue, May 25, 2010 at 6:24 PM, Joris Meys jorism...@gmail.com wrote: What kind

Re: [R] Cohen's Kappa for beginners

Thanks for you quick responses, all! Bill, it looks like that's just what I want, but I'm not sure where you're getting the cohen.kappa() function. The only function I could find by that name is in the concord library, and it gives me: x-c(red, yellow, blue, red) #coder number 1 y-c(red,

[R] Calculation time of isoMDS and the optimal number of dimensions

Dear all, I'm running a set of nonparametric MDS analyses, using a wrapper for isoMDS, on a 800x800 distance matrix. I noticed that setting the parameter k to larger numbers seriously increases the calculation time. Actually, with k=10 it calculates already longer than for k=2 and k=5 together.

Re: [R] File normalization

?scale is specifically written for this. See also ?sweep Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Joris Meys Sent: Tuesday, May 25, 2010 9:54 AM To: cobbler_squad Cc:

Re: [R] R eat my data

Changbin, It looks you're trying to read in a gene annotation file and usually it has many strange characters, e.g. #, , (as other people also suggest). I encounter this all the time. So try to be very thorough about your search (the first place I'll look for is the line where R stop

Re: [R] rounding up to nearest integer

-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Mohan L Sent: Monday, May 24, 2010 6:26 PM To: r-help@r-project.org Subject: [R] rounding up to nearest integer Dear All, I have a data frame data and the below is the str

Re: [R] File normalization

Scale is written to do that IF you want to normalize according to the mean and the sd. For any other form of normalization, apply or sweep constructs will have to be used. I couldn't really see a way of using the absolute median value in a sweep-statement. On Tue, May 25, 2010 at 7:11 PM, Bert

[R] General Question regarding Lists

Hello, Here is a general question that I think many of you will have insight to. I have 40 independent dataframes. Each has a dimension of 1359 x 15. For example dim(meanAnnualWaterDepth) 1539 15 I need to calculate the average value for each dataframe but only for columns 7: 15. I can do

Re: [R] summary of arima model in R

Check http://cran.r-project.org/doc/contrib/Ricci-refcard-ts.pdf for some ideas on testing time series in R. I'd go with the acf() and pacf() on the residuals of the arima model. If arima works, both plots will indicate absence of autocorrelation. also check ?tsdiag And if you're really going

Re: [R] Cohen's Kappa for beginners

Jason, It seems that your version of psych may be outdated. CRAN currently has version 1.0-88, in which wkappa is listed as deprecated. Might be time to upgrade. -Peter Ehlers On 2010-05-25 10:55, Jason Priem wrote: Thanks for you quick responses, all! Bill, it looks like that's just what

Re: [R] File normalization

The scale function can use whatever vector you choose for subtraction and division. (It's basically a wrapper for the sweep function.) For example, to subtract the median and divide by the median absolute deviation, use scale(x,center=apply(x,2,median),scale=apply(x,2,mad)) Either the

Re: [R] Cohen's Kappa for beginners

Thanks; i used update.packages() before I asked this, but apparently it didn't work. A manual upgrade did the trick, and now I'm Kappa-ing to my heart's content. Thanks again to everyone for your help! Best, Jason On 5/25/2010 1:34 PM, Peter Ehlers [via R] wrote: Jason, It seems that

Re: [R] File normalization

On Tue, May 25, 2010 at 7:57 PM, Phil Spector spec...@stat.berkeley.eduwrote: The scale function can use whatever vector you choose for subtraction and division. (It's basically a wrapper for the sweep function.) Yeah, I know, I said it a bit strong. In this case it becomes

[R] Pipe

Hi, I'm trying to use the pipe function to read data from another process on my server. Here is the code I have tried. con - pipe(/var/matlab/scripts/stream.pl) while(con_read - readLines(con)) { print(con_read) } Problem is that the data from the perl script just keeps appending to con_read

[R] Non-unique Values

I might be missing something really obvious, but is there an easy way to locate all non-unique values in a data frame? Example mydata - numeric() mydata$id - 0:8 mydata$unique - c(1:5, 1:4) mydata$result - c(1:3, 1:3, 1:3) mydata $id [1] 0 1 2 3 4 5 6 7 8 $unique [1] 1 2 3 4 5 1 2 3 4

[R] appending objects to file created with save()

Dears, is there a way to append R objects similar to the function save() to a binary file that already consists some previously saved R objects? I browsed the mailing list archive and only found some suggestions that include reading in the old file first and then saving the new objects

Re: [R] R eat my data

Thanks, Tao, I will try to do it. On Tue, May 25, 2010 at 10:13 AM, Shi, Tao shida...@yahoo.com wrote: Changbin, It looks you're trying to read in a gene annotation file and usually it has many strange characters, e.g. #, , (as other people also suggest). I encounter this all the

Re: [R] R eat my data

gene_name-read.delim(/home/cdu/operon/id_name_gh5.txt, sep=\t, skip=0, header=F, fill=T) dim(gene_name) [1] 19323 Thanks, Tao! Now you see, read.delim works! Thanks all for your imputs! I really appreciated! On Tue, May 25, 2010 at 10:13 AM, Shi, Tao shida...@yahoo.com wrote:

Re: [R] adding one line to a plot

Your line does show up, but the x values start at ~6 and the y values are incredibly small, so it is masked by the y=0 line. You probably have to check your calculations! --- Dimitri Liakhovitski dimitri.liakhovit...@gmail.com schrieb am Mo, 24.5.2010: Von: Dimitri Liakhovitski

Re: [R] appending objects to file created with save()

If you work with large data you might want to look at the ff package - useful if your data is close or above your RAM. The package has ffsave where with option add=TRUE you can add data to an existing ff archive. With ff data is stored outside of R in files, only meta-data is stored within R.

Re: [R] Non-unique Values

The really obvious thing that you missed ;-) was trying: help(unique) and looking at 'see also' which would have led you to help(duplicated) HTH Jannis --- Polwart Calum (County Durham and Darlington NHS Foundation Trust) calum.polw...@nhs.net schrieb am Di, 25.5.2010: Von: Polwart Calum

Re: [R] Lattice: relation = 'free' in scales

Dear Peter, thank you for your help. This helped. Albart -- View this message in context: http://r.789695.n4.nabble.com/Lattice-relation-free-in-scales-tp2229644p2230511.html Sent from the R help mailing list archive at Nabble.com. __

Re: [R] Getting sink to work with message on R 2.11.0 - what didI miss?

OK, I have uploaded a few new functions to the TeachingDemos package on R-forge (it will be a while before the CRAN version is updated, but you can install directly from R-forge once the changes show up there). The main functions to use (after loading TeachingDemos) are wdtxtStart and

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